References.bib

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@article{Ling2013,
author = {Ling, Hong-Qing and Zhao, Shancen and Liu, Dongcheng and Wang, Junyi and Sun, Hua and Zhang, Chi and Fan, Huajie and Li, Dong and Dong, Lingli and Tao, Yong and Gao, Chuan and Wu, Huilan and Li, Yiwen and Cui, Yan and Guo, Xiaosen and Zheng, Shusong and Wang, Biao and Yu, Kang and Liang, Qinsi and Yang, Wenlong and Lou, Xueyuan and Chen, Jie and Feng, Mingji and Jian, Jianbo and Zhang, Xiaofei and Luo, Guangbin and Jiang, Ying and Liu, Junjie and Wang, Zhaobao and Sha, Yuhui and Zhang, Bairu and Wu, Huajun and Tang, Dingzhong and Shen, Qianhua and Xue, Pengya and Zou, Shenhao and Wang, Xiujie and Liu, Xin and Wang, Famin and Yang, Yanping and An, Xueli and Dong, Zhenying and Zhang, Kunpu and Zhang, Xiangqi and Luo, Ming-Cheng and Dvorak, Jan and Tong, Yiping and Wang, Jian and Yang, Huanming and Li, Zhensheng and Wang, Daowen and Zhang, Aimin and Wang, Jun},
doi = {10.1038/nature11997},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Ling et al/Nature/2013-Nature-Draft sequencing of the wheat A genome.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
month = mar,
pages = {3--6},
publisher = {Nature Publishing Group},
title = {{Draft genome of the wheat A-genome progenitor Triticum urartu}},
url = {http://www.nature.com/doifinder/10.1038/nature11997},
year = {2013}
}
@article{Chapman2015,
author = {Chapman, Jarrod a and Mascher, Martin and Bulu\c{c}, Aydın and Barry, Kerrie and Georganas, Evangelos and Session, Adam and Strnadova, Veronika and Jenkins, Jerry and Sehgal, Sunish and Oliker, Leonid and Schmutz, Jeremy and Yelick, Katherine a and Scholz, Uwe and Waugh, Robbie and Poland, Jesse a and Muehlbauer, Gary J and Stein, Nils and Rokhsar, Daniel S},
doi = {10.1186/s13059-015-0582-8},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Chapman et al/Genome Biology/s13059-015-0582-8.pdf:pdf},
issn = {1465-6906},
journal = {Genome Biology},
number = {1},
pages = {1--17},
title = {{A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome}},
url = {http://genomebiology.com/2015/16/1/26},
volume = {16},
year = {2015}
}
@article{Lozano2012,
abstract = {The majority of disease resistance (R) genes identified to date in plants encode a nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain containing protein. Additional domains such as coiled-coil (CC) and TOLL/interleukin-1 receptor (TIR) domains can also be present. In the recently sequenced Solanum tuberosum group phureja genome we used HMM models and manual curation to annotate 435 NBS-encoding R gene homologs and 142 NBS-derived genes that lack the NBS domain. Highly similar homologs for most previously documented Solanaceae R genes were identified. A surprising ∼41\% (179) of the 435 NBS-encoding genes are pseudogenes primarily caused by premature stop codons or frameshift mutations. Alignment of 81.80\% of the 577 homologs to S. tuberosum group phureja pseudomolecules revealed non-random distribution of the R-genes; 362 of 470 genes were found in high density clusters on 11 chromosomes.},
author = {Lozano, Roberto and Ponce, Olga and Ramirez, Manuel and Mostajo, Nelly and Orjeda, Gisella},
doi = {10.1371/journal.pone.0034775},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Lozano et al/PloS one/journal.pone.0034775.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Amino Acid Sequence,Base Sequence,Binding Sites,Chromosome Mapping,Chromosomes, Plant,Conserved Sequence,Disease Resistance,Disease Resistance: genetics,Disease Resistance: immunology,Genome, Plant,Genome-Wide Association Study,Molecular Sequence Data,Multigene Family,Nucleotides,Nucleotides: metabolism,Phylogeny,Plant Diseases,Plant Diseases: genetics,Plant Diseases: immunology,Plant Proteins,Plant Proteins: chemistry,Plant Proteins: genetics,Protein Binding,Protein Structure, Tertiary,Proteins,Proteins: chemistry,Proteins: genetics,Pseudogenes,Pseudogenes: genetics,Sequence Homology, Amino Acid,Solanum tuberosum,Solanum tuberosum: genetics},
month = jan,
number = {4},
pages = {e34775},
pmid = {22493716},
title = {{Genome-wide identification and mapping of NBS-encoding resistance genes in Solanum tuberosum group phureja.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3321028\&tool=pmcentrez\&rendertype=abstract},
volume = {7},
year = {2012}
}
@book{casavaBCL,
author = {Illumina},
edition = {RevC},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Illumina/Unknown/CASAVA\_1\_8\_2\_UG\_15011196C.pdf:pdf},
pages = {19--46},
title = {{CASAVA v1.8.2 User guide}},
url = {http://support.illumina.com/sequencing/sequencing\_software/casava/documentation.ilmn},
year = {2011}
}
@article{Michelmore1991,
abstract = {We developed bulked segregant analysis as a method for rapidly identifying markers linked to any specific gene or genomic region. Two bulked DNA samples are generated from a segregating population from a single cross. Each pool, or bulk, contains individuals that are identical for a particular trait or genomic region but arbitrary at all unlinked regions. The two bulks are therefore genetically dissimilar in the selected region but seemingly heterozygous at all other regions. The two bulks can be made for any genomic region and from any segregating population. The bulks are screened for differences using restriction fragment length polymorphism probes or random amplified polymorphic DNA primers. We have used bulked segregant analysis to identify three random amplified polymorphic DNA markers in lettuce linked to a gene for resistance to downy mildew. We showed that markers can be reliably identified in a 25-centimorgan window on either side of the targeted locus. Bulked segregant analysis has several advantages over the use of near-isogenic lines to identify markers in specific regions of the genome. Genetic walking will be possible by multiple rounds of bulked segregation analysis; each new pair of bulks will differ at a locus identified in the previous round of analysis. This approach will have widespread application both in those species where selfing is possible and in those that are obligatorily outbreeding.},
author = {Michelmore, R. W. and Paran, I. and Kesseli, R. V.},
doi = {10.1073/pnas.88.21.9828},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Michelmore, Paran, Kesseli/Proceedings of the National Academy of Sciences/pnas01071-0462.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
month = nov,
number = {21},
pages = {9828--9832},
title = {{Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations.}},
url = {http://www.pnas.org/content/88/21/9828.short},
volume = {88},
year = {1991}
}
@article{Wang2014,
abstract = {High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.},
author = {Wang, Shichen and Wong, Debbie and Forrest, Kerrie and Allen, Alexandra and Chao, Shiaoman and Huang, Bevan E and Maccaferri, Marco and Salvi, Silvio and Milner, Sara G and Cattivelli, Luigi and Mastrangelo, Anna M and Whan, Alex and Stephen, Stuart and Barker, Gary and Wieseke, Ralf and Plieske, Joerg and Lillemo, Morten and Mather, Diane and Appels, Rudi and Dolferus, Rudy and Brown-Guedira, Gina and Korol, Abraham and Akhunova, Alina R and Feuillet, Catherine and Salse, Jerome and Morgante, Michele and Pozniak, Curtis and Luo, Ming-Cheng and Dvorak, Jan and Morell, Matthew and Dubcovsky, Jorge and Ganal, Martin and Tuberosa, Roberto and Lawley, Cindy and Mikoulitch, Ivan and Cavanagh, Colin and Edwards, Keith J and Hayden, Matthew and Akhunov, Eduard},
doi = {10.1111/pbi.12183},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Wang et al/Plant biotechnology journal/Unknown - Unknown - No Title.pdf:pdf},
issn = {1467-7652},
journal = {Plant biotechnology journal},
month = mar,
number = {6},
pages = {787--796},
pmid = {24646323},
title = {{Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24646323},
volume = {12},
year = {2014}
}
@article{Birol2013,
author = {Birol, I. and Raymond, a. and Jackman, S. D. and Pleasance, S. and Coope, R. and Taylor, G. a. and Yuen, M. M. S. and Keeling, C. I. and Brand, D. and Vandervalk, B. P. and Kirk, H. and Pandoh, P. and Moore, R. a. and Zhao, Y. and Mungall, a. J. and Jaquish, B. and Yanchuk, a. and Ritland, C. and Boyle, B. and Bousquet, J. and Ritland, K. and MacKay, J. and Bohlmann, J. and Jones, S. J. M.},
doi = {10.1093/bioinformatics/btt178},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Birol et al/Bioinformatics/Bioinformatics 2013 Birol.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
month = may,
pages = {1--6},
title = {{Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btt178},
year = {2013}
}
@article{DeSmet2012,
abstract = {Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Therefore, understanding the development and architecture of roots holds potential for the manipulation of root traits to improve the productivity and sustainability of agricultural systems and to better understand and manage natural ecosystems. While lateral root development is a traceable process along the primary root and different stages can be found along this longitudinal axis of time and development, root system architecture is complex and difficult to quantify. Here, we comment on assays to describe lateral root phenotypes and propose ways to move forward regarding the description of root system architecture, also considering crops and the environment.},
author = {{De Smet}, Ive and White, Philip J and Bengough, a Glyn and Dupuy, Lionel and Parizot, Boris and Casimiro, Ilda and Heidstra, Renze and Laskowski, Marta and Lepetit, Marc and Hochholdinger, Frank and Draye, Xavier and Zhang, Hanma and Broadley, Martin R and P\'{e}ret, Benjamin and Hammond, John P and Fukaki, Hidehiro and Mooney, Sacha and Lynch, Jonathan P and Nacry, Phillipe and Schurr, Ulrich and Laplaze, Laurent and Benfey, Philip and Beeckman, Tom and Bennett, Malcolm},
doi = {10.1105/tpc.111.094292},
file = {:Users/ramirezr/Documents/Mendeley Desktop/De Smet et al/The Plant cell/EWAC-Eucarpia proceedings2012 Eversole.pdf:pdf},
issn = {1532-298X},
journal = {The Plant cell},
keywords = {Models, Theoretical,Plant Roots,Plant Roots: growth \& development},
month = jan,
number = {1},
pages = {15--20},
pmid = {22227890},
title = {{Analyzing lateral root development: how to move forward.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3289553\&tool=pmcentrez\&rendertype=abstract},
volume = {24},
year = {2012}
}
@article{Mckinley2011,
author = {Mckinley, Trevelyan J and Murcia, Pablo R and Gog, Julia R and Varela, Mariana and Wood, James L N},
doi = {10.1371/journal.pcbi.1002027},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Mckinley et al/Unknown/McKinleyetalPLoSCompBio2011.pdf:pdf},
number = {3},
title = {{A Bayesian Approach to Analyse Genetic Variation within RNA Viral Populations}},
volume = {7},
year = {2011}
}
@article{Krichevsky2011,
abstract = {Covalent modifications of histones, such as acetylation, methylation and ubiquitination, are central for regulation of gene expression. Heterochromatic gene silencing, for example, is associated with hypoacetylation, methylation and demethylation, and deubiquitination of specific amino acid residues in histone molecules. Many of these changes can be effected by histone-modifying repressor complexes that include histone lysine demethylases, such as KDM1 in animals and KDM1C in plants. However, whereas KDM1-containing repressor complexes have been implicated in histone demethylation, methylation and deacetylation, whether or not they can also mediate histone deubiquitination remains unknown. We identify an Arabidopsis otubain-like deubiquitinase OTLD1 which directly interacts with the Arabidopsis KDM1C in planta, and use one target gene to exemplify that both OTLD1 and KDM1C are involved in transcriptional gene repression via histone deubiquitination and demethylation. We also show that OTLD1 binds plant chromatin and has enzymatic histone deubiquitinase activity, specific for the H2B histone. Thus, we suggest that, during gene repression, lysine demethylases can directly interact and function in a protein complex with histone deubiquitinases.},
author = {Krichevsky, Alexander and Zaltsman, Adi and Lacroix, Beno\^{\i}t and Citovsky, Vitaly},
doi = {10.1073/pnas.1014030108},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Krichevsky et al/Proceedings of the National Academy of Sciences of the United States of America/PNAS-2011-Krichevsky-1014030108.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
month = jul,
number = {27},
pages = {11157--62},
pmid = {21690391},
title = {{Involvement of KDM1C histone demethylase-OTLD1 otubain-like histone deubiquitinase complexes in plant gene repression.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3131378\&tool=pmcentrez\&rendertype=abstract},
volume = {108},
year = {2011}
}
@article{Duan2010,
abstract = {Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes. Interphase chromosomes are not positioned randomly within the nucleus, but instead adopt preferred conformations. Disparate DNA elements co-localize into functionally defined aggregates or 'factories' for transcription and DNA replication. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. The map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between DNA sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among transfer RNA genes, among origins of early DNA replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome.},
annote = {From Duplicate 1 ( A three-dimensional model of the yeast genome. - Duan, Zhijun; Andronescu, Mirela; Schutz, Kevin; McIlwain, Sean; Kim, Yoo Jung; Lee, Choli; Shendure, Jay; Fields, Stanley; Blau, C Anthony; Noble, William S )},
author = {Duan, Zhijun and Andronescu, Mirela and Schutz, Kevin and Mcllwain, Sean and Kim, Yoo Jung and Lee, Choli and Shendure, Jay and Fields, Stanley and Blau, C Anthony and William, S and McIlwain, Sean and Noble, William S},
doi = {10.1038/nature08973},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Duan et al/Nature/7e1a6024041eb5b18a9044e9cca13336f9b09e9f.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Cell Nucleolus,Cell Nucleolus: genetics,Cell Nucleolus: metabolism,Cell Nucleus,Cell Nucleus: genetics,Cell Nucleus: metabolism,Centromere,Centromere: genetics,Centromere: metabolism,Chromosome Breakpoints,Chromosome Positioning,Chromosome Positioning: physiology,Chromosomes,DNA Replication,Fungal,Fungal: genetics,Fungal: metabolism,Genome,Genome Modelling,Haploidy,Imaging,Intranuclear Space,Intranuclear Space: metabolism,RNA,Replication Origin,Replication Origin: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae: cytology,Saccharomyces cerevisiae: genetics,Three-Dimensional,Transfer,Transfer: genetics},
mendeley-tags = {Genome Modelling},
month = may,
number = {7296},
pages = {363--7},
pmid = {20436457},
title = {{A three-dimensional model of the yeast genome.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2874121\&tool=pmcentrez\&rendertype=abstract},
volume = {465},
year = {2010}
}
@article{Paux2010,
abstract = {In wheat, the deployment of marker-assisted selection has long been hampered by the lack of markers compatible with high-throughput cost-effective genotyping techniques. Recently, insertion site-based polymorphism (ISBP) markers have appeared as very powerful new tools for genomics and genetic studies in hexaploid wheat. To demonstrate their possible use in wheat breeding programmes, we assessed their potential to meet the five main requirements for utilization in MAS: flexible and high-throughput detection methods, low quantity and quality of DNA required, low cost per assay, tight link to target loci and high level of polymorphism in breeding material. Toward this aim, we developed a programme, IsbpFinder, for the automated design of ISBP markers and adapted three detection methods (melting curve analysis, SNaPshot Multiplex System and Illumina BeadArray technology) for high throughput and flexible detection of ISBP or ISBP-derived SNP markers. We demonstrate that the high level of polymorphism of the ISBPs combined with cost-effective genotyping methods can be used to efficiently saturate genetic maps, discriminate between elite cultivars, and design tightly linked diagnostic markers for virtually all target loci in the wheat genome. All together, our results suggest that ISBP markers have the potential to lead to a breakthrough in wheat marker-assisted selection.},
author = {Paux, Etienne and Faure, S\'{e}bastien and Choulet, Fr\'{e}d\'{e}ric and Roger, Delphine and Gauthier, Val\'{e}rie and Martinant, Jean-Pierre and Sourdille, Pierre and Balfourier, Fran\c{c}ois and {Le Paslier}, Marie-Christine and Chauveau, Aur\'{e}lie and Cakir, Mehmet and Gandon, B\'{e}atrice and Feuillet, Catherine},
doi = {10.1111/j.1467-7652.2009.00477.x},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Paux et al/Plant biotechnology journal/j.1467-7652.2009.00477.x.pdf:pdf},
issn = {1467-7652},
journal = {Plant biotechnology journal},
keywords = {Base Sequence,Chromosome Mapping,DNA,DNA: methods,Genome,Genomics,Genomics: methods,Genotype,High-Throughput Screening Assays,ISBPFinder.pl,Molecular Sequence Data,Plant,Plant: genetics,Polymorphism,Sequence Analysis,Single Nucleotide,Triticum,Triticum: genetics},
mendeley-tags = {ISBPFinder.pl},
month = feb,
number = {2},
pages = {196--210},
pmid = {20078842},
title = {{Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat.}},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00477.x/full http://www.ncbi.nlm.nih.gov/pubmed/20078842},
volume = {8},
year = {2010}
}
@article{Edenberg2009,
abstract = {The genetics of complex diseases has been given a tremendous boost in recent years by the introduction of high-throughput laboratory methods that make it possible to approach larger questions in larger populations and to cover the genome more comprehensively. The ability to determine genotypes of many individuals accurately and efficiently has allowed genetic studies that cover more of the variation within individual genes, instead of focusing only on one or a few coding variants, and to do so in study samples of reasonable power. Chip-based genotyping assays, combined with knowledge of the patterns of coinheritance of markers (linkage disequilibrium [LD]), have stimulated genome-wide association studies (GWAS) of complex diseases. Recent successes of GWAS in identifying specific genes that affect risk for common diseases are dramatic illustrations of how improved technology can lead to scientific breakthroughs. A key issue in high-throughput genotyping is to choose the appropriate technology for your goals and for the stage of your experiment, being cognizant of your sample numbers and resources. This article introduces some of the commonly used methods of high-throughput single-nucleotide polymorphism (SNP) genotyping for different stages of genetic studies and briefly reviews some of the high-throughput sequencing methods just coming into use. It also mentions some recent developments in "next-generation" sequencing that will enable other kinds of studies. This article is not intended to be comprehensive, and because technology in this area is rapidly changing, our comments should be taken as a starting point for further investigation.},
author = {Edenberg, Howard J and Liu, Yunlong},
doi = {10.1101/pdb.top62},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Edenberg, Liu/Cold Spring Harbor protocols/Cold Spring Harb Protoc-2009-Edenberg-pdb.top62.pdf:pdf},
issn = {1559-6095},
journal = {Cold Spring Harbor protocols},
keywords = {Clinical Laboratory Techniques,Genetic Linkage,Genome-Wide Association Study,Genotype,High-Throughput Screening Assays,High-Throughput Screening Assays: methods,Humans,Physical Chromosome Mapping,Polymorphism, Single Nucleotide,Polymorphism, Single Nucleotide: genetics,Quality Control,Sequence Analysis, DNA},
month = nov,
number = {11},
pages = {pdb.top62},
pmid = {20150074},
title = {{Laboratory methods for high-throughput genotyping.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20150074},
volume = {2009},
year = {2009}
}
@article{Bernardo2008,
author = {Bernardo, Rex},
doi = {10.2135/cropsci2008.03.0131},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Bernardo/Crop Science/cs-48-5-1649.pdf:pdf},
issn = {1435-0653},
journal = {Crop Science},
number = {5},
pages = {1649},
title = {{Molecular Markers and Selection for Complex Traits in Plants: Learning from the Last 20 Years}},
url = {https://www.crops.org/publications/cs/abstracts/48/5/1649},
volume = {48},
year = {2008}
}
@article{Resendis-Antonio2007,
abstract = {Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. This symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific challenge with direct applications in agronomy and plant development. Rhizobium etli is a bacteria which provides legumes with ammonia (among other chemical compounds), thereby stimulating plant growth. A genome-scale approach, integrating the biochemical information available for R. etli, constitutes an important step toward understanding the symbiotic relationship and its possible improvement. In this work we present a genome-scale metabolic reconstruction (iOR363) for R. etli CFN42, which includes 387 metabolic and transport reactions across 26 metabolic pathways. This model was used to analyze the physiological capabilities of R. etli during stages of nitrogen fixation. To study the physiological capacities in silico, an objective function was formulated to simulate symbiotic nitrogen fixation. Flux balance analysis (FBA) was performed, and the predicted active metabolic pathways agreed qualitatively with experimental observations. In addition, predictions for the effects of gene deletions during nitrogen fixation in Rhizobia in silico also agreed with reported experimental data. Overall, we present some evidence supporting that FBA of the reconstructed metabolic network for R. etli provides results that are in agreement with physiological observations. Thus, as for other organisms, the reconstructed genome-scale metabolic network provides an important framework which allows us to compare model predictions with experimental measurements and eventually generate hypotheses on ways to improve nitrogen fixation.},
author = {Resendis-Antonio, Osbaldo and Reed, Jennifer L and Encarnaci\'{o}n, Sergio and Collado-Vides, Julio and Palsson, Bernhard \O},
doi = {10.1371/journal.pcbi.0030192},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Resendis-Antonio et al/PLoS computational biology/journal.pcbi.0030192.pdf:pdf},
issn = {1553-7358},
journal = {PLoS computational biology},
keywords = {Gene Expression Regulation, Bacterial,Gene Expression Regulation, Bacterial: physiology,Genome, Bacterial,Genome, Bacterial: physiology,Metabolic Networks and Pathways,Models, Biological,Nitrogen Fixation,Nitrogen Fixation: genetics,Rhizobium etli,Rhizobium etli: genetics,Rhizobium etli: metabolism,Symbiosis},
month = oct,
number = {10},
pages = {1887--95},
pmid = {17922569},
title = {{Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2000972\&tool=pmcentrez\&rendertype=abstract},
volume = {3},
year = {2007}
}
@article{Collard2005,
author = {Collard, B. C. Y. and Jahufer, M. Z. Z. and Brouwer, J. B. and Pang, E. C. K.},
doi = {10.1007/s10681-005-1681-5},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Collard et al/Euphytica/ab5b86d33fd71ca838139387d60eeb2fa635c1fb.pdf:pdf},
isbn = {1068100516},
issn = {0014-2336},
journal = {Euphytica},
keywords = {bulked-segregant analysis,dna markers,linkage map,marker-assisted selection,qtl analysis,qtl mapping,qtls,quantitative trait loci},
month = jan,
number = {1-2},
pages = {169--196},
title = {{An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts}},
url = {http://www.springerlink.com/index/10.1007/s10681-005-1681-5},
volume = {142},
year = {2005}
}
@article{Clarke2013,
author = {Clarke, J.},
doi = {10.1126/science.1235463},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Clarke/Science/b2caeab1418413513bb45930a5dba6be3e1a2b58.pdf:pdf},
issn = {0036-8075},
journal = {Science},
month = may,
number = {6133},
pages = {690--692},
title = {{Feathers Before Flight}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1235463},
volume = {340},
year = {2013}
}
@article{Foster2012,
abstract = {BACKGROUND: In interphase nuclei of a wide range of species chromosomes are organised into their own specific locations termed territories. These chromosome territories are non-randomly positioned in nuclei which is believed to be related to a spatial aspect of regulatory control over gene expression. In this study we have adopted the pig as a model in which to study interphase chromosome positioning and follows on from other studies from our group of using pig cells and tissues to study interphase genome re-positioning during differentiation. The pig is an important model organism both economically and as a closely related species to study human disease models. This is why great efforts have been made to accomplish the full genome sequence in the last decade. RESULTS: This study has positioned most of the porcine chromosomes in in vitro cultured adult and embryonic fibroblasts, early passage stromal derived mesenchymal stem cells and lymphocytes. The study is further expanded to position four chromosomes in ex vivo tissue derived from pig kidney, lung and brain. CONCLUSIONS: It was concluded that porcine chromosomes are also non-randomly positioned within interphase nuclei with few major differences in chromosome position in interphase nuclei between different cell and tissue types. There were also no differences between preferred nuclear location of chromosomes in in vitro cultured cells as compared to cells in tissue sections. Using a number of analyses to ascertain by what criteria porcine chromosomes were positioned in interphase nuclei; we found a correlation with DNA content.},
author = {Foster, Helen A and Griffin, Darren K and Bridger, Joanna M},
doi = {10.1186/1471-2121-13-30},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Foster, Griffin, Bridger/BMC cell biology/1471-2121-13-30.pdf:pdf},
issn = {1471-2121},
journal = {BMC cell biology},
keywords = {Animals,Cells,Chromosome Positioning,Chromosome Positioning: physiology,Chromosomes,Chromosomes: physiology,Confocal,Cultured,Fibroblasts,Fibroblasts: cytology,Fibroblasts: metabolism,Fluorescence,In Situ Hybridization,Interphase,Lymphocytes,Lymphocytes: cytology,Lymphocytes: metabolism,Mesenchymal Stromal Cells,Mesenchymal Stromal Cells: cytology,Mesenchymal Stromal Cells: metabolism,Microscopy,Swine},
month = jan,
number = {1},
pages = {30},
pmid = {23151271},
publisher = {BMC Cell Biology},
title = {{Interphase chromosome positioning in in vitro porcine cells and ex vivo porcine tissues.}},
url = {BMC Cell Biology http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3499214\&tool=pmcentrez\&rendertype=abstract},
volume = {13},
year = {2012}
}
@article{HernandezPatino2012,
abstract = {One of the main objectives in systems biology is to understand the biological mechanisms that give rise to the phenotype of a microorganism by using high-throughput technologies (HTs) and genome-scale mathematical modeling. The computational modeling of genome-scale metabolic reconstructions is one systemic and quantitative strategy for characterizing the metabolic phenotype associated with human diseases and potentially for designing drugs with optimal clinical effects. The purpose of this short review is to describe how computational modeling, including the specific case of constraint-based modeling, can be used to explore, characterize, and predict the metabolic capacities that distinguish the metabolic phenotype of cancer cell lines. As we show herein, this computational framework is far from a pure theoretical description, and to ensure proper biological interpretation, it is necessary to integrate high-throughput data and generate predictions for later experimental assessment. Hence, genome-scale modeling serves as a platform for the following: (1) the integration of data from HTs, (2) the assessment of how metabolic activity is related to phenotype in cancer cell lines, and (3) the design of new experiments to evaluate the outcomes of the in silico analysis. By combining the functions described above, we show that computational modeling is a useful methodology to construct an integrative, systemic, and quantitative scheme for understanding the metabolic profiles of cancer cell lines, a first step to determine the metabolic mechanism by which cancer cells maintain and support their malignant phenotype in human tissues.},
author = {{Hern\'{a}ndez Pati\~{n}o}, Claudia E and Jaime-Mu\~{n}oz, Gustavo and Resendis-Antonio, Osbaldo},
doi = {10.3389/fphys.2012.00481},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Hern\'{a}ndez Pati\~{n}o, Jaime-Mu\~{n}oz, Resendis-Antonio/Frontiers in physiology/fphys-03-00481.pdf:pdf},
issn = {1664-042X},
journal = {Frontiers in physiology},
keywords = {cancer metabolic phenotype,computational modeling of metabolism,computational modeling of metabolism, cancer metab,constraint-based modeling,genome scale metabolic reconstruction,high throughput biology},
month = jan,
number = {January},
pages = {481},
pmid = {23316163},
title = {{Systems biology of cancer: moving toward the integrative study of the metabolic alterations in cancer cells.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3539652\&tool=pmcentrez\&rendertype=abstract},
volume = {3},
year = {2012}
}
@article{Fonseca2010,
abstract = {Biodiversity is of crucial importance for ecosystem functioning, sustainability and resilience, but the magnitude and organization of marine diversity at a range of spatial and taxonomic scales are undefined. In this paper, we use second-generation sequencing to unmask putatively diverse marine metazoan biodiversity in a Scottish temperate benthic ecosystem. We show that remarkable differences in diversity occurred at microgeographical scales and refute currently accepted ecological and taxonomic paradigms of meiofaunal identity, rank abundance and concomitant understanding of trophic dynamics. Richness estimates from the current benchmarked Operational Clustering of Taxonomic Units from Parallel UltraSequencing analyses are broadly aligned with those derived from morphological assessments. However, the slope of taxon rarefaction curves for many phyla remains incomplete, suggesting that the true alpha diversity is likely to exceed current perceptions. The approaches provide a rapid, objective and cost-effective taxonomic framework for exploring links between ecosystem structure and function of all hitherto intractable, but ecologically important, communities.},
author = {Fonseca, Vera G and Carvalho, Gary R and Sung, Way and Johnson, Harriet F and Power, Deborah M and Neill, Simon P and Packer, Margaret and Blaxter, Mark L and Lambshead, P John D and Thomas, W Kelley and Creer, Simon},
doi = {10.1038/ncomms1095},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Fonseca et al/Nature communications/Fonseca et al. - 2010 - Second-generation environmental sequencing unmasks marine metazoan biodiversity.pdf:pdf},
issn = {2041-1723},
journal = {Nature communications},
month = oct,
number = {7},
pages = {98},
pmid = {20981026},
publisher = {Nature Publishing Group},
title = {{Second-generation environmental sequencing unmasks marine metazoan biodiversity.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20981026},
volume = {1},
year = {2010}
}
@article{Kundeti2010,
abstract = {Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories - based on the data structures which they employ. The first class uses an overlap/string graph and the second type uses a de Bruijn graph. However with the recent advances in short read sequencing technology, de Bruijn graph based algorithms seem to play a vital role in practice. Efficient algorithms for building these massive de Bruijn graphs are very essential in large sequencing projects based on short reads. In an earlier work, an O(n/p) time parallel algorithm has been given for this problem. Here n is the size of the input and p is the number of processors. This algorithm enumerates all possible bi-directed edges which can overlap with a node and ends up generating $\Theta$(n$\Sigma$) messages ($\Sigma$ being the size of the alphabet).},
author = {Kundeti, Vamsi K and Rajasekaran, Sanguthevar and Dinh, Hieu and Vaughn, Matthew and Thapar, Vishal},
doi = {10.1186/1471-2105-11-560},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Kundeti et al/BMC bioinformatics/Kundeti et al. - 2010 - Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs.pdf:pdf},
issn = {1471-2105},
journal = {BMC bioinformatics},
keywords = {Algorithms,Base Sequence,Computational Biology,Computational Biology: methods,DNA,DNA: methods,Genome,Sequence Analysis},
month = jan,
number = {1},
pages = {560},
pmid = {21078174},
title = {{Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21078174 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2996408\&tool=pmcentrez\&rendertype=abstract},
volume = {11},
year = {2010}
}
@article{Li2009a,
abstract = {SUMMARY: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. AVAILABILITY: http://samtools.sourceforge.net.},
author = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard},
doi = {10.1093/bioinformatics/btp352},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Li et al/Bioinformatics (Oxford, England)/Li et al. - 2009 - The Sequence AlignmentMap format and SAMtools.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
keywords = {Algorithms,Base Sequence,Computational Biology,Computational Biology: methods,Genome,Genomics,Molecular Sequence Data,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Software},
month = aug,
number = {16},
pages = {2078--9},
pmid = {19505943},
title = {{The Sequence Alignment/Map format and SAMtools.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2723002\&tool=pmcentrez\&rendertype=abstract},
volume = {25},
year = {2009}
}
@article{Stephens2001,
abstract = {Current routine genotyping methods typically do not provide haplotype information, which is essential for many analyses of fine-scale molecular-genetics data. Haplotypes can be obtained, at considerable cost, experimentally or (partially) through genotyping of additional family members. Alternatively, a statistical method can be used to infer phase and to reconstruct haplotypes. We present a new statistical method, applicable to genotype data at linked loci from a population sample, that improves substantially on current algorithms; often, error rates are reduced by > 50\%, relative to its nearest competitor. Furthermore, our algorithm performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping additional family members may be an inefficient use of resources.},
author = {Stephens, M and Smith, N J and Donnelly, P},
doi = {10.1086/319501},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Stephens, Smith, Donnelly/American journal of human genetics/f73e738b801f48c8823ba31d7a229c14f89a6225.pdf:pdf},
issn = {0002-9297},
journal = {American journal of human genetics},
keywords = {Algorithms,Calibration,Computer Simulation,Gene Frequency,Gene Frequency: genetics,Haplotypes,Haplotypes: genetics,Humans,Research Design,Sensitivity and Specificity,Statistics as Topic},
month = apr,
number = {4},
pages = {978--89},
pmid = {11254454},
title = {{A new statistical method for haplotype reconstruction from population data.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1275651\&tool=pmcentrez\&rendertype=abstract},
volume = {68},
year = {2001}
}
@article{Rozen,
author = {Rozen, Steve and Skaletsky, Helen},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Rozen, Skaletsky/Methods in molecular biology (Clifton, N.J.)/e26b2804e4d12e0391893c496d46fdbd832dd1a2.pdf:pdf},
issn = {1064-3745},
journal = {Methods in molecular biology (Clifton, N.J.)},
keywords = {Base Sequence,DNA Primers,Database Management Systems,Internet,Molecular Sequence Data,Nucleic Acid,Polymerase Chain Reaction,Sequence Homology,User-Computer Interface},
month = jan,
pages = {365--86},
pmid = {10547847},
title = {{Primer3 on the WWW for general users and for biologist programmers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10547847},
volume = {132},
year = {2000}
}
@article{Needleman1970,
abstract = {A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed. From these findings it is possible to determine whether significant homology exists between the proteins. This information is used to trace their possible evolutionary development. The maximum match is a number dependent upon the similarity of the sequences. One of its definitions is the largest number of amino acids of one protein that can be matched with those of a second protein allowing for all possible interruptions in either of the sequences. While the interruptions give rise to a very large number of comparisons, the method efficiently excludes from consideration those comparisons that cannot contribute to the maximum match. Comparisons are made from the smallest unit of significance, a pair of amino acids, one from each protein. All possible pairs are represented by a two-dimensional array, and all possible comparisons are represented by pathways through the array. For this maximum match only certain of the possible pathways must be evaluated. A numerical value, one in this case, is assigned to every cell in the array representing like amino acids. The maximum match is the largest number that would result from summing the cell values of every pathway.},
author = {Needleman, Saul B. and Wunsch, Christian D.},
doi = {10.1016/0022-2836(70)90057-4},
issn = {00222836},
journal = {Journal of Molecular Biology},
month = mar,
number = {3},
pages = {443--453},
title = {{A general method applicable to the search for similarities in the amino acid sequence of two proteins}},
url = {http://dx.doi.org/10.1016/0022-2836(70)90057-4},
volume = {48},
year = {1970}
}
@article{Patel2014,
abstract = {Human cancers are complex ecosystems composed of cells with distinct phenotypes, genotypes, and epigenetic states, but current models do not adequately reflect tumor composition in patients. We used single-cell RNA sequencing (RNA-seq) to profile 430 cells from five primary glioblastomas, which we found to be inherently variable in their expression of diverse transcriptional programs related to oncogenic signaling, proliferation, complement/immune response, and hypoxia. We also observed a continuum of stemness-related expression states that enabled us to identify putative regulators of stemness in vivo. Finally, we show that established glioblastoma subtype classifiers are variably expressed across individual cells within a tumor and demonstrate the potential prognostic implications of such intratumoral heterogeneity. Thus, we reveal previously unappreciated heterogeneity in diverse regulatory programs central to glioblastoma biology, prognosis, and therapy.},
author = {Patel, Anoop P and Tirosh, Itay and Trombetta, John J and Shalek, Alex K and Gillespie, Shawn M and Wakimoto, Hiroaki and Cahill, Daniel P and Nahed, Brian V and Curry, William T and Martuza, Robert L and Louis, David N and Rozenblatt-Rosen, Orit and Suv\`{a}, Mario L and Regev, Aviv and Bernstein, Bradley E},
doi = {10.1126/science.1254257},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Patel et al/Science (New York, N.Y.)/Unknown - Unknown - No Title.pdf:pdf},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Brain Neoplasms,Brain Neoplasms: classification,Brain Neoplasms: drug therapy,Brain Neoplasms: genetics,Gene Expression Profiling,Genetic Variation,Glioblastoma,Glioblastoma: classification,Glioblastoma: drug therapy,Glioblastoma: genetics,Humans,Messenger,Messenger: genetics,Prognosis,RNA,RNA: methods,Sequence Analysis,Single-Cell Analysis,Single-Cell Analysis: methods},
month = jun,
number = {6190},
pages = {1396--401},
pmid = {24925914},
title = {{Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24925914},
volume = {344},
year = {2014}
}
@article{Hahn2014,
abstract = {Current de novo whole genome sequencing approaches are often inadequate for organisms lacking substantial pre-existing genetic data. Problems with these methods are manifest as: large numbers of scaffolds that are not ordered within chromosomes or assigned to individual chromosomes, misassembly of allelic sequences as separate loci when the individual(s) being sequenced are heterozygous, and the collapse of recently duplicated sequences into a single locus, regardless of levels of heterozygosity. Here we propose a new approach for producing de novo whole genome sequences-which we call recombinant population genome construction (RPGC)-that solves many of the problems encountered in standard genome assembly, and that can be applied in model and non-model organisms. Our approach takes advantage of next-generation sequencing technologies to simultaneously barcode and sequence a large number of individuals from a recombinant population. The sequences of all recombinants can be combined to create an initial de novo assembly, followed by the use of individual recombinant genotypes to correct assembly splitting/collapsing and to order and orient scaffolds within linkage groups. RPGC can rapidly accelerate the transformation of non-model species into genome-enabled systems by simultaneously producing a high quality genome assembly and providing genomic tools (e.g. high-confidence SNPs) for immediate applications. In populations segregating for important functional traits, this approach also enables simultaneous mapping of quantitative trait loci. We demonstrate our method using simulated Illumina data from a recombinant population of Caenorhabditis elegans, and show that the method can produce a high-fidelity, high-quality genome assembly for both parents of the cross.},
author = {Hahn, Matthew W and Zhang, Simo V and Moyle, Leonie C},
doi = {10.1534/g3.114.010264},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Hahn, Zhang, Moyle/G3 (Bethesda, Md.)/uyghmi-g3.114.010264.full.pdf:pdf},
issn = {2160-1836},
journal = {G3 (Bethesda, Md.)},
keywords = {assembly,duplication,genetics,genome,next-generation sequencing},
month = feb,
pmid = {24531727},
title = {{Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24531727},
year = {2014}
}
@article{Cavanagh2013,
abstract = {Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.},
author = {Cavanagh, Colin R and Chao, Shiaoman and Wang, Shichen and Huang, Bevan Emma and Stephen, Stuart and Kiani, Seifollah and Forrest, Kerrie and Saintenac, Cyrille and Brown-Guedira, Gina L and Akhunova, Alina and See, Deven and Bai, Guihua and Pumphrey, Michael and Tomar, Luxmi and Wong, Debbie and Kong, Stephan and Reynolds, Matthew and da Silva, Marta Lopez and Bockelman, Harold and Talbert, Luther and Anderson, James A and Dreisigacker, Susanne and Baenziger, Stephen and Carter, Arron and Korzun, Viktor and Morrell, Peter Laurent and Dubcovsky, Jorge and Morell, Matthew K and Sorrells, Mark E and Hayden, Matthew J and Akhunov, Eduard},
doi = {10.1073/pnas.1217133110},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Cavanagh et al/Proceedings of the National Academy of Sciences of the United States of America/Cavanagh et al. - 2013 - Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat lan.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Alleles,Crops, Agricultural,Crops, Agricultural: genetics,Gene Frequency,Genes, Plant,Genetic Variation,Genome, Plant,Genotype,Haplotypes,Oligonucleotide Array Sequence Analysis,Ploidies,Polymorphism, Single Nucleotide,Triticum,Triticum: genetics},
month = may,
number = {20},
pages = {8057--62},
pmid = {23630259},
title = {{Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars.}},
url = {http://www.pnas.org/content/110/20/8057.short},
volume = {110},
year = {2013}
}
@article{Kim2013,
abstract = {TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2 is available at http://ccb.jhu.edu/software/tophat.},
author = {Kim, Daehwan and Pertea, Geo and Trapnell, Cole and Pimentel, Harold and Kelley, Ryan and Salzberg, Steven L},
doi = {10.1186/gb-2013-14-4-r36},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Kim et al/Genome biology/gb-2013-14-4-r36.pdf:pdf},
issn = {1465-6914},
journal = {Genome biology},
month = apr,
number = {4},
pages = {R36},
pmid = {23618408},
publisher = {BioMed Central Ltd},
title = {{TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4053844\&tool=pmcentrez\&rendertype=abstract},
volume = {14},
year = {2013}
}
@article{Keating2013,
abstract = {Highly pathogenic avian influenza viruses pose a continuing global threat. Current vaccines will not protect against newly evolved pandemic viruses. The creation of 'universal' vaccines has been unsuccessful because the immunological mechanisms that promote heterosubtypic immunity are incompletely defined. We found here that rapamycin, an immunosuppressive drug that inhibits the kinase mTOR, promoted cross-strain protection against lethal infection with influenza virus of various subtypes when administered during immunization with influenza virus subtype H3N2. Rapamycin reduced the formation of germinal centers and inhibited class switching in B cells, which yielded a unique repertoire of antibodies that mediated heterosubtypic protection. Our data established a requirement for the mTORC1 complex in B cell class switching and demonstrated that rapamycin skewed the antibody response away from high-affinity variant epitopes and targeted more conserved elements of hemagglutinin. Our findings have implications for the design of a vaccine against influenza virus.},
author = {Keating, Rachael and Hertz, Tomer and Wehenkel, Marie and Harris, Tarsha L and Edwards, Benjamin A and McClaren, Jennifer L and Brown, Scott A and Surman, Sherri and Wilson, Zachary S and Bradley, Philip and Hurwitz, Julia and Chi, Hongbo and Doherty, Peter C and Thomas, Paul G and McGargill, Maureen A},
doi = {10.1038/ni.2741},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Keating et al/Nature immunology/d2d729432855e986db551b5120fe5cc5d5032e5f.pdf:pdf},
issn = {1529-2916},
journal = {Nature immunology},
month = oct,
pmid = {24141387},
title = {{The kinase mTOR modulates the antibody response to provide cross-protective immunity to lethal infection with influenza virus.}},
url = {http://www.nature.com/ni/journal/vaop/ncurrent/pdf/ni.2741.pdf http://www.ncbi.nlm.nih.gov/pubmed/24141387},
year = {2013}
}
@article{Jupe2013,
abstract = {RenSeq is a NB-LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB-LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB-LRRs and can be accessed through a genome browser that we provide. We compared these NB-LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that \~{}80\% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum 'Heinz 1706' extended the NB-LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi-ber2) and S. ruiz-ceballosii (Rpi-rzc1), we were able to apply RenSeq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines.},
author = {Jupe, Florian and Witek, Kamil and Verweij, Walter and Sliwka, Jadwiga and Pritchard, Leighton and Etherington, Graham J and Maclean, Dan and Cock, Peter J and Leggett, Richard M and Bryan, Glenn J and Cardle, Linda and Hein, Ingo and Jones, Jonathan D G},
doi = {10.1111/tpj.12307},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Jupe et al/The Plant journal for cell and molecular biology/tpj12307.pdf:pdf},
issn = {1365-313X},
journal = {The Plant journal : for cell and molecular biology},
keywords = {clone dm1-3 516 r44,lycopersicum,nb-lrr,next-generation sequencing,num tuberosum group phureja,pathogen resistance,sola-,solanaceae,solanum,solanum berthaultii,solanum ruiz-ceballosii,target enrichment,technical advance},
month = nov,
number = {3},
pages = {530--544},
pmid = {23937694},
title = {{Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23937694},
volume = {76},
year = {2013}
}
@article{Bian2013,
author = {Bian, G. and Joshi, D. and Dong, Y. and Lu, P. and Zhou, G. and Pan, X. and Xu, Y. and Dimopoulos, G. and Xi, Z.},
doi = {10.1126/science.1236192},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Bian et al/Science/92b2f19b5de6fbad01c6b96c5933b7c463738228.pdf:pdf},
issn = {0036-8075},
journal = {Science},
month = may,
number = {6133},
pages = {748--751},
title = {{Wolbachia Invades Anopheles stephensi Populations and Induces Refractoriness to Plasmodium Infection}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1236192},
volume = {340},
year = {2013}
}
@article{Trapnell2012,
abstract = {Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression analysis of high-throughput mRNA sequencing (RNA-seq) data. Together, they allow biologists to identify new genes and new splice variants of known ones, as well as compare gene and transcript expression under two or more conditions. This protocol describes in detail how to use TopHat and Cufflinks to perform such analyses. It also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-seq analysis results. Although the procedure assumes basic informatics skills, these tools assume little to no background with RNA-seq analysis and are meant for novices and experts alike. The protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results. The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time.},
author = {Trapnell, Cole and Roberts, Adam and Goff, Loyal and Pertea, Geo and Kim, Daehwan and Kelley, David R and Pimentel, Harold and Salzberg, Steven L and Rinn, John L and Pachter, Lior},
doi = {10.1038/nprot.2012.016},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Trapnell et al/Nature protocols/nprot.2012.016.pdf:pdf},
issn = {1750-2799},
journal = {Nature protocols},
keywords = {DNA, Complementary,DNA, Complementary: genetics,Gene Expression Profiling,Gene Expression Profiling: methods,Genetic Association Studies,Genetic Association Studies: methods,Genomics,Genomics: methods,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Software},
month = mar,
number = {3},
pages = {562--78},
pmid = {22383036},
title = {{Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3334321\&tool=pmcentrez\&rendertype=abstract},
volume = {7},
year = {2012}
}
@article{Woo2012,
abstract = {Recently, we reported the discovery of three novel coronaviruses, bulbul coronavirus HKU11, thrush coronavirus HKU12, and munia coronavirus HKU13, which were identified as representatives of a novel genus, Deltacoronavirus, in the subfamily Coronavirinae. In this territory-wide molecular epidemiology study involving 3,137 mammals and 3,298 birds, we discovered seven additional novel deltacoronaviruses in pigs and birds, which we named porcine coronavirus HKU15, white-eye coronavirus HKU16, sparrow coronavirus HKU17, magpie robin coronavirus HKU18, night heron coronavirus HKU19, wigeon coronavirus HKU20, and common moorhen coronavirus HKU21. Complete genome sequencing and comparative genome analysis showed that the avian and mammalian deltacoronaviruses have similar genome characteristics and structures. They all have relatively small genomes (25.421 to 26.674 kb), the smallest among all coronaviruses. They all have a single papain-like protease domain in the nsp3 gene; an accessory gene, NS6 open reading frame (ORF), located between the M and N genes; and a variable number of accessory genes (up to four) downstream of the N gene. Moreover, they all have the same putative transcription regulatory sequence of ACACCA. Molecular clock analysis showed that the most recent common ancestor of all coronaviruses was estimated at approximately 8100 BC, and those of Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus were at approximately 2400 BC, 3300 BC, 2800 BC, and 3000 BC, respectively. From our studies, it appears that bats and birds, the warm blooded flying vertebrates, are ideal hosts for the coronavirus gene source, bats for Alphacoronavirus and Betacoronavirus and birds for Gammacoronavirus and Deltacoronavirus, to fuel coronavirus evolution and dissemination.},
author = {Woo, Patrick C Y and Lau, Susanna K P and Lam, Carol S F and Lau, Candy C Y and Tsang, Alan K L and Lau, John H N and Bai, Ru and Teng, Jade L L and Tsang, Chris C C and Wang, Ming and Zheng, Bo-Jian and Chan, Kwok-Hung and Yuen, Kwok-Yung},
doi = {10.1128/JVI.06540-11},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Woo et al/Journal of virology/Delta en China.pdf:pdf},
issn = {1098-5514},
journal = {Journal of virology},
keywords = {Animals,Base Sequence,Bird Diseases,Bird Diseases: virology,Cats,Chiroptera,Chiroptera: virology,Coronaviridae,Coronaviridae Infections,Coronaviridae Infections: veterinary,Coronaviridae Infections: virology,Coronaviridae: classification,Coronaviridae: genetics,Coronaviridae: isolation \& purification,Coronavirus,Coronavirus: classification,Coronavirus: genetics,Coronavirus: isolation \& purification,Dogs,Evolution,Genome,Haplorhini,Humans,Mammals,Mammals: virology,Molecular,Molecular Sequence Data,Phylogeny,Rodentia,Swine,Viral,Viral Proteins,Viral Proteins: genetics},
month = apr,
number = {7},
pages = {3995--4008},
pmid = {22278237},
title = {{Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavi}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3302495\&tool=pmcentrez\&rendertype=abstract},
volume = {86},
year = {2012}
}
@article{Scholz2012,
abstract = {The recent technological advances in next generation sequencing have brought the field closer to the goal of reconstructing all genomes within a community by presenting high throughput sequencing at much lower costs. While these next-generation sequencing technologies have allowed a massive increase in available raw sequence data, there are a number of new informatics challenges and difficulties that must be addressed to improve the current state, and fulfill the promise of, metagenomics.},
author = {Scholz, Matthew B and Lo, Chien-Chi and Chain, Patrick S G},
doi = {10.1016/j.copbio.2011.11.013},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Scholz, Lo, Chain/Current opinion in biotechnology/1-s2.0-S0958166911007245-main.pdf:pdf},
issn = {1879-0429},
journal = {Current opinion in biotechnology},
keywords = {Algorithms,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: economics,High-Throughput Nucleotide Sequencing: methods,Metagenomics,Metagenomics: economics,Metagenomics: methods,Sequence Analysis, DNA,Sequence Analysis, DNA: economics,Sequence Analysis, DNA: methods},
month = feb,
number = {1},
pages = {9--15},
pmid = {22154470},
title = {{Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22154470},
volume = {23},
year = {2012}
}
@article{Casals2012,
abstract = {The advent of next generation sequencing technologies has opened new possibilities in the analysis of human disease. In this review we present the main next-generation sequencing technologies, with their major contributions and possible applications to the study of the genetic etiology of complex diseases.},
author = {Casals, Ferran and Idaghdour, Youssef and Hussin, Julie and Awadalla, Philip},
doi = {10.1016/j.jneuroim.2011.12.017},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Casals et al/Journal of neuroimmunology/NGSCOMPLEX DISEASES.pdf:pdf},
issn = {1872-8421},
journal = {Journal of neuroimmunology},
keywords = {Chromosome Mapping,Chromosome Mapping: methods,Chromosome Mapping: trends,Genetic Diseases, Inborn,Genetic Diseases, Inborn: diagnosis,Genetic Diseases, Inborn: genetics,Genetic Diseases, Inborn: physiopathology,Genetic Predisposition to Disease,Genetic Predisposition to Disease: genetics,Genotyping Techniques,Genotyping Techniques: methods,Genotyping Techniques: trends,Humans,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Sequence Analysis, DNA: trends},
month = jul,
number = {1-2},
pages = {10--22},
pmid = {22285396},
publisher = {Elsevier B.V.},
title = {{Next-generation sequencing approaches for genetic mapping of complex diseases.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22285396},
volume = {248},
year = {2012}
}
@article{Abe2012,
abstract = {The majority of agronomic traits are controlled by multiple genes that cause minor phenotypic effects, making the identification of these genes difficult. Here we introduce MutMap, a method based on whole-genome resequencing of pooled DNA from a segregating population of plants that show a useful phenotype. In MutMap, a mutant is crossed directly to the original wild-type line and then selfed, allowing unequivocal segregation in second filial generation (F(2)) progeny of subtle phenotypic differences. This approach is particularly amenable to crop species because it minimizes the number of genetic crosses (n = 1 or 0) and mutant F(2) progeny that are required. We applied MutMap to seven mutants of a Japanese elite rice cultivar and identified the unique genomic positions most probable to harbor mutations causing pale green leaves and semidwarfism, an agronomically relevant trait. These results show that MutMap can accelerate the genetic improvement of rice and other crop plants.},
author = {Abe, Akira and Kosugi, Shunichi and Yoshida, Kentaro and Natsume, Satoshi and Takagi, Hiroki and Kanzaki, Hiroyuki and Matsumura, Hideo and Yoshida, Kakoto and Mitsuoka, Chikako and Tamiru, Muluneh and Innan, Hideki and Cano, Liliana and Kamoun, Sophien and Terauchi, Ryohei},
doi = {10.1038/nbt.2095},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Abe et al/Nature biotechnology/c0245086bbef07634ac7ea1c364e6103919712e7.pdf:pdf},
issn = {1546-1696},
journal = {Nature biotechnology},
keywords = {Chromosome Mapping,Crops, Agricultural,Crops, Agricultural: genetics,Crosses, Genetic,Genome, Plant,Genotype,Mutation,Mutation: genetics,Oryza sativa,Oryza sativa: genetics,Phenotype,Plant Leaves,Plant Leaves: genetics,Polymorphism, Single Nucleotide,Quantitative Trait Loci,Quantitative Trait Loci: genetics,Sequence Analysis, DNA,Sequence Analysis, DNA: methods},
month = feb,
number = {2},
pages = {174--8},
pmid = {22267009},
publisher = {Nature Publishing Group},
title = {{Genome sequencing reveals agronomically important loci in rice using MutMap.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22267009},
volume = {30},
year = {2012}
}
@article{Schuenemann2011,
author = {Schuenemann, V. J. and Bos, K. and DeWitte, S. and Schmedes, S. and Jamieson, J. and Mittnik, a. and Forrest, S. and Coombes, B. K. and Wood, J. W. and Earn, D. J. D. and White, W. and Krause, J. and Poinar, H. N.},
doi = {10.1073/pnas.1105107108},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Schuenemann et al/Proceedings of the National Academy of Sciences/PNAS-2011-Schuenemann-1105107108.pdf:pdf},
isbn = {1105107108},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
month = aug,
pages = {1--7},
title = {{PNAS Plus: Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1105107108},
year = {2011}
}
@article{Currat2011,
author = {Currat, M. and Excoffier, L.},
doi = {10.1073/pnas.1107450108},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Currat, Excoffier/Proceedings of the National Academy of Sciences/PNAS-2011-Currat-15129-34.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
month = sep,
number = {37},
pages = {15129--15134},
title = {{Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1107450108},
volume = {108},
year = {2011}
}
@article{,
file = {:Users/ramirezr/Documents/Mendeley Desktop/Unknown/Unknown/G38\_Wheat\_Disease\_Guide\_2011.pdf:pdf},
title = {{The HGCA wheat disease management guide 2011}},
year = {2011}
}
@misc{TheMendeleySupportTeam2011d,
abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.},
address = {London},
author = {{The Mendeley Support Team}},
booktitle = {Mendeley Desktop},
file = {:Users/ramirezr/Documents/Mendeley Desktop/The Mendeley Support Team/Mendeley Desktop/The Mendeley Support Team - 2011 - Getting Started with Mendeley(2).pdf:pdf},
keywords = {Mendeley,how-to,user manual},
pages = {1--16},
publisher = {Mendeley Ltd.},
title = {{Getting Started with Mendeley}},
url = {http://www.mendeley.com},
year = {2011}
}
@article{Morrell2011,
abstract = {The completion of reference genome sequences for many important crops and the ability to perform high-throughput resequencing are providing opportunities for improving our understanding of the history of plant domestication and to accelerate crop improvement. Crop plant comparative genomics is being transformed by these data and a new generation of experimental and computational approaches. The future of crop improvement will be centred on comparisons of individual plant genomes, and some of the best opportunities may lie in using combinations of new genetic mapping strategies and evolutionary analyses to direct and optimize the discovery and use of genetic variation. Here we review such strategies and insights that are emerging.},
author = {Morrell, Peter L and Buckler, Edward S and Ross-Ibarra, Jeffrey},
doi = {10.1038/nrg3097},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Morrell, Buckler, Ross-Ibarra/Nature reviews. Genetics/Crop breeding.pdf:pdf},
issn = {1471-0064},
journal = {Nature reviews. Genetics},
keywords = {Agricultural,Agricultural: genetics,Crops,Evolution,Genome,Genomics,High-Throughput Nucleotide Sequencing,Molecular,Plant},
month = feb,
number = {2},
pages = {85--96},
pmid = {22207165},
publisher = {Nature Publishing Group},
title = {{Crop genomics: advances and applications.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22207165},
volume = {13},
year = {2011}
}
@article{Procedure2010,
author = {Procedure, Installation},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Procedure/PDA journal of pharmaceutical science and technology PDA/Procedure - 2010 - Technical Bulletin no. 2003-03 freezing of microbial samples prior to testing. Parenteral Drug Association.pdf:pdf},
issn = {1079-7440},
journal = {PDA journal of pharmaceutical science and technology / PDA},
keywords = {Drug Contamination,Drug Contamination: prevention \& control,Freezing,Microbiological Techniques,Microbiological Techniques: methods,Pharmaceutical Preparations,Research Design},
number = {5},
pages = {323},
pmid = {14677623},
title = {{Technical Bulletin no. 2003-03: freezing of microbial samples prior to testing. Parenteral Drug Association.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19007651},
volume = {57},
year = {2010}
}
@article{Geer2010,
abstract = {The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets.},
author = {Geer, Lewis Y and Marchler-Bauer, Aron and Geer, Renata C and Han, Lianyi and He, Jane and He, Siqian and Liu, Chunlei and Shi, Wenyao and Bryant, Stephen H},
doi = {10.1093/nar/gkp858},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Geer et al/Nucleic acids research/Geer et al. - 2010 - The NCBI BioSystems database.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Animals,Cell Membrane,Cell Membrane: metabolism,Computational Biology,Computational Biology: methods,Computational Biology: trends,Databases, Genetic,Databases, Nucleic Acid,Databases, Protein,Genes,Genomics,Humans,Information Storage and Retrieval,Information Storage and Retrieval: methods,Internet,National Library of Medicine (U.S.),Software,Systems Biology,United States},
month = jan,
number = {Database issue},
pages = {D492--6},
pmid = {19854944},
title = {{The NCBI BioSystems database.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2808896\&tool=pmcentrez\&rendertype=abstract},
volume = {38},
year = {2010}
}
@article{Shendure2008,
abstract = {DNA sequence represents a single format onto which a broad range of biological phenomena can be projected for high-throughput data collection. Over the past three years, massively parallel DNA sequencing platforms have become widely available, reducing the cost of DNA sequencing by over two orders of magnitude, and democratizing the field by putting the sequencing capacity of a major genome center in the hands of individual investigators. These new technologies are rapidly evolving, and near-term challenges include the development of robust protocols for generating sequencing libraries, building effective new approaches to data-analysis, and often a rethinking of experimental design. Next-generation DNA sequencing has the potential to dramatically accelerate biological and biomedical research, by enabling the comprehensive analysis of genomes, transcriptomes and interactomes to become inexpensive, routine and widespread, rather than requiring significant production-scale efforts.},
author = {Shendure, Jay and Ji, Hanlee},
doi = {10.1038/nbt1486},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Shendure, Ji/Nature biotechnology/fca2673e087784f17c09ec865013ac22dcbf9fe9.pdf:pdf},
issn = {1546-1696},
journal = {Nature biotechnology},
keywords = {Chromosome Mapping,Chromosome Mapping: trends,Forecasting,Genomics,Genomics: trends,Sequence Alignment,Sequence Alignment: trends,Sequence Analysis, DNA,Sequence Analysis, DNA: trends},
month = oct,
number = {10},
pages = {1135--45},
pmid = {18846087},
title = {{Next-generation DNA sequencing.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18846087},
volume = {26},
year = {2008}
}
@article{Miller2007,
abstract = {Restriction site associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allows RAD tags to serve as genetic markers spread at a high density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and using an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and nonmodel systems.},
author = {Miller, Michael R and Dunham, Joseph P and Amores, Angel and Cresko, William a and Johnson, Eric a},
doi = {10.1101/gr.5681207},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Miller et al/Genome research/Miller et al. - 2007 - Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) m.pdf:pdf},
issn = {1088-9051},
journal = {Genome research},
keywords = {Animals,Base Sequence,Cost-Benefit Analysis,DNA,DNA: genetics,Drosophila,Drosophila: genetics,Gene Library,Genetic Markers,Genotype,Oligonucleotide Array Sequence Analysis,Oligonucleotide Array Sequence Analysis: economics,Oligonucleotide Array Sequence Analysis: methods,Polymorphism, Single Nucleotide,Smegmamorpha,Smegmamorpha: genetics},
month = feb,
number = {2},
pages = {240--8},
pmid = {17189378},
title = {{Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17189378},
volume = {17},
year = {2007}
}
@article{Ross2007,
author = {Ross, CA and Liu, Yue and Shen, QJ},
doi = {10.1111/j.1672-9072.2007.00504.x},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Ross, Liu, Shen/Journal of Integrative Plant Biology/e6dd2701d0b85265ac87481ee520a551df7fc82a.pdf:pdf},
journal = {Journal of Integrative Plant Biology},
keywords = {2007,49,6,827,842,available online at www,because of their inability,blackwell-synergy,com,envi-,gene family,in rice,indica,integr,j,japonica,jipb,links,liu y,net,oryza sativa,plant biol,plants,rice,ross ca,shen qj,the wrky gene family,to escape predation or,toc,wrky,www},
number = {6},
pages = {827--842},
title = {{The WRKY gene family in rice (Oryza sativa)}},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1744-7909.2007.00504.x/full},
volume = {49},
year = {2007}
}
@article{Somers2004,
abstract = {A microsatellite consensus map was constructed by joining four independent genetic maps of bread wheat. Three of the maps were F(1)-derived, doubled-haploid line populations and the fourth population was 'Synthetic' x 'Opata', an F(6)-derived, recombinant-inbred line population. Microsatellite markers from different research groups including the Wheat Microsatellite Consortium, GWM, GDM, CFA, CFD, and BARC were used in the mapping. A sufficient number of common loci between genetic maps, ranging from 52 to 232 loci, were mapped on different populations to facilitate joining the maps. Four genetic maps were developed using MapMaker V3.0 and JoinMap V3.0. The software CMap, a comparative map viewer, was used to align the four maps and identify potential errors based on consensus. JoinMap V3.0 was used to calculate marker order and recombination distances based on the consensus of the four maps. A total of 1,235 microsatellite loci were mapped, covering 2,569 cM, giving an average interval distance of 2.2 cM. This consensus map represents the highest-density public microsatellite map of wheat and is accompanied by an allele database showing the parent allele sizes for every marker mapped. This enables users to predict allele sizes in new breeding populations and develop molecular breeding and genomics strategies.},
author = {Somers, Daryl J and Isaac, Peter and Edwards, Keith},
doi = {10.1007/s00122-004-1740-7},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Somers, Isaac, Edwards/TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik/art\%3A10.1007\%2Fs00122-004-1740-7.pdf:pdf},
isbn = {0012200417},
issn = {0040-5752},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
keywords = {Bread,Chromosome Mapping,Chromosomes,Consensus Sequence,DNA,Genetic Markers,Haploidy,Microsatellite Repeats,Plant,Plant: genetics,Triticum},
month = oct,
number = {6},
pages = {1105--14},
pmid = {15490101},
title = {{A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.).}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15490101},
volume = {109},
year = {2004}
}
@article{Vanvoorst,
author = {Voorst, B Van and Seidel, Steven},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Voorst, Seidel/Parallel and Distributed Processing/Vanvoorst, Seidel - Unknown - Comparison of MPI Implementations on a Shared Memory Machine.pdf:pdf},
journal = {Parallel and Distributed Processing},
title = {{Comparison of MPI implementations on a shared memory machine}},
url = {http://link.springer.com/chapter/10.1007/3-540-45591-4\_116},
year = {2000}
}
@article{Michelmore1998,
abstract = {Classical genetic and molecular data show that genes determining disease resistance in plants are frequently clustered in the genome. Genes for resistance (R genes) to diverse pathogens cloned from several species encode proteins that have motifs in common. These motifs indicate that R genes are part of signal-transduction systems. Most of these R genes encode a leucine-rich repeat (LRR) region. Sequences encoding putative solvent-exposed residues in this region are hypervariable and have elevated ratios of nonsynonymous to synonymous substitutions; this suggests that they have evolved to detect variation in pathogen-derived ligands. Generation of new resistance specificities previously had been thought to involve frequent unequal crossing-over and gene conversions. However, comparisons between resistance haplotypes reveal that orthologs are more similar than paralogs implying a low rate of sequence homogenization from unequal crossing-over and gene conversion. We propose a new model adapted and expanded from one proposed for the evolution of vertebrate major histocompatibility complex and immunoglobulin gene families. Our model emphasizes divergent selection acting on arrays of solvent-exposed residues in the LRR resulting in evolution of individual R genes within a haplotype. Intergenic unequal crossing-over and gene conversions are important but are not the primary mechanisms generating variation.},
author = {Michelmore, RW W and Meyers, BC C},
doi = {10.1101/gr.8.11.1113},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Michelmore, Meyers/Genome research/45e18c2513af90be65fe45e31d41be8612e17d48.pdf:pdf;:Users/ramirezr/Documents/Mendeley Desktop/Michelmore, Meyers/Genome research/662c6b70baa68bcb3b76ea056432cf6ba7bced11.pdf:pdf},
issn = {1088-9051},
journal = {Genome research},
keywords = {Evolution,Genetic,Genetic Variation,Genome,Models,Molecular,Multigene Family,Plant,Plant Diseases,Plant Diseases: genetics,Plants,Plants: genetics},
month = nov,
number = {11},
pages = {1113--30},
pmid = {9847076},
title = {{Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process.}},
url = {http://genome.cshlp.org/content/8/11/1113.short http://www.ncbi.nlm.nih.gov/pubmed/9847076},
volume = {8},
year = {1998}
}
@article{Bjo1973,
abstract = {The nucleotide substitution matrix inferred from avian data sets using cytochrome b differs considerably from the models commonly used in phylogenetic analyses. To analyze the possible effects of this particular pattern of change in phylogeny estimation we performed a computer simulation in which we started with a real sequence and used the inferred model of change to produce a tree of 10 species. Maximum parsimony (MP), maximum likelihood (ML), and various distance methods were then used to recover the topology and the branch lengths. We used two kinds of data with varying levels of variation. In addition, we tested with the removal of third positions and different weighting schemes. At low levels of variation, MP was outstanding in recovering the topology (90\% correct), while unweighted pair-group method, arithmetic average (UPGMA), regardless of distances used, was poor (40\%). At the higher level, most methods had a chance of around 40\%-58\% of finding the true tree. However, in most cases, the trees found were only slightly wrong, with only one or a few branches misplaced. On the other hand, the use of a "wrong" model had serious effects on the estimation of branch lengths (distances). Although precision was high, accuracy was poor with most methods, giving branch lengths that were biased downward. When seeded with the true distance matrix, Fitch and NJ always found the true tree, while UPGMA frequently failed to do so. The effect of removing third positions was dramatic at low levels of variation, because only one MP program was able to find a true tree at all, albeit rarely, while none of the others ever did so. At higher levels, the situation was better, but still much worse than with the whole data set.},
author = {H\aa stad, O and Bj\"{o}rklund, M},
file = {:Users/ramirezr/Documents/Mendeley Desktop/H\aa stad, Bj\"{o}rklund/Molecular biology and evolution/Bjo - 1973 - Nucleotide Substitution Models and Estimation of Phylogeny Olle Ha.pdf:pdf},
issn = {0737-4038},
journal = {Molecular biology and evolution},
keywords = {Animals,Avian Proteins,Avian Proteins: genetics,Birds,Computational Biology,Computational Biology: methods,Computational Biology: statistics \& numerical data,Computer Simulation,Computer Simulation: statistics \& numerical data,Cytochrome b Group,Cytochrome b Group: genetics,Evolution,Genetic,Models,Molecular,Nucleotides,Nucleotides: genetics,Phylogeny},
month = nov,
number = {11},
pages = {1381--9},
pmid = {12572602},
title = {{Nucleotide substitution models and estimation of phylogeny.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12572602},
volume = {15},
year = {1998}
}
@article{Michelmore1998b,
abstract = {Classical genetic and molecular data show that genes determining disease resistance in plants are frequently clustered in the genome. Genes for resistance (R genes) to diverse pathogens cloned from several species encode proteins that have motifs in common. These motifs indicate that R genes are part of signal-transduction systems. Most of these R genes encode a leucine-rich repeat (LRR) region. Sequences encoding putative solvent-exposed residues in this region are hypervariable and have elevated ratios of nonsynonymous to synonymous substitutions; this suggests that they have evolved to detect variation in pathogen-derived ligands. Generation of new resistance specificities previously had been thought to involve frequent unequal crossing-over and gene conversions. However, comparisons between resistance haplotypes reveal that orthologs are more similar than paralogs implying a low rate of sequence homogenization from unequal crossing-over and gene conversion. We propose a new model adapted and expanded from one proposed for the evolution of vertebrate major histocompatibility complex and immunoglobulin gene families. Our model emphasizes divergent selection acting on arrays of solvent-exposed residues in the LRR resulting in evolution of individual R genes within a haplotype. Intergenic unequal crossing-over and gene conversions are important but are not the primary mechanisms generating variation.},
author = {Michelmore, Richard W and Meyers, Blake C},
doi = {10.1101/gr.8.11.1113},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Michelmore, Meyers/Genome research/fa62d5580e1751e8af66dcf94e81d954361d98ca.pdf:pdf},
issn = {1088-9051},
journal = {Genome research},
keywords = {Evolution,Genetic,Genetic Variation,Genome,Models,Molecular,Multigene Family,Plant,Plant Diseases,Plant Diseases: genetics,Plants,Plants: genetics},
month = nov,
number = {11},
pages = {1113--30},
pmid = {9847076},
title = {{Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9847076},
volume = {8},
year = {1998}
}
@article{Committee1985,
author = {Committee, Nomenclature and Union, International},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Committee, Union/Eur. J. Biochem/b7cdc31bc57f51117531628b51582cd4ccfaa6eb.pdf:pdf},
journal = {Eur. J. Biochem},
pages = {281--286},
title = {{Nomenclature for incompletely specified bases in nucleic acid sequences}},
url = {http://scholar.google.com/scholar?hl=en\&btnG=Search\&q=intitle:Nomenclature+for+incompletely+specified+bases+in+nucleic+acid+sequences\#8},
volume = {229},
year = {1985}
}
@article{Flavell1974,
author = {Flavell, R. B. and Bennett, M. D. and Smith, J. B. and Smith, D. B.},
doi = {10.1007/BF00485947},
issn = {0006-2928},
journal = {Biochemical Genetics},
month = oct,
number = {4},
pages = {257--269},
title = {{Genome size and the proportion of repeated nucleotide sequence DNA in plants}},
url = {http://link.springer.com/10.1007/BF00485947},
volume = {12},
year = {1974}
}
@article{Etherington2015,
author = {Etherington, Graham J and Ramirez-Gonzalez, R. H. and MacLean, D.},
doi = {10.1093/bioinformatics/btv178},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Etherington, Ramirez-Gonzalez, MacLean/Bioinformatics/Bioinformatics-2015-Etherington-bioinformatics\_btv178.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
pages = {1--2},
title = {{bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btv178},
year = {2015}
}
@article{Hubbard2015,
author = {Hubbard, Amelia and Lewis, Clare M and Yoshida, Kentaro and Ramirez-Gonzalez, Ricardo H and de Vallavieille-Pope, Claude and Thomas, Jane and Kamoun, Sophien and Bayles, Rosemary and Uauy, Cristobal and Saunders, Diane Go},
doi = {10.1186/s13059-015-0590-8},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Hubbard et al/Genome Biology/s13059-015-0590-8.pdf:pdf},
issn = {1465-6906},
journal = {Genome Biology},
number = {1},
pages = {1--15},
title = {{Field pathogenomics reveals the emergence of a diverse wheat yellow rust population}},
url = {http://genomebiology.com/2015/16/1/23},
volume = {16},
year = {2015}
}
@article{Ramirez-Gonzalez2015a,
author = {Ramirez-Gonzalez, R. H. and Uauy, Cristobal and Caccamo, Mario},
doi = {10.1093/bioinformatics/btv069},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Ramirez-Gonzalez, Uauy, Caccamo/Bioinformatics/bioinformatics.btv069.full.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
pages = {2--3},
pmid = {25649618},
title = {{PolyMarker: A fast polyploid primer design pipeline}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btv069},
year = {2015}
}
@misc{TheHSQLDBGroup,
author = {{The HSQLDB Group}},
title = {{H2 SQL}},
url = {http://www.h2database.com/}
}
@misc{,
file = {:Users/ramirezr/Documents/Mendeley Desktop/Unknown/Unknown/Unknown - Unknown - Import documents to Mendeley.html:html},
title = {{Import documents to Mendeley}},
url = {http://www.mendeley.com/import/bookmarklet/?pu=1\&key=e3eaa56a475780fb1dd46ab62d441138},
urldate = {2013-04-15}
}
@article{Schmid2014,
author = {Schmid, Marc W and Grossniklaus, Ueli},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Schmid, Grossniklaus/Unknown/Bioinformatics-2014-Schmid-bioinformatics\_btu680.pdf:pdf},
pages = {1--2},
title = {{Rcount : simple and flexible RNA-Seq read counting}},
year = {2014}
}
@article{Misasi2014,
author = {Misasi, John and Sullivan, Nancy J.},
doi = {10.1016/j.cell.2014.10.006},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Misasi, Sullivan/Cell/PIIS0092867414012938.pdf:pdf},
issn = {00928674},
journal = {Cell},
month = oct,
number = {3},
pages = {477--486},
publisher = {Elsevier Inc.},
title = {{Camouflage and Misdirection: The Full-On Assault of Ebola Virus Disease}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867414012938},
volume = {159},
year = {2014}
}
@article{Krasileva2013,
abstract = {BACKGROUND: The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. RESULTS: A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96\% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22\% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7\% of SNPs analyzed are correctly separated by phasing. CONCLUSIONS: Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.},
author = {Krasileva, Ksenia V and Buffalo, Vince and Bailey, Paul and Pearce, Stephen and Ayling, Sarah and Tabbita, Facundo and Soria, Marcelo and Wang, Shichen and Consortium, Iwgs and Akhunov, Eduard and Uauy, Cristobal and Dubcovsky, Jorge},
doi = {10.1186/gb-2013-14-6-r66},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Krasileva et al/Genome biology/gb-2013-14-6-r66.pdf:pdf},
issn = {1465-6914},
journal = {Genome biology},
month = jun,
number = {6},
pages = {R66},
pmid = {23800085},
title = {{Separating homeologs by phasing in the tetraploid wheat transcriptome.}},
url = {http://genomebiology.com/2013/14/6/R66 http://www.ncbi.nlm.nih.gov/pubmed/23800085},
volume = {14},
year = {2013}
}
@article{James2013,
abstract = {Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.},
author = {James, Geo Velikkakam and Patel, Vipul and Nordstr\"{o}m, Karl Jv and Klasen, Jonas R and Salom\'{e}, Patrice a and Weigel, Detlef and Schneeberger, Korbinian},
doi = {10.1186/gb-2013-14-6-r61},
file = {:Users/ramirezr/Documents/Mendeley Desktop/James et al/Genome biology/fa84dcf6f4fccdb45d91ee562d92f053c5bfaf79.pdf:pdf},
issn = {1465-6914},
journal = {Genome biology},
keywords = {arabidopsis,genetic mapping,mapping-by-sequencing,shoremapping,whole-genome sequencing},
month = jun,
number = {6},
pages = {R61},
pmid = {23773572},
publisher = {BioMed Central Ltd},
title = {{User guide for mapping-by-sequencing in Arabidopsis.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3706810\&tool=pmcentrez\&rendertype=abstract},
volume = {14},
year = {2013}
}
@article{Leimena2013,
abstract = {BACKGROUND: Next generation sequencing (NGS) technologies can be applied in complex microbial ecosystems for metatranscriptome analysis by employing direct cDNA sequencing, which is known as RNA sequencing (RNA-seq). RNA-seq generates large datasets of great complexity, the comprehensive interpretation of which requires a reliable bioinformatic pipeline. In this study, we focus on the development of such a metatranscriptome pipeline, which we validate using Illumina RNA-seq datasets derived from the small intestine microbiota of two individuals with an ileostomy.

RESULTS: The metatranscriptome pipeline developed here enabled effective removal of rRNA derived sequences, followed by confident assignment of the predicted function and taxonomic origin of the mRNA reads. Phylogenetic analysis of the small intestine metatranscriptome datasets revealed a strong similarity with the community composition profiles obtained from 16S rDNA and rRNA pyrosequencing, indicating considerable congruency between community composition (rDNA), and the taxonomic distribution of overall (rRNA) and specific (mRNA) activity among its microbial members. Reproducibility of the metatranscriptome sequencing approach was established by independent duplicate experiments. In addition, comparison of metatranscriptome analysis employing single- or paired-end sequencing methods indicated that the latter approach does not provide improved functional or phylogenetic insights. Metatranscriptome functional-mapping allowed the analysis of global, and genus specific activity of the microbiota, and illustrated the potential of these approaches to unravel syntrophic interactions in microbial ecosystems.

CONCLUSIONS: A reliable pipeline for metatransciptome data analysis was developed and evaluated using RNA-seq datasets obtained for the human small intestine microbiota. The set-up of the pipeline is very generic and can be applied for (bacterial) metatranscriptome analysis in any chosen niche.},
author = {Leimena, Milkha M and Ramiro-Garcia, Javier and Davids, Mark and van den Bogert, Bartholomeus and Smidt, Hauke and Smid, Eddy J and Boekhorst, Jos and Zoetendal, Erwin G and Schaap, Peter J and Kleerebezem, Michiel},
doi = {10.1186/1471-2164-14-530},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Leimena et al/BMC genomics/1471-2164-14-530.pdf:pdf},
issn = {1471-2164},
journal = {BMC genomics},
keywords = {Aged,Computational Biology,Computational Biology: methods,Computational Biology: standards,Databases, Genetic,Female,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Expression Profiling: standards,Humans,Intestine, Small,Intestine, Small: microbiology,Metabolic Networks and Pathways,Metabolic Networks and Pathways: genetics,Metagenome,Metagenome: genetics,Middle Aged,Phylogeny,RNA, Messenger,RNA, Messenger: genetics,Reference Standards,Sequence Analysis, RNA},
month = jan,
number = {1},
pages = {530},
pmid = {23915218},
publisher = {BMC Genomics},
title = {{A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3750648\&tool=pmcentrez\&rendertype=abstract},
volume = {14},
year = {2013}
}
@book{Myllykangas2012,
address = {New York, NY},
author = {Myllykangas, Samuel and Buenrostro, Jason and Ji, Hanlee P},
doi = {10.1007/978-1-4614-0782-9},
editor = {Rodr\'{\i}guez-Ezpeleta, Naiara and Hackenberg, Michael and Aransay, Ana M.},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Myllykangas, Buenrostro, Ji/Unknown/9781461407812-c1 (1).pdf:pdf},
isbn = {978-1-4614-0781-2},
pages = {11--26},
publisher = {Springer New York},
title = {{Bioinformatics for High Throughput Sequencing}},
url = {http://www.springerlink.com/index/10.1007/978-1-4614-0782-9},
year = {2012}
}
@article{Liu2012a,
abstract = {BACKGROUND: Common bean (Phaseolus vulgaris L.) is one of the most important legumes in the world. Several diseases severely reduce bean production and quality; therefore, it is very important to better understand disease resistance in common bean in order to prevent these losses. More than 70 resistance (R) genes which confer resistance against various pathogens have been cloned from diverse plant species. Most R genes share highly conserved domains which facilitates the identification of new candidate R genes from the same species or other species. The goals of this study were to isolate expressed R gene-like sequences (RGLs) from 454-derived transcriptomic sequences and expressed sequence tags (ESTs) of common bean, and to develop RGL-tagged molecular markers.

RESULTS: A data-mining approach was used to identify tentative P. vulgaris R gene-like sequences from approximately 1.69 million 454-derived sequences and 116,716 ESTs deposited in GenBank. A total of 365 non-redundant sequences were identified and named as common bean (P. vulgaris = Pv) resistance gene-like sequences (PvRGLs). Among the identified PvRGLs, about 60\% (218 PvRGLs) were from 454-derived sequences. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis confirmed that PvRGLs were actually expressed in the leaves of common bean. Upon comparison to P. vulgaris genomic sequences, 105 (28.77\%) of the 365 tentative PvRGLs could be integrated into the existing common bean physical map. Based on the syntenic blocks between common bean and soybean, 237 (64.93\%) PvRGLs were anchored on the P. vulgaris genetic map and will need to be mapped to determine order. In addition, 11 sequence-tagged-site (STS) and 19 cleaved amplified polymorphic sequence (CAPS) molecular markers were developed for 25 unique PvRGLs.

CONCLUSIONS: In total, 365 PvRGLs were successfully identified from 454-derived transcriptomic sequences and ESTs available in GenBank and about 65\% of PvRGLs were integrated into the common bean genetic map. A total of 30 RGL-tagged markers were developed for 25 unique PvRGLs, including 11 STS and 19 CAPS markers. The expressed PvRGLs identified in this study provide a large sequence resource for development of RGL-tagged markers that could be used further for genetic mapping of disease resistant candidate genes and quantitative trait locus/loci (QTLs). This work also represents an additional method for identifying expressed RGLs from next generation sequencing data.},
author = {Liu, Zhanji and Crampton, Mollee and Todd, Antonette and Kalavacharla, Venu},
doi = {10.1186/1471-2229-12-42},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Liu et al/BMC plant biology/Rgeneslike expressed in Phaseolus\#.pdf:pdf},
issn = {1471-2229},
journal = {BMC plant biology},
keywords = {Amino Acid Sequence,Chromosome Mapping,DNA, Plant,DNA, Plant: genetics,Data Mining,Databases, Genetic,Disease Resistance,Expressed Sequence Tags,Gene Expression Profiling,Genes, Plant,Genetic Markers,Phaseolus,Phaseolus: genetics,Phaseolus: immunology,Plant Diseases,Plant Diseases: genetics,Plant Diseases: immunology,Plant Leaves,Plant Leaves: genetics,Reverse Transcriptase Polymerase Chain Reaction,Sequence Analysis, DNA,Soybeans,Soybeans: genetics,Synteny,Transcriptome},
month = jan,
number = {1},
pages = {42},
pmid = {22443214},
publisher = {BioMed Central Ltd},
title = {{Identification of expressed resistance gene-like sequences by data mining in 454-derived transcriptomic sequences of common bean (Phaseolus vulgaris L.).}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3353201\&tool=pmcentrez\&rendertype=abstract},
volume = {12},
year = {2012}
}
@article{Hernandez2012,
abstract = {Wheat is the third most important crop for human nutrition in the world. The availability of high-resolution genetic and physical maps and ultimately a complete genome sequence holds great promise for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread wheat (Triticum aestivum) genome (approximately 17 Gb/1C) and the triplication of genic sequence resulting from its hexaploid status have impeded genome sequencing of this important crop species. Here we describe the use of mitotic chromosome flow sorting to separately purify and then shotgun-sequence a pair of telocentric chromosomes that together form chromosome 4A (856 Mb/1C) of wheat. The isolation of this much reduced template and the consequent avoidance of the problem of sequence duplication, in conjunction with synteny-based comparisons with other grass genomes, have facilitated construction of an ordered gene map of chromosome 4A, embracing ≥85\% of its total gene content, and have enabled precise localization of the various translocation and inversion breakpoints on chromosome 4A that differentiate it from its progenitor chromosome in the A genome diploid donor. The gene map of chromosome 4A, together with the emerging sequences of homoeologous wheat chromosome groups 4, 5 and 7, represent unique resources that will allow us to obtain new insights into the evolutionary dynamics between homoeologous chromosomes and syntenic chromosomal regions.},
author = {Hernandez, Pilar and Martis, Mihaela and Dorado, Gabriel and Pfeifer, Matthias and G\'{a}lvez, Sergio and Schaaf, Sebastian and Jouve, Nicol\'{a}s and \v{S}imkov\'{a}, Hana and Val\'{a}rik, Miroslav and Dole\v{z}el, Jaroslav and Mayer, Klaus F X},
doi = {10.1111/j.1365-313X.2011.04808.x},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Hernandez et al/The Plant journal for cell and molecular biology/HernandezetalPTJ2011.pdf:pdf},
issn = {1365-313X},
journal = {The Plant journal : for cell and molecular biology},
keywords = {Chromosome Mapping,Chromosomes, Plant,DNA, Plant,DNA, Plant: genetics,Genome, Plant,Sequence Analysis, DNA,Synteny,Triticum,Triticum: genetics},
month = feb,
number = {3},
pages = {377--86},
pmid = {21974774},
title = {{Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21974774},
volume = {69},
year = {2012}
}
@article{Mayer2012,
abstract = {Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.},
author = {Mayer, Klaus F X and Waugh, Robbie and Brown, John W S and Schulman, Alan and Langridge, Peter and Platzer, Matthias and Fincher, Geoffrey B and Muehlbauer, Gary J and Sato, Kazuhiro and Close, Timothy J and Wise, Roger P and Stein, Nils},
doi = {10.1038/nature11543},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Mayer et al/Nature/nature11543.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Alternative Splicing,Alternative Splicing: genetics,Codon, Nonsense,Codon, Nonsense: genetics,Crops, Agricultural,Crops, Agricultural: genetics,Evolution, Molecular,Gene Expression Regulation, Plant,Genes, Plant,Genes, Plant: genetics,Genome, Plant,Genome, Plant: genetics,Genomics,Hordeum,Hordeum: classification,Hordeum: genetics,Molecular Sequence Annotation,Physical Chromosome Mapping,Polymorphism, Single Nucleotide,Polymorphism, Single Nucleotide: genetics,Repetitive Sequences, Nucleic Acid,Repetitive Sequences, Nucleic Acid: genetics,Sequence Analysis, DNA,Transcriptome,Transcriptome: genetics},
month = nov,
number = {7426},
pages = {711--6},
pmid = {23075845},
publisher = {Nature Publishing Group},
title = {{A physical, genetic and functional sequence assembly of the barley genome.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23075845},
volume = {491},
year = {2012}
}
@book{Reynolds2012,
author = {Reynolds, MP and Pask, AJD and Mullan, DM},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Reynolds, Pask, Mullan/Unknown/PhysBreeding1.pdf:pdf},
isbn = {9789706481818},
title = {{Physiological breeding I: interdisciplinary approaches to improve crop adaptation}},
url = {http://books.google.com/books?hl=en\&lr=\&id=bYdVb1JuCDoC\&oi=fnd\&pg=PR5\&dq=Physiological+Breeding+I:+Interdisciplinary+Approaches+to+Improve+Crop+Adaptation\&ots=PTRT3TjrVF\&sig=RdmSXFjINn1d1klh30HGqOoWUL0},
year = {2012}
}
@misc{fastqc,
annote = {Babraham Bioinformatics},
author = {{Babraham Bioinformatics}},
keywords = {Babraham Bioinformatics},
mendeley-tags = {Babraham Bioinformatics},
title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/},
year = {2012}
}
@article{Mayer2011,
abstract = {We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign \~{}86\% of the estimated \~{}32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.},
author = {Mayer, Klaus F X and Martis, Mihaela and Hedley, Pete E and Simkov\'{a}, Hana and Liu, Hui and Morris, Jenny a and Steuernagel, Burkhard and Taudien, Stefan and Roessner, Stephan and Gundlach, Heidrun and Kubal\'{a}kov\'{a}, Marie and Such\'{a}nkov\'{a}, Pavla and Murat, Florent and Felder, Marius and Nussbaumer, Thomas and Graner, Andreas and Salse, Jerome and Endo, Takashi and Sakai, Hiroaki and Tanaka, Tsuyoshi and Itoh, Takeshi and Sato, Kazuhiro and Platzer, Matthias and Matsumoto, Takashi and Scholz, Uwe and Dolezel, Jaroslav and Waugh, Robbie and Stein, Nils},
doi = {10.1105/tpc.110.082537},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Mayer et al/The Plant cell/1249.full.pdf:pdf},
issn = {1532-298X},
journal = {The Plant cell},
keywords = {Centromere,Centromere: genetics,Chromosomes, Plant,Chromosomes, Plant: genetics,Evolution, Molecular,Gene Order,Gene Order: genetics,Gene Rearrangement,Gene Rearrangement: genetics,Genes, Plant,Genes, Plant: genetics,Genome, Plant,Genome, Plant: genetics,Genomics,Genomics: methods,Hordeum,Hordeum: genetics,Models, Genetic,Oryza sativa,Oryza sativa: genetics,Sequence Analysis, DNA,Triticum,Triticum: genetics},
month = apr,
number = {4},
pages = {1249--63},
pmid = {21467582},
title = {{Unlocking the barley genome by chromosomal and comparative genomics.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3101540\&tool=pmcentrez\&rendertype=abstract},
volume = {23},
year = {2011}
}
@article{Hajibabaei2011,
author = {Hajibabaei, Mehrdad and Shokralla, Shadi and Zhou, Xin and Singer, Gregory a. C. and Baird, Donald J.},
doi = {10.1371/journal.pone.0017497},
editor = {Voolstra, Christian R.},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Hajibabaei et al/PLoS ONE/Hajibabaei et al. - 2011 - Environmental Barcoding A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Bent.pdf:pdf},
issn = {1932-6203},
journal = {PLoS ONE},
month = apr,
number = {4},
pages = {e17497},
title = {{Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos}},
url = {http://dx.plos.org/10.1371/journal.pone.0017497},
volume = {6},
year = {2011}
}
@article{Senshu2011,
abstract = {Viruses encode RNA silencing suppressors to counteract host antiviral silencing. In this study, we analyzed the suppressors encoded by potato virus M (PVM), a member of the genus Carlavirus. In the conventional green fluorescent protein transient coexpression assay, the cysteine-rich protein (CRP) of PVM inhibited both local and systemic silencing, whereas the triple gene block protein 1 (TGBp1) showed suppressor activity only on systemic silencing. Furthermore, to elucidate the roles of these two suppressors during an active viral infection, we performed PVX vector-based assays and viral movement complementation assays. CRP increased the accumulation of viral RNA at the single-cell level and also enhanced viral cell-to-cell movement by inhibiting RNA silencing. However, TGBp1 facilitated viral movement but did not affect viral accumulation in protoplasts. These data suggest that CRP inhibits RNA silencing primarily at the viral replication step, whereas TGBp1 is a suppressor that acts at the viral movement step. Thus, our findings demonstrate a sophisticated viral infection strategy that suppresses host antiviral silencing at two different steps via two mechanistically distinct suppressors. This study is also the first report of the RNA silencing suppressor in the genus Carlavirus.},
author = {Senshu, Hiroko and Yamaji, Yasuyuki and Minato, Nami and Shiraishi, Takuya and Maejima, Kensaku and Hashimoto, Masayoshi and Miura, Chihiro and Neriya, Yutaro and Namba, Shigetou},
doi = {10.1128/JVI.05273-11},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Senshu et al/Journal of virology/10269.pdf:pdf},
issn = {1098-5514},
journal = {Journal of virology},
month = oct,
number = {19},
pages = {10269--78},
pmid = {21752911},
title = {{A dual strategy for the suppression of host antiviral silencing: two distinct suppressors for viral replication and viral movement encoded by potato virus m.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21752911},
volume = {85},
year = {2011}
}
@article{Sam2010,
author = {Sam, The and Specification, Format},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Sam, Specification/Read/Sam, Specification - 2010 - The SAM Format Specification (v1.3-r882).pdf:pdf},
journal = {Read},
pages = {1--11},
title = {{The SAM Format Specification (v1.3-r882)}},
year = {2010}
}
@article{Geraci2010,
abstract = {Single nucleotide polymorphisms are the most common form of variation in human DNA, and are involved in many research fields, from molecular biology to medical therapy. The technological opportunity to deal with long DNA sequences using shotgun sequencing has raised the problem of fragment recombination. In this regard, Single Individual Haplotyping (SIH) problem has received considerable attention over the past few years.},
author = {Geraci, Filippo},
doi = {10.1093/bioinformatics/btq411},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Geraci/Bioinformatics (Oxford, England)/de1d184c110812191f705a11842fe648ca583698.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
keywords = {Algorithms,Base Sequence,Haplotypes,Humans,Polymorphism, Single Nucleotide,Software},
month = oct,
number = {18},
pages = {2217--25},
pmid = {20624781},
title = {{A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2935405\&tool=pmcentrez\&rendertype=abstract},
volume = {26},
year = {2010}
}
@article{Resendis-Antonio2010,
abstract = {BACKGROUND: Alterations on glucose consumption and biosynthetic activity of amino acids, lipids and nucleotides are metabolic changes for sustaining cell proliferation in cancer cells. Irrevocable evidence of this fact is the Warburg effect which establishes that cancer cells prefers glycolysis over oxidative phosphorylation to generate ATP. Regulatory action over metabolic enzymes has opened a new window for designing more effective anti-cancer treatments. This enterprise is not trivial and the development of computational models that contribute to identifying potential enzymes for breaking the robustness of cancer cells is a priority.

METHODOLOGY/PRINCIPAL FINDINGS: This work presents a constraint-base modeling of the most experimentally studied metabolic pathways supporting cancer cells: glycolysis, TCA cycle, pentose phosphate, glutaminolysis and oxidative phosphorylation. To evaluate its predictive capacities, a growth kinetics study for Hela cell lines was accomplished and qualitatively compared with in silico predictions. Furthermore, based on pure computational criteria, we concluded that a set of enzymes (such as lactate dehydrogenase and pyruvate dehydrogenase) perform a pivotal role in cancer cell growth, findings supported by an experimental counterpart.

CONCLUSIONS/SIGNIFICANCE: Alterations on metabolic activity are crucial to initiate and sustain cancer phenotype. In this work, we analyzed the phenotype capacities emerged from a constructed metabolic network conformed by the most experimentally studied pathways sustaining cancer cell growth. Remarkably, in silico model was able to resemble the physiological conditions in cancer cells and successfully identified some enzymes currently studied by its therapeutic effect. Overall, we supplied evidence that constraint-based modeling constitutes a promising computational platform to: 1) integrate high throughput technology and establish a crosstalk between experimental validation and in silico prediction in cancer cell phenotype; 2) explore the fundamental metabolic mechanism that confers robustness in cancer; and 3) suggest new metabolic targets for anticancer treatments. All these issues being central to explore cancer cell metabolism from a systems biology perspective.},
author = {Resendis-Antonio, Osbaldo and Checa, Alberto and Encarnaci\'{o}n, Sergio},
doi = {10.1371/journal.pone.0012383},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Resendis-Antonio, Checa, Encarnaci\'{o}n/PloS one/journal.pone.0012383.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Cell Proliferation,Citric Acid Cycle,Computational Biology,Glycolysis,HeLa Cells,Humans,Models, Biological,Neoplasms,Neoplasms: metabolism,Neoplasms: pathology,Oxidative Phosphorylation,Pentose Phosphate Pathway,Phenotype},
month = jan,
number = {8},
pages = {e12383},
pmid = {20811631},
title = {{Modeling core metabolism in cancer cells: surveying the topology underlying the Warburg effect.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2928278\&tool=pmcentrez\&rendertype=abstract},
volume = {5},
year = {2010}
}
@article{Metzker2010,
abstract = {Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest.},
author = {Metzker, Michael L},
doi = {10.1038/nrg2626},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Metzker/Nature reviews. Genetics/39660ec8b45a41fc82ef048e2a7cd67762b646bf.pdf:pdf},
issn = {1471-0064},
journal = {Nature reviews. Genetics},
keywords = {Automation,Genetic Techniques,Genome,Genome, Human,Genomics,Genomics: methods,Humans,Models, Genetic,Molecular Biology,Molecular Biology: methods,Oligonucleotides,Oligonucleotides: genetics,Polymerase Chain Reaction,Sequence Analysis, DNA,Sequence Analysis, DNA: economics,Sequence Analysis, DNA: instrumentation,Sequence Analysis, DNA: methods,Sequence Analysis, DNA: trends},
month = jan,
number = {1},
pages = {31--46},
pmid = {19997069},
publisher = {Nature Publishing Group},
title = {{Sequencing technologies - the next generation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19997069},
volume = {11},
year = {2010}
}
@article{Goecks2010,
abstract = {Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.},
author = {Goecks, Jeremy and Nekrutenko, Anton and Taylor, James},
doi = {10.1186/gb-2010-11-8-r86},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Goecks, Nekrutenko, Taylor/Genome Biology/gb-2010-11-8-r86.pdf:pdf},
issn = {1465-6914},
journal = {Genome Biology},
keywords = {Algorithms,Animals,Computational Biology,Computational Biology: methods,Databases,Genomics,Genomics: methods,Humans,Internet,Nucleic Acid},
month = jan,
number = {8},
pages = {R86},
pmid = {20738864},
title = {{Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2945788\&tool=pmcentrez\&rendertype=abstract},
volume = {11},
year = {2010}
}
@article{Murphy2009,
author = {Murphy, Lesley R. and Santra, Dipak and Kidwell, Kimberlee and Yan, Guiping and Chen, Xianming and Campbell, Kimberly Garland},
doi = {10.2135/cropsci2008.10.0621},
issn = {1435-0653},
journal = {Crop Science},
language = {en},
number = {5},
pages = {1786},
publisher = {Crop Science Society of America},
title = {{Linkage Maps of Wheat Stripe Rust Resistance Genes and for Use in Marker-Assisted Selection}},
url = {https://www.crops.org/publications/cs/articles/49/5/1786},
volume = {49},
year = {2009}
}
@article{Randhawa2009,
abstract = {A marker-assisted background selection (MABS)-based gene introgression approach in wheat (Triticum aestivum L.) was optimized, where 97\% or more of a recurrent parent genome (RPG) can be recovered in just two backcross (BC) generations. A four-step MABS method was developed based on 'Plabsim' computer simulations and wheat genome structure information. During empirical optimization of this method, double recombinants around the target gene were selected in a step-wise fashion during the two BC cycles followed by selection for recurrent parent genotype on non-carrier chromosomes. The average spacing between carrier chromosome markers was <4 cM. For non-carrier chromosome markers that flanked each of the 48 wheat gene-rich regions, this distance was approximately 12 cM. Employed to introgress seedling stripe rust (Puccinia striiformis f. sp. tritici) resistance gene Yr15 into the spring wheat cultivar 'Zak', marker analysis of 2,187 backcross-derived progeny resulted in the recovery of a BC(2)F(2ratio3) plant with 97\% of the recurrent parent genome. In contrast, only 82\% of the recurrent parent genome was recovered in phenotypically selected BC(4)F(7) plants developed without MABS. Field evaluation results from 17 locations indicated that the MABS-derived line was either equal or superior to the recurrent parent for the tested agronomic characteristics. Based on these results, MABS is recommended as a strategy for rapidly introgressing a targeted gene into a wheat genotype in just two backcross generations while recovering 97\% or more of the recurrent parent genotype.},
author = {Randhawa, Harpinder S and Mutti, Jasdeep S and Kidwell, Kim and Morris, Craig F and Chen, Xianming and Gill, Kulvinder S},
doi = {10.1371/journal.pone.0005752},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Randhawa et al/PloS one/bff65a9ea72186b7aa5dac549f3e687d585d47ef.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Chromosome Mapping,Chromosomes,Chromosomes: ultrastructure,Computer Simulation,Crosses,Genes,Genetic,Genetic Markers,Genome,Genotype,Heterozygote,Models,Plant,Plant Diseases,Plant Diseases: genetics,Probability,Recombination,Triticum,Triticum: genetics},
month = jan,
number = {6},
pages = {e5752},
pmid = {19484121},
title = {{Rapid and targeted introgression of genes into popular wheat cultivars using marker-assisted background selection.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2684585\&tool=pmcentrez\&rendertype=abstract},
volume = {4},
year = {2009}
}
@article{Gupta2008,
abstract = {Wheat (Triticum aestivum L.), with a large genome (16000 Mb) and high proportion ( approximately 80\%) of repetitive sequences, has been a difficult crop for genomics research. However, the availability of extensive cytogenetics stocks has been an asset, which facilitated significant progress in wheat genomic research in recent years. For instance, fairly dense molecular maps (both genetic and physical maps) and a large set of ESTs allowed genome-wide identification of gene-rich and gene-poor regions as well as QTL including eQTL. The availability of markers associated with major economic traits also allowed development of major programs on marker-assisted selection (MAS) in some countries, and facilitated map-based cloning of a number of genes/QTL. Resources for functional genomics including TILLING and RNA interference (RNAi) along with some new approaches like epigenetics and association mapping are also being successfully used for wheat genomics research. BAC/BIBAC libraries for the subgenome D and some individual chromosomes have also been prepared to facilitate sequencing of gene space. In this brief review, we discuss all these advances in some detail, and also describe briefly the available resources, which can be used for future genomics research in this important crop.},
author = {Gupta, P. K. and Mir, R. R. and Mohan, A. and Kumar, J.},
doi = {10.1155/2008/896451},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Gupta et al/International journal of plant genomics/ca46109d1b9effbbecea2bb824e25af47144cac9.pdf:pdf},
issn = {1687-5370},
journal = {International journal of plant genomics},
month = jan,
pages = {896451},
pmid = {18528518},
title = {{Wheat genomics: present status and future prospects.}},
url = {http://www.hindawi.com/journals/ijpg/2008/896451/ http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2397558\&tool=pmcentrez\&rendertype=abstract},
volume = {2008},
year = {2008}
}
@article{Bennetzen2008,
author = {Bennetzen, Jeffrey L. and Chen, Mingsheng},
doi = {10.1007/s12284-008-9015-6},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Bennetzen, Chen/Rice/9a4f51a74d1a7bc3e09b51b5a3154b828a8e4aca.pdf:pdf},
issn = {1939-8425},
journal = {Rice},
keywords = {comparative genomics,genome evolution,microcolinearity,recombination,transposable elements},
month = nov,
number = {2},
pages = {109--118},
title = {{Grass Genomic Synteny Illuminates Plant Genome Function and Evolution}},
url = {http://www.springerlink.com/index/10.1007/s12284-008-9015-6},
volume = {1},
year = {2008}
}
@article{Collard2008,
abstract = {DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). The large number of quantitative trait loci (QTLs) mapping studies for diverse crops species have provided an abundance of DNA marker-trait associations. In this review, we present an overview of the advantages of MAS and its most widely used applications in plant breeding, providing examples from cereal crops. We also consider reasons why MAS has had only a small impact on plant breeding so far and suggest ways in which the potential of MAS can be realized. Finally, we discuss reasons why the greater adoption of MAS in the future is inevitable, although the extent of its use will depend on available resources, especially for orphan crops, and may be delayed in less-developed countries. Achieving a substantial impact on crop improvement by MAS represents the great challenge for agricultural scientists in the next few decades.},
author = {Collard, Bertrand C Y and Mackill, David J},
doi = {10.1098/rstb.2007.2170},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Collard, Mackill/Philosophical transactions of the Royal Society of London. Series B, Biological sciences/32db29a29a187f8592755945fb73d4dd9480c466.pdf:pdf},
issn = {0962-8436},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
keywords = {Agriculture,Agriculture: methods,Crops, Agricultural,Crops, Agricultural: genetics,Crops, Agricultural: growth \& development,Genetic Markers,Genetic Variation,Humans,Plants, Genetically Modified,Quantitative Trait Loci,Selection, Genetic},
month = feb,
number = {1491},
pages = {557--72},
pmid = {17715053},
title = {{Marker-assisted selection: an approach for precision plant breeding in the twenty-first century.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2610170\&tool=pmcentrez\&rendertype=abstract},
volume = {363},
year = {2008}
}
@article{Joshi2005,
author = {Joshi, Shantanu and Arumugam, S},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Joshi, Arumugam/Information Sciences/Joshi - 2005 - An Online approach to Overlap Detection for DNA Fragment Assembly.pdf:pdf},
journal = {Information Sciences},
pages = {1--17},
title = {{An Online approach to Overlap Detection for DNA Fragment Assembly}},
url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.60.1502\&rep=rep1\&type=pdf},
year = {2005}
}
@article{Sardiello2005,
abstract = {In metazoan organisms, energy production is the only example of a process that is under dual genetic control: nuclear and mitochondrial. We used a genomic approach to examine how energy genes of both the nuclear and mitochondrial genomes are coordinated, and discovered a novel genetic regulatory circuit in Drosophila melanogaster that is surprisingly simple and parsimonious. This circuit is based on a single DNA regulatory element and can explain both intra- and inter-genomic coordinated expression of genes involved in energy production, including the full complement of mitochondrial and nuclear oxidative phosphorylation genes, and the genes involved in the Krebs cycle.},
author = {Sardiello, Marco and Tripoli, Gaetano and Romito, Antonio and Minervini, Crescenzio and Viggiano, Luigi and Caggese, Corrado and Pesole, Graziano},
doi = {10.1016/j.tig.2004.11.009},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Sardiello et al/Trends in genetics TIG/1-s2.0-S0168952504003129-main.pdf:pdf},
issn = {0168-9525},
journal = {Trends in genetics : TIG},
keywords = {Animals,Anopheles,Anopheles: genetics,DNA, Mitochondrial,DNA, Mitochondrial: genetics,Drosophila,Drosophila melanogaster,Drosophila melanogaster: genetics,Drosophila: genetics,Energy Metabolism,Energy Metabolism: genetics,Genome},
month = jan,
number = {1},
pages = {12--6},
pmid = {15680507},
title = {{Energy biogenesis: one key for coordinating two genomes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15680507},
volume = {21},
year = {2005}
}
@incollection{Singh2002,
abstract = {Wheat is the most widely known grown cereal crop in the world, with an ever increasing demand. It plays a fundamental role in food security, and a major challenge is to meet additional requirements with new cultivars and improved cropping technologies. This book provides extensive information from a number of international experts on the current status of research on wheat improvement and productions, as well as on other aspetcs, from its evolutionary origins to seed production technologies. It will be particularly useful to researchers and development specialists.},
author = {Singh and Huerta-Espino and Roelfs},
booktitle = {The wheat rusts},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Singh, Huerta-Espino, Roelfs/The wheat rusts/Unknown - Unknown - The wheat rusts - R.P. Singh, J. Huerta-Espino, A.P. Roelfs.html:html},
isbn = {9251048096},
pages = {567},
title = {{Bread Wheat}},
url = {http://www.fao.org/docrep/006/Y4011E/y4011e0g.htm},
year = {2002}
}
@article{Ellsworth1999,
abstract = {To outline potential benefits of integrating recent developments in bioinformatics and statistical genetics with traditional epidemiologic studies to localize genes influencing complex phenotypes and examine genetic effects on disease susceptibility.},
author = {Ellsworth, D L and Manolio, T a},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Ellsworth, Manolio/Annals of epidemiology/442880cfe49504263baab9e3d839cb7c810c22f9.pdf:pdf},
issn = {1047-2797},
journal = {Annals of epidemiology},
keywords = {Data Interpretation,Databases,Factual,Genetic Linkage,Genetic Predisposition to Disease,Humans,Medical Informatics Computing,Molecular Epidemiology,Molecular Epidemiology: methods,Mutation,Statistical},
month = may,
number = {4},
pages = {207--24},
pmid = {10332927},
title = {{The Emerging Importance of Genetics in Epidemiologic Research III. Bioinformatics and statistical genetic methods.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10332927},
volume = {9},
year = {1999}
}
@article{Devos1997,
abstract = {Comparative genetic studies have demonstrated that gene content and orders are highly conserved, both at the map and megabase level, between different species within the grass family. Integration of the genetic maps of rice, foxtail millet, sugar cane, sorghum, maize, the Triticeae cereals and oats into a single synthesis reveals that some chromosome arrangements characterise taxonomic groups, while others have arisen during or after speciation. A detailed analysis of the comparative maps of seven species, belonging to three subfamilies, and their applications are described below.},
author = {Devos, K M and Gale, M D},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Devos, Gale/Plant molecular biology/ecdd83551ce24969900b079f75913c5176805f7d.pdf:pdf},
issn = {0167-4412},
journal = {Plant molecular biology},
keywords = {Avena sativa,Avena sativa: genetics,Cereals,Cereals: genetics,Genome, Plant,Oryza sativa,Oryza sativa: genetics,Panicum,Panicum: genetics,Poaceae,Poaceae: genetics,Triticum,Triticum: genetics,Zea mays,Zea mays: genetics},
month = sep,
number = {1-2},
pages = {3--15},
pmid = {9291955},
title = {{Comparative genetics in the grasses.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9291955},
volume = {35},
year = {1997}
}
@article{Moore1995,
abstract = {The genomes of six major grass species can be aligned by dissecting the individual chromosomes into segments and rearranging these linkage blocks into highly similar structures.},
author = {Moore, G. and Devos, K.M. and Wang, Z. and Gale, M.D.},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Moore et al/Current Biology/Moore et al. - 1995 - Cereal Genome Evolution Grasses, line up and form a circle.pdf:pdf},
journal = {Current Biology},
number = {7},
pages = {737--739},
title = {{Cereal Genome Evolution: Grasses, line up and form a circle}},
url = {http://www.sciencedirect.com/science/article/pii/S0960982295001485},
volume = {5},
year = {1995}
}
@article{Cornish-Bowden1985,
author = {Cornish-Bowden, A},
issn = {0305-1048},
journal = {Nucleic acids research},
keywords = {Animals,Base Sequence,DNA,DNA Restriction Enzymes,DNA Restriction Enzymes: metabolism,DNA: analysis,Humans,RNA,RNA: analysis,Terminology as Topic},
month = may,
number = {9},
pages = {3021--30},
pmid = {2582368},
title = {{Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=341218\&tool=pmcentrez\&rendertype=abstract},
volume = {13},
year = {1985}
}
@article{Smith1981,
author = {Smith, T.F. and Waterman, M.S.},
doi = {10.1016/0022-2836(81)90087-5},
issn = {00222836},
journal = {Journal of Molecular Biology},
month = mar,
number = {1},
pages = {195--197},
title = {{Identification of common molecular subsequences}},
url = {http://dx.doi.org/10.1016/0022-2836(81)90087-5},
volume = {147},
year = {1981}
}
@article{Ariyaratne2011,
abstract = {Many de novo genome assemblers have been proposed recently. The basis for most existing methods relies on the de bruijn graph: a complex graph structure that attempts to encompass the entire genome. Such graphs can be prohibitively large, may fail to capture subtle information and is difficult to be parallelized.},
author = {Ariyaratne, Pramila Nuwantha and Sung, Wing-Kin},
doi = {10.1093/bioinformatics/btq626},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Ariyaratne, Sung/Bioinformatics (Oxford, England)/Ariyaratne, Sung - 2011 - PE-Assembler de novo assembler using short paired-end reads.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
keywords = {Computer Simulation,DNA,DNA: methods,Escherichia coli,Escherichia coli: genetics,Genome,Genomics,Genomics: methods,Schizosaccharomyces,Schizosaccharomyces: genetics,Sequence Analysis,Software},
month = jan,
number = {2},
pages = {167--74},
pmid = {21149345},
title = {{PE-Assembler: de novo assembler using short paired-end reads.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21149345},
volume = {27},
year = {2011}
}
@article{Ehrenreich2010,
abstract = {Most heritable traits, including many human diseases, are caused by multiple loci. Studies in both humans and model organisms, such as yeast, have failed to detect a large fraction of the loci that underlie such complex traits. A lack of statistical power to identify multiple loci with small effects is undoubtedly one of the primary reasons for this problem. We have developed a method in yeast that allows the use of much larger sample sizes than previously possible and hence permits the detection of multiple loci with small effects. The method involves generating very large numbers of progeny from a cross between two Saccharomyces cerevisiae strains and then phenotyping and genotyping pools of these offspring. We applied the method to 17 chemical resistance traits and mitochondrial function, and identified loci for each of these phenotypes. We show that the level of genetic complexity underlying these quantitative traits is highly variable, with some traits influenced by one major locus and others by at least 20 loci. Our results provide an empirical demonstration of the genetic complexity of a number of traits and show that it is possible to identify many of the underlying factors using straightforward techniques. Our method should have broad applications in yeast and can be extended to other organisms.},
author = {Ehrenreich, Ian M and Torabi, Noorossadat and Jia, Yue and Kent, Jonathan and Martis, Stephen and Shapiro, Joshua a and Gresham, David and Caudy, Amy a and Kruglyak, Leonid},
doi = {10.1038/nature08923},
issn = {1476-4687},
journal = {Nature},
keywords = {4-Nitroquinoline-1-oxide,4-Nitroquinoline-1-oxide: pharmacology,Chromosome Mapping,Chromosome Mapping: methods,Crosses, Genetic,Diploidy,Drug Resistance, Fungal,Drug Resistance, Fungal: drug effects,Drug Resistance, Fungal: genetics,Gene Frequency,Genotype,Haploidy,Mitochondria,Mitochondria: metabolism,Multifactorial Inheritance,Multifactorial Inheritance: genetics,Oligonucleotide Array Sequence Analysis,Phenotype,Polymorphism, Single Nucleotide,Polymorphism, Single Nucleotide: genetics,Quantitative Trait Loci,Quantitative Trait Loci: genetics,Quinolones,Quinolones: pharmacology,Saccharomyces cerevisiae,Saccharomyces cerevisiae: cytology,Saccharomyces cerevisiae: drug effects,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Sample Size},
month = apr,
number = {7291},
pages = {1039--42},
pmid = {20393561},
publisher = {Nature Publishing Group},
title = {{Dissection of genetically complex traits with extremely large pools of yeast segregants.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2862354\&tool=pmcentrez\&rendertype=abstract},
volume = {464},
year = {2010}
}
@article{Shewry2009,
abstract = {Wheat is the dominant crop in temperate countries being used for human food and livestock feed. Its success depends partly on its adaptability and high yield potential but also on the gluten protein fraction which confers the viscoelastic properties that allow dough to be processed into bread, pasta, noodles, and other food products. Wheat also contributes essential amino acids, minerals, and vitamins, and beneficial phytochemicals and dietary fibre components to the human diet, and these are particularly enriched in whole-grain products. However, wheat products are also known or suggested to be responsible for a number of adverse reactions in humans, including intolerances (notably coeliac disease) and allergies (respiratory and food). Current and future concerns include sustaining wheat production and quality with reduced inputs of agrochemicals and developing lines with enhanced quality for specific end-uses, notably for biofuels and human nutrition.},
author = {Shewry, P R},
doi = {10.1093/jxb/erp058},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Shewry/Journal of experimental botany/7ea09633a002551fa7287cb1fb1c96d42865bebf.pdf:pdf;:Users/ramirezr/Documents/Mendeley Desktop/Shewry/Journal of experimental botany/29b123fea180439e5ee03eab2ca4a11cb60212be.pdf:pdf},
issn = {1460-2431},
journal = {Journal of experimental botany},
keywords = {Celiac Disease,Celiac Disease: etiology,Gardening,Glutens,Glutens: immunology,Humans,Nutritive Value,Triticum,Triticum: chemistry,Triticum: immunology,Triticum: metabolism,Wheat Hypersensitivity,Wheat Hypersensitivity: etiology},
month = jan,
number = {6},
pages = {1537--53},
pmid = {19386614},
title = {{Wheat.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19386614},
volume = {60},
year = {2009}
}
@article{Bilgic2007,
abstract = {Wheat-barley disomic and ditelosomic chromosome addition lines have been used as genetic tools for a range of applications since their development in the 1980s. In the present study, we used the Affymetrix Barley1 GeneChip for comparative transcript analysis of the barley cultivar Betzes, the wheat cultivar Chinese Spring, and Chinese Spring - Betzes ditelosomic chromosome addition lines to physically map barley genes to their respective chromosome arm locations. We mapped 1257 barley genes to chromosome arms 1HS, 2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 5HS, 5HL, 7HS, and 7HL based on their transcript levels in the ditelosomic addition lines. The number of genes assigned to individual chromosome arms ranged from 24 to 197. We validated the physical locations of the genes through comparison with our previous chromosome-based physical mapping, comparative in silico mapping with rice and wheat, and single feature polymorphism (SFP) analysis. We found our physical mapping of barley genes to chromosome arms to be consistent with our previous physical mapping to whole chromosomes. In silico comparative mapping of barley genes assigned to chromosome arms revealed that the average genomic synteny to wheat and rice chromosome arms was 63.2\% and 65.5\%, respectively. In the 1257 mapped genes, we identified SFPs in 924 genes between the appropriate ditelosomic line and Chinese Spring that supported physical map placements. We also identified a single small rearrangement event between rice chromosome 9 and barley chromosome 4H that accounts for the loss of synteny for several genes.},
author = {Bilgic, Hatice and Cho, Seungho and Garvin, David F and Muehlbauer, Gary J},
doi = {10.1139/g07-059},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Bilgic et al/Genome National Research Council Canada = G\'{e}nome Conseil national de recherches Canada/c6ed69480560caf23b63126094a19c944e6e94f6.pdf:pdf},
issn = {0831-2796},
journal = {Genome / National Research Council Canada = G\'{e}nome / Conseil national de recherches Canada},
keywords = {Chimera,Chimera: genetics,Gene Expression Profiling,Gene Expression Profiling: methods,Genes,Genetic,Genetic Markers,Hordeum,Hordeum: genetics,Oligonucleotide Array Sequence Analysis,Physical Chromosome Mapping,Physical Chromosome Mapping: methods,Plant,Plant: genetics,Polymorphism,Transcription,Triticum,Triticum: genetics},
month = oct,
number = {10},
pages = {898--906},
pmid = {18059553},
title = {{Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18059553},
volume = {50},
year = {2007}
}
@article{KosakovskyPond2006,
abstract = {The evolution of homologous sequences affected by recombination or gene conversion cannot be adequately explained by a single phylogenetic tree. Many tree-based methods for sequence analysis, for example, those used for detecting sites evolving nonneutrally, have been shown to fail if such phylogenetic incongruity is ignored. However, it may be possible to propose several phylogenies that can correctly model the evolution of nonrecombinant fragments. We propose a model-based framework that uses a genetic algorithm to search a multiple-sequence alignment for putative recombination break points, quantifies the level of support for their locations, and identifies sequences or clades involved in putative recombination events. The software implementation can be run quickly and efficiently in a distributed computing environment, and various components of the methods can be chosen for computational expediency or statistical rigor. We evaluate the performance of the new method on simulated alignments and on an array of published benchmark data sets. Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection.},
author = {{Kosakovsky Pond}, Sergei L and Posada, David and Gravenor, Michael B and Woelk, Christopher H and Frost, Simon D W},
doi = {10.1093/molbev/msl051},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Kosakovsky Pond et al/Molecular biology and evolution/Mol Biol Evol-2006-Kosakovsky Pond-1891-901.pdf:pdf},
issn = {0737-4038},
journal = {Molecular biology and evolution},
keywords = {Algorithms,Computer Simulation,Evolution, Molecular,HIV-1,HIV-1: genetics,Models, Genetic,Phylogeny,Recombination, Genetic,Selection, Genetic,Sequence Alignment,Sequence Alignment: statistics \& numerical data,Software},
month = oct,
number = {10},
pages = {1891--901},
pmid = {16818476},
title = {{Automated phylogenetic detection of recombination using a genetic algorithm.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16818476},
volume = {23},
year = {2006}
}
@article{Panconesi2004,
author = {Panconesi, A and Sozio, M},
doi = {10.1007/978-3-540-30219-3\_23},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Panconesi, Sozio/Algorithms in Bioinformatics/4d7d76432cfee3d52f5d83dc8d5909c32d73297b.ps:ps},
journal = {Algorithms in Bioinformatics},
title = {{Fast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstruction}},
url = {http://link.springer.com/chapter/10.1007/978-3-540-30219-3\_23},
year = {2004}
}
@incollection{PontiusJUWagnerL2002,
author = {Pontius, JU and Wagner, L and Schuler, GD.},
booktitle = {The NCBI Handbook [Internet]},
chapter = {21},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Pontius, Wagner, Schuler/The NCBI Handbook Internet/ch21.pdf:pdf},
language = {en},
month = oct,
publisher = {National Center for Biotechnology Information (US)},
title = {{UniGene: A Unified View of the Transcriptome}},
url = {http://www.ncbi.nlm.nih.gov/books/NBK21083/},
year = {2002}
}
@article{Chague1999,
author = {Chagu\'{e}, V and Fahima, T and Dahan, A and Sun, G L and Korol, A B and Ronin, Y I and Grama, A and R\"{o}der, M S and Nevo, E},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Chagu\'{e} et al/Unknown/Chague1999.pdf:pdf},
keywords = {gene,genetic mapping,microsatellite markers,triticum dicoccoides,wheat,yr15 stripe rust resistance},
pages = {1050--1056},
title = {Isolation of microsatellite and RAPD markers flanking the \textit{Yr15} gene of wheat using NILs and bulked segregant analysis},
volume = {1056},
year = {1999}
}

@Inbook{Ramirez-Gonzalez2015c,
author={Ramirez-Gonzalez, Ricardo H.
and Segovia, Vanesa
and Bird, Nicholas
and Caccamo, Mario
and Uauy, Cristobal},
editor={Ogihara, Yasunari
and Takumi, Shigeo
and Handa, Hirokazu},
title={Next Generation Sequencing Enabled Genetics in Hexaploid Wheat},
bookTitle={Advances in Wheat Genetics: From Genome to Field: Proceedings of the 12th International Wheat Genetics Symposium},
year={2015},
publisher={Springer Japan},
address={Tokyo},
pages={201--209},
isbn={978-4-431-55675-6},
doi={10.1007/978-4-431-55675-6\_22},
url={http://dx.doi.org/10.1007/978-4-431-55675-6\_22}
}

@Inbook{VanOoijen2013,
author={Van Ooijen, J.W.
and Jansen, J. },
title={Estimation of recombination frequencies; Genetic Mapping in Experimental Populations},
bookTitle={Genetic Mapping in Experimental Populations},
year={2013},
pages={73--133},
publisher={Cambridge University Press},
address={Cambridge},
isbn={978-1-107-0132-16}

}

@Inbook{VanOoijen2013Intro,
author={Van Ooijen, J.W.
and Jansen, J. },
title={Introduction; Genetic Mapping in Experimental Populations},
bookTitle={Genetic Mapping in Experimental Populations},
year={2013},
pages={15--31},
publisher={Cambridge University Press},
address={Cambridge},
isbn={978-1-107-0132-16}

}


@article{Ramirez-Gonzalez2015b,
author = {Ramirez-Gonzalez, Ricardo H. and Segovia, Vanesa and Bird, Nicholas and Fenwick, Paul and Holdgate, Sarah and Berry, Simon and Jack, Peter and Caccamo, Mario and Uauy, Cristobal},
title = {RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat},
journal = {Plant Biotechnology Journal},
volume = {13},
number = {5},
issn = {1467-7652},
url = {http://dx.doi.org/10.1111/pbi.12281},
doi = {10.1111/pbi.12281},
pages = {613--624},
keywords = {bulk frequency ratio, Yr15, marker-assisted selection, haplotype, yellow rust, SRA project numbers, PolyMarker},
year = {2015}
}
@misc{,
file = {:Users/ramirezr/Documents/Mendeley Desktop/Unknown/Unknown/798ac8c0abe47a8c83f2c0ee0a1cb033ddb86b60.pdf:pdf},
title = {798ac8c0abe47a8c83f2c0ee0a1cb033ddb86b60.pdf}
}
@article{Rapaport2013,
abstract = {A large number of computational methods have been developed for analyzing differential gene expression in RNA-seq data. We describe a comprehensive evaluation of common methods using the SEQC benchmark dataset and ENCODE data. We consider a number of key features, including normalization, accuracy of differential expression detection and differential expression analysis when one condition has no detectable expression. We find significant differences among the methods, but note that array-based methods adapted to RNA-seq data perform comparably to methods designed for RNA-seq. Our results demonstrate that increasing the number of replicate samples significantly improves detection power over increased sequencing depth.},
author = {Rapaport, Franck and Khanin, Raya and Liang, Yupu and Pirun, Mono and Krek, Azra and Zumbo, Paul and Mason, Christopher E and Socci, Nicholas D and Betel, Doron},
doi = {10.1186/gb-2013-14-9-r95},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Rapaport et al/Genome biology/gb-2013-14-9-r95.pdf:pdf},
issn = {1465-6914},
journal = {Genome biology},
month = jan,
number = {9},
pages = {R95},
pmid = {24020486},
publisher = {BioMed Central Ltd},
title = {{Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4054597\&tool=pmcentrez\&rendertype=abstract},
volume = {14},
year = {2013}
}
@article{Wilhelm2013,
abstract = {The introgression of Reduced height (Rht)-B1b and Rht-D1b into bread wheat (Triticum aestivum) varieties beginning in the 1960s led to improved lodging resistance and yield, providing a major contribution to the 'green revolution'. Although wheat Rht-1 and surrounding sequence is available, the genetic composition of this region has not been examined in a homoeologous series. To determine this, three Rht-1-containing bacterial artificial chromosome (BAC) sequences derived from the A, B, and D genomes of the bread wheat variety Chinese Spring (CS) were fully assembled and analyzed. This revealed that Rht-1 and two upstream genes were highly conserved among the homoeologs. In contrast, transposable elements (TEs) were not conserved among homoeologs with the exception of intronic miniature inverted-repeat TEs (MITEs). In relation to the Triticum urartu ancestral line, CS-A genic sequences were highly conserved and several colinear TEs were present. Comparative analysis of the CS wheat BAC sequences with assembled Poaceae genomes showed gene synteny and amino acid sequences were well preserved. Further 5' and 3' of the wheat BAC sequences, a high degree of gene colinearity is present among the assembled Poaceae genomes. In the 20 kb of sequence flanking Rht-1, five conserved non-coding sequences (CNSs) were present among the CS wheat homoeologs and among all the Poaceae members examined. Rht-A1 was mapped to the long arm of chromosome 4 and three closely flanking genetic markers were identified. The tools developed herein will enable detailed studies of Rht-1 and linked genes that affect abiotic and biotic stress response in wheat.},
author = {Wilhelm, Edward P and Howells, Rhian M and Al-Kaff, Nadia and Jia, Jizeng and Baker, Catherine and Leverington-Waite, Michelle a and Griffiths, Simon and Greenland, Andy J and Boulton, Margaret I and Powell, Wayne},
doi = {10.1007/s00122-013-2055-3},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Wilhelm et al/TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik/Wilhelm et al. - 2013 - Genetic characterization and mapping of the Rht-1 homoeologs and flanking sequences in wheat.pdf:pdf},
issn = {1432-2242},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
keywords = {Chromosome Mapping,Chromosomes, Artificial, Bacterial,Chromosomes, Plant,Chromosomes, Plant: genetics,DNA, Plant,DNA, Plant: genetics,Genes, Plant,Genes, Plant: genetics,Genetic Markers,Genome, Plant,Genome, Plant: genetics,Phylogeny,Poaceae,Poaceae: classification,Poaceae: genetics,Triticum,Triticum: genetics,Triticum: growth \& development},
month = may,
number = {5},
pages = {1321--36},
pmid = {23381809},
title = {{Genetic characterization and mapping of the Rht-1 homoeologs and flanking sequences in wheat.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23381809},
volume = {126},
year = {2013}
}
@article{Bevan2013,
abstract = {The sequencing of large and complex genomes of crop species, facilitated by new sequencing technologies and bioinformatic approaches, has provided new opportunities for crop improvement. Current challenges include understanding how genetic variation translates into phenotypic performance in the field.},
author = {Bevan, Michael W and Uauy, Cristobal},
doi = {10.1186/gb-2013-14-6-206},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Bevan, Uauy/Genome biology/gb-2013-14-6-206.pdf:pdf},
issn = {1465-6914},
journal = {Genome biology},
keywords = {crop improvement,genomic,genomics,selection,systems breeding},
month = jun,
number = {6},
pages = {206},
pmid = {23796126},
title = {{Genomics reveals new landscapes for crop improvement.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23796126},
volume = {14},
year = {2013}
}
@article{Trick2012,
abstract = {Next generation sequencing (NGS) technologies are providing new ways to accelerate fine-mapping and gene isolation in many species. To date, the majority of these efforts have focused on diploid organisms with readily available whole genome sequence information. In this study, as a proof of concept, we tested the use of NGS for SNP discovery in tetraploid wheat lines differing for the previously cloned grain protein content (GPC) gene GPC-B1. Bulked segregant analysis (BSA) was used to define a subset of putative SNPs within the candidate gene region, which were then used to fine-map GPC-B1.},
author = {Trick, Martin and Adamski, Nikolai and Mugford, Sarah G and Jiang, Cong-Cong and Febrer, Melanie and Uauy, Cristobal},
doi = {10.1186/1471-2229-12-14},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Trick et al/BMC plant biology/e494a329069ccc121d432ce3ca3fac5c55e42708.pdf:pdf},
issn = {1471-2229},
journal = {BMC plant biology},
keywords = {Chromosome Mapping,Computational Biology,DNA, Plant,DNA, Plant: genetics,Gene Library,Genome, Plant,Molecular Sequence Data,Polymorphism, Single Nucleotide,Polyploidy,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Synteny,Triticum,Triticum: genetics},
month = jan,
number = {1},
pages = {14},
pmid = {22280551},
publisher = {BioMed Central Ltd},
title = {{Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3296661},
volume = {12},
year = {2012}
}
@article{Flicek2012,
abstract = {The Ensembl project (http://www.Ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.Ensembl.org) with preliminary support. The past year has also seen improvements across the project.},
author = {Flicek, Paul and Amode, M Ridwan and Barrell, Daniel and Beal, Kathryn and Brent, Simon and Carvalho-Silva, Denise and Clapham, Peter and Coates, Guy and Fairley, Susan and Fitzgerald, Stephen and Gil, Laurent and Gordon, Leo and Hendrix, Maurice and Hourlier, Thibaut and Johnson, Nathan and K\"{a}h\"{a}ri, Andreas K and Keefe, Damian and Keenan, Stephen and Kinsella, Rhoda and Komorowska, Monika and Koscielny, Gautier and Kulesha, Eugene and Larsson, Pontus and Longden, Ian and McLaren, William and Muffato, Matthieu and Overduin, Bert and Pignatelli, Miguel and Pritchard, Bethan and Riat, Harpreet Singh and Ritchie, Graham R S and Ruffier, Magali and Schuster, Michael and Sobral, Daniel and Tang, Y Amy and Taylor, Kieron and Trevanion, Stephen and Vandrovcova, Jana and White, Simon and Wilson, Mark and Wilder, Steven P and Aken, Bronwen L and Birney, Ewan and Cunningham, Fiona and Dunham, Ian and Durbin, Richard and Fern\'{a}ndez-Suarez, Xos\'{e} M and Harrow, Jennifer and Herrero, Javier and Hubbard, Tim J P and Parker, Anne and Proctor, Glenn and Spudich, Giulietta and Vogel, Jan and Yates, Andy and Zadissa, Amonida and Searle, Stephen M J},
doi = {10.1093/nar/gkr991},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Flicek et al/Nucleic acids research/Flicek et al. - 2012 - Ensembl 2012.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Animals,Databases, Genetic,Gene Expression Regulation,Genetic Variation,Genomics,Humans,Mice,Molecular Sequence Annotation,Rats},
month = jan,
number = {Database issue},
pages = {D84--90},
pmid = {22086963},
title = {{Ensembl 2012.}},
url = {http://nar.oxfordjournals.org/content/40/D1/D84},
volume = {40},
year = {2012}
}
@article{Greer2012,
abstract = {Despite possessing multiple sets of related (homoeologous) chromosomes, hexaploid wheat (Triticum aestivum) restricts pairing to just true homologs at meiosis. Deletion of a single major locus, Pairing homoeologous1 (Ph1), allows pairing of homoeologs. How can the same chromosomes be processed as homologs instead of being treated as nonhomologs? Ph1 was recently defined to a cluster of defective cyclin-dependent kinase (Cdk)-like genes showing some similarity to mammalian Cdk2. We reasoned that the cluster might suppress Cdk2-type activity and therefore affect replication and histone H1 phosphorylation. Our study does indeed reveal such effects, suggesting that Cdk2-type phosphorylation has a major role in determining chromosome specificity during meiosis.},
author = {Greer, Emma and Mart\'{\i}n, Azahara C and Pendle, Ali and Colas, Isabelle and Jones, Alexandra M E and Moore, Graham and Shaw, Peter},
doi = {10.1105/tpc.111.094771},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Greer et al/The Plant cell/Greer et al. - 2012 - The Ph1 locus suppresses Cdk2-type activity during premeiosis and meiosis in wheat.pdf:pdf},
issn = {1532-298X},
journal = {The Plant cell},
keywords = {Cyclin-Dependent Kinase 2,Cyclin-Dependent Kinase 2: genetics,Cyclin-Dependent Kinase 2: metabolism,Gene Expression Regulation, Plant,Gene Expression Regulation, Plant: genetics,Gene Expression Regulation, Plant: physiology,Meiosis,Meiosis: genetics,Meiosis: physiology,Molecular Sequence Data,Plant Proteins,Plant Proteins: genetics,Plant Proteins: metabolism,Triticum,Triticum: genetics,Triticum: metabolism},
month = jan,
number = {1},
pages = {152--62},
pmid = {22274628},
title = {{The Ph1 locus suppresses Cdk2-type activity during premeiosis and meiosis in wheat.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3289575\&tool=pmcentrez\&rendertype=abstract},
volume = {24},
year = {2012}
}
@article{Maclean2012,
author = {Maclean, Daniel and Kamoun, Sophien},
doi = {10.1038/nbt.2079},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Maclean, Kamoun/Nature biotechnology/0fa535f988af7615e0cee2637c8ecca9d8bf5eed.pdf:pdf},
issn = {1546-1696},
journal = {Nature biotechnology},
keywords = {Academies and Institutes,Academies and Institutes: trends,Automatic Data Processing,Computational Biology,Computational Biology: methods,Computational Biology: trends,Data Mining,Data Mining: methods,Data Mining: trends,Drug Industry,Drug Industry: trends,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: methods,Humans,Polymorphism,Single Nucleotide,Single Nucleotide: genetics},
month = jan,
number = {1},
pages = {33--4},
pmid = {22231089},
publisher = {Nature Publishing Group},
title = {{Big data in small places.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22231089},
volume = {30},
year = {2012}
}
@article{Fossdal2012,
abstract = {NB-LRR resistance proteins are involved in recognizing pathogens and other exogenous stressors in plants. Resistance proteins are the first step in induced defence responses and a better understanding of their regulation is important to understand the mechanisms of plant defence. Much of the post-transcriptional regulation in plants is controlled by microRNAs (miRNA). We examined the expression of five Norway spruce miRNA that may regulate NB-LRR related transcripts in secondary phloem (bark) of resistant Norway spruce after wounding and inoculation with the necrotrophic blue stain fungus Ceratocystis polonica.},
author = {Fossdal, Carl Gunnar and Yaqoob, Nadeem and Krokene, Paal and Kvaalen, Harald and Solheim, Halvor and Yakovlev, Igor a},
doi = {10.1186/1471-2229-12-105},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Fossdal et al/BMC plant biology/NBS\_LRR expresion.pdf:pdf},
issn = {1471-2229},
journal = {BMC plant biology},
keywords = {carl,ceratocystis polonica,correspondence,fossdal,microrna,necrotroph,no,pcr,picea abies,qRT�PCR,qrt,resistance,skogoglandskap},
month = jan,
number = {1},
pages = {105},
pmid = {22776433},
publisher = {BMC Plant Biology},
title = {{Local and systemic changes in expression of resistance genes, nb-lrr genes and their putative microRNAs in norway spruce after wounding and inoculation with the pathogen Ceratocystis polonica.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3431983\&tool=pmcentrez\&rendertype=abstract},
volume = {12},
year = {2012}
}
@article{Westermann2012,
abstract = {A comprehensive understanding of host-pathogen interactions requires a knowledge of the associated gene expression changes in both the pathogen and the host. Traditional, probe-dependent approaches using microarrays or reverse transcription PCR typically require the pathogen and host cells to be physically separated before gene expression analysis. However, the development of the probe-independent RNA sequencing (RNA-seq) approach has begun to revolutionize transcriptomics. Here, we assess the feasibility of taking transcriptomics one step further by performing 'dual RNA-seq', in which gene expression changes in both the pathogen and the host are analysed simultaneously.},
author = {Westermann, Alexander J and Gorski, Stanislaw a and Vogel, J\"{o}rg},
doi = {10.1038/nrmicro2852},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Westermann, Gorski, Vogel/Nature reviews. Microbiology/RNAseq for pathogen and host.pdf:pdf},
issn = {1740-1534},
journal = {Nature reviews. Microbiology},
keywords = {Animals,Bacterial Infections,Bacterial Infections: pathology,Computational Biology,Computational Biology: methods,Disease Models, Animal,Gene Expression Profiling,Gene Expression Profiling: methods,Host-Pathogen Interactions,Humans,Mycoses,Mycoses: pathology,Plant Diseases,Plant Diseases: microbiology,Protozoan Infections,Protozoan Infections: pathology,Sequence Analysis, RNA,Sequence Analysis, RNA: methods},
month = oct,
number = {9},
pages = {618--30},
pmid = {22890146},
publisher = {Nature Publishing Group},
title = {{Dual RNA-seq of pathogen and host.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22890146},
volume = {10},
year = {2012}
}
@book{Rifkin2012,
address = {New York, NY},
author = {Rifkin, Scott A.},
doi = {10.1007/978-1-61779-785-9},
editor = {Rifkin, Scott A.},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Rifkin/Unknown/Rifkin - 2012 - Quantitative Trait Loci (QTL).pdf:pdf},
isbn = {978-1-61779-784-2},
pages = {331},
publisher = {Humana Press},
series = {Methods in Molecular Biology},
title = {{Quantitative Trait Loci (QTL)}},
volume = {871},
year = {2012}
}
@article{Schneeberger2011,
abstract = {New sequencing technologies are dramatically accelerating progress in forward genetics, and the use of such methods for the rapid identification of mutant alleles will be soon routine in many laboratories. A straightforward extension will be the cloning of major-effect genetic variants in crop species. In the near future, it can be expected that mapping by sequencing will become a centerpiece in efforts to discover the genes responsible for quantitative trait loci. The largest impact, however, might come from the use of these strategies to extract genes from non-model, non-crop plants that exhibit heritable variation in important traits. Deployment of such genes to improve crops or engineer microbes that produce valuable compounds heralds a potential paradigm shift for plant biology.},
author = {Schneeberger, Korbinian and Weigel, Detlef},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Schneeberger, Weigel/Trends in Plant Science/Schneeberger, Weigel - 2011 - Fast-forward genetics enabled by new sequencing technologies.pdf:pdf},
journal = {Trends in Plant Science},
number = {5},
pages = {282--288},
title = {{Fast-forward genetics enabled by new sequencing technologies}},
url = {http://www.sciencedirect.com/science/article/pii/S136013851100029X},
volume = {16},
year = {2011}
}
@article{Chance2011,
abstract = {Researchers have documented many cases in which individuals rationalize their regrettable actions. Four experiments examine situations in which people go beyond merely explaining away their misconduct to actively deceiving themselves. We find that those who exploit opportunities to cheat on tests are likely to engage in self-deception, inferring that their elevated performance is a sign of intelligence. This short-term psychological benefit of self-deception, however, can come with longer-term costs: when predicting future performance, participants expect to perform equally well-a lack of awareness that persists even when these inflated expectations prove costly. We show that although people expect to cheat, they do not foresee self-deception, and that factors that reinforce the benefits of cheating enhance self-deception. More broadly, the findings of these experiments offer evidence that debates about the relative costs and benefits of self-deception are informed by adopting a temporal view that assesses the cumulative impact of self-deception over time.},
author = {Chance, Zo\"{e} and Norton, Michael I and Gino, Francesca and Ariely, Dan},
doi = {10.1073/pnas.1010658108},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Chance et al/Proceedings of the National Academy of Sciences of the United States of America/Chance et al. - 2011 - Quantification of Behavior Sackler Colloquium Temporal view of the costs and benefits of self-deception.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Sociology},
mendeley-tags = {Sociology},
month = mar,
pages = {1010658108--},
pmid = {21383150},
title = {{Quantification of Behavior Sackler Colloquium: Temporal view of the costs and benefits of self-deception.}},
url = {http://www.pnas.org/cgi/content/abstract/1010658108v1},
year = {2011}
}
@article{Lieberman-aiden2009,
abstract = {We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.},
author = {Lieberman-aiden, Erez and van Berkum, Nynke L and Williams, Louise and Imakaev, Maxim and Ragoczy, Tobias and Telling, Agnes and Amit, Ido and Lajoie, Bryan R and Sabo, Peter J and Dorschner, Michael O and Sandstrom, Richard and Bernstein, Bradley and Bender, M A and Groudine, Mark and Gnirke, Andreas and Stamatoyannopoulos, John and Mirny, Leonid A and Lander, Eric S and Dekker, Job and Berkum, Nynke L Van and Peter, J and Leonid, A},
doi = {10.1126/science.1181369},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Lieberman-aiden et al/Science (New York, N.Y.)/079f4061c5e467c5e407507dd0f555de381ac33e.pdf:pdf},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Biotin,Cell Line,Cell Nucleus,Cell Nucleus: ultrastructure,Chromatin,Chromatin Immunoprecipitation,Chromatin: chemistry,Chromosomes,Computational Biology,DNA,DNA: chemistry,Fluorescence,Gene Library,Genome,Genome Modeling,Human,Human: chemistry,Human: ultrastructure,Humans,In Situ Hybridization,Models,Molecular,Monte Carlo Method,Nucleic Acid Conformation,Principal Component Analysis,Protein Conformation,Sequence Analysis,Transformed},
mendeley-tags = {Genome Modeling},
month = oct,
number = {5950},
pages = {289--93},
pmid = {19815776},
title = {{Comprehensive mapping of long-range interactions reveals folding principles of the human genome.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2858594\&tool=pmcentrez\&rendertype=abstract},
volume = {326},
year = {2009}
}
@article{Bansal2008,
abstract = {The goal of the haplotype assembly problem is to reconstruct the two haplotypes (chromosomes) for an individual using a mix of sequenced fragments from the two chromosomes. This problem has been shown to be computationally intractable for various optimization criteria. Polynomial time algorithms have been proposed for restricted versions of the problem. In this article, we consider the haplotype assembly problem in the most general setting, i.e. fragments of any length and with an arbitrary number of gaps.},
author = {Bansal, Vikas and Bafna, Vineet},
doi = {10.1093/bioinformatics/btn298},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Bansal, Bafna/Bioinformatics (Oxford, England)/df389ddda71df2355d8b8f78118fd58a711dd3ac.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
keywords = {Algorithms,Base Sequence,Chromosome Mapping,Chromosome Mapping: methods,Haplotypes,Haplotypes: genetics,Molecular Sequence Data,Reproducibility of Results,Sensitivity and Specificity,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis, DNA,Sequence Analysis, DNA: methods},
month = aug,
number = {16},
pages = {i153--9},
pmid = {18689818},
title = {{HapCUT: an efficient and accurate algorithm for the haplotype assembly problem.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18689818},
volume = {24},
year = {2008}
}
@article{Macgregor2003,
abstract = {This year marks the 50th anniversary of the proposal of a double helical structure for DNA by James Watson and Francis Crick. The place of this proposal in the history and development of molecular biology is discussed. Several other discoveries that occurred in the middle of the twentieth century were perhaps equally important to our understanding of cellular processes; however, none of these captured the attention and imagination of the public to the same extent as the double helix. The existence of multiple forms of DNA and the uses of DNA in biological technologies is presented. DNA is also finding increasing use as a material due to its rather unusual structural and physical characteristics as well as its ready availability.},
author = {Macgregor, Robert B. and Poon, Gregory M.K.},
doi = {10.1016/j.compbiolchem.2003.08.001},
issn = {14769271},
journal = {Computational Biology and Chemistry},
keywords = {dna,double helix,molecular biology,nanotechnology},
month = oct,
number = {4-5},
pages = {461--467},
title = {{The DNA double helix fifty years on}},
url = {http://dx.doi.org/10.1016/j.compbiolchem.2003.08.001},
volume = {27},
year = {2003}
}
@incollection{CooperGM2000,
author = {GM, Cooper},
booktitle = {The Cell: A Molecular Approach},
language = {en},
publisher = {Sinauer Associates},
title = {{Chloroplasts and Other Plastids}},
url = {http://www.ncbi.nlm.nih.gov/books/NBK9905/?redirect-on-error=\_\_HOME\_\_},
year = {2000}
}
@article{Steed1999,
author = {Quarrie, SA and Lazi\'{c}-Jan\v{c}i\'{c}, V},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Quarrie, Lazi\'{c}-Jan\v{c}i\'{c}/Journal of experimental botany/1e37e7296d68695dc4b9272707ff8231e1cd2be5.pdf:pdf},
journal = {Journal of experimental botany},
keywords = {bsa,bulk segregant analysis,drought,genetic maps,maize,molecular markers,resistance,zea},
number = {337},
pages = {1299--1306},
title = {{Bulk segregant analysis with molecular markers and its use for improving drought resistance in maize}},
url = {http://jxb.oxfordjournals.org/content/50/337/1299.short},
volume = {50},
year = {1999}
}
@article{Altschul1990,
abstract = {A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.},
author = {Altschul, S F and Gish, W and Miller, W and Myers, E W and Lipman, D J},
doi = {10.1016/S0022-2836(05)80360-2},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Algorithms,Amino Acid Sequence,Base Sequence,Databases, Factual,Mutation,Sensitivity and Specificity,Sequence Homology, Nucleic Acid,Software},
month = oct,
number = {3},
pages = {403--10},
pmid = {2231712},
title = {{Basic local alignment search tool.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/2231712},
volume = {215},
year = {1990}
}
@article{Cucurbitaceae1985,
author = {Cucurbitaceae, Jacq Swartz},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Cucurbitaceae/Unknown/54ccbb9ad628bd27167da651705a4bfa4a05149e.pdf:pdf},
title = {{SCHIUM EDULE (Jacq) Swartz CUCURBITACEAE}},
year = {1985}
}
@article{Buettner2015,
author = {Buettner, Florian and Natarajan, Kedar N and Casale, F Paolo and Proserpio, Valentina and Scialdone, Antonio and Theis, Fabian J and Teichmann, Sarah a and Marioni, John C and Stegle, Oliver},
doi = {10.1038/nbt.3102},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Buettner et al/Nature Biotechnology/nbt.3102.pdf:pdf},
issn = {1087-0156},
journal = {Nature Biotechnology},
month = jan,
number = {2},
title = {{Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells}},
url = {http://www.nature.com/doifinder/10.1038/nbt.3102},
volume = {33},
year = {2015}
}
@article{Campus,
author = {Campus, Cayirova and Scientific, The and Engineering, Genetic and Sciences, Natural and Sciences, Biological},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Campus et al/Unknown/050768425ec6fe5f0e3c3695697a7f605a1ab693.pdf:pdf},
title = {{A Microsatellite Marker for Yellow Rust Resistance in Wheat}}
}
@article{,
doi = {10.1126/science.1251385},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Unknown/Unknown/Unknown - Unknown - whole-genome analyses resolve early branches in the tree of life of modern birds.pdf:pdf},
title = {whole-genome analyses resolve early branches in the tree of life of modern birds}
}
@article{Henry2014,
abstract = {Chemical mutagenesis efficiently generates phenotypic variation in otherwise homogeneous genetic backgrounds, enabling functional analysis of genes. Advances in mutation detection have brought the utility of induced mutant populations on par with those produced by insertional mutagenesis, but systematic cataloguing of mutations would further increase their utility. We examined the suitability of multiplexed global exome capture and sequencing coupled with custom-developed bioinformatics tools to identify mutations in well-characterized mutant populations of rice (Oryza sativa) and wheat (Triticum aestivum). In rice, we identified ∼18,000 induced mutations from 72 independent M2 individuals. Functional evaluation indicated the recovery of potentially deleterious mutations for >2600 genes. We further observed that specific sequence and cytosine methylation patterns surrounding the targeted guanine residues strongly affect their probability to be alkylated by ethyl methanesulfonate. Application of these methods to six independent M2 lines of tetraploid wheat demonstrated that our bioinformatics pipeline is applicable to polyploids. In conclusion, we provide a method for developing large-scale induced mutation resources with relatively small investments that is applicable to resource-poor organisms. Furthermore, our results demonstrate that large libraries of sequenced mutations can be readily generated, providing enhanced opportunities to study gene function and assess the effect of sequence and chromatin context on mutations.},
author = {Henry, Isabelle M and Nagalakshmi, Ugrappa and Lieberman, Meric C and Ngo, Kathie J and Krasileva, Ksenia V and Vasquez-Gross, Hans and Akhunova, Alina and Akhunov, Eduard and Dubcovsky, Jorge and Tai, Thomas H and Comai, Luca},
doi = {10.1105/tpc.113.121590},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Henry et al/The Plant cell/Plant Cell-2014-Henry-tpc.113.121590.pdf:pdf},
issn = {1532-298X},
journal = {The Plant cell},
month = apr,
number = {4},
pages = {1382--1397},
pmid = {24728647},
title = {{Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24728647},
volume = {26},
year = {2014}
}
@article{Saintenac2013,
abstract = {The emergence of new sequencing technologies has provided fast and cost-efficient strategies for high-resolution mapping of complex genomes. Although these approaches hold great promise to accelerate genome analysis, their application in studying genetic variation in wheat has been hindered by the complexity of its polyploid genome. Here, we applied the next-generation sequencing of a wheat doubled-haploid mapping population for high-resolution gene mapping and tested its utility for ordering shotgun sequence contigs of a flow-sorted wheat chromosome. A bioinformatical pipeline was developed for reliable variant analysis of sequence data generated for polyploid wheat mapping populations. The results of variant mapping were consistent with the results obtained using the wheat 9000 SNP iSelect assay. A reference map of the wheat genome integrating 2740 gene-associated single-nucleotide polymorphisms from the wheat iSelect assay, 1351 diversity array technology, 118 simple sequence repeat/sequence-tagged sites, and 416,856 genotyping-by-sequencing markers was developed. By analyzing the sequenced megabase-size regions of the wheat genome we showed that mapped markers are located within 40-100 kb from genes providing a possibility for high-resolution mapping at the level of a single gene. In our population, gene loci controlling a seed color phenotype cosegregated with 2459 markers including one that was located within the red seed color gene. We demonstrate that the high-density reference map presented here is a useful resource for gene mapping and linking physical and genetic maps of the wheat genome.},
author = {Saintenac, Cyrille and Jiang, Dayou and Wang, Shichen and Akhunov, Eduard},
doi = {10.1534/g3.113.005819},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Saintenac et al/G3 (Bethesda, Md.)/1105.full.pdf:pdf},
issn = {2160-1836},
journal = {G3 (Bethesda, Md.)},
keywords = {Chromosome Mapping,Chromosomes,DNA,Expressed Sequence Tags,Genetic Variation,Genome,Humans,Plant,Plant: genetics,Polymorphism,Polyploidy,Sequence Analysis,Single Nucleotide},
month = jul,
number = {7},
pages = {1105--14},
pmid = {23665877},
title = {{Sequence-based mapping of the polyploid wheat genome.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23665877},
volume = {3},
year = {2013}
}
@article{Macalalad2012,
abstract = {Viruses diversify over time within hosts, often undercutting the effectiveness of host defenses and therapeutic interventions. To design successful vaccines and therapeutics, it is critical to better understand viral diversification, including comprehensively characterizing the genetic variants in viral intra-host populations and modeling changes from transmission through the course of infection. Massively parallel sequencing technologies can overcome the cost constraints of older sequencing methods and obtain the high sequence coverage needed to detect rare genetic variants (< 1\%) within an infected host, and to assay variants without prior knowledge. Critical to interpreting deep sequence data sets is the ability to distinguish biological variants from process errors with high sensitivity and specificity. To address this challenge, we describe V-Phaser, an algorithm able to recognize rare biological variants in mixed populations. V-Phaser uses covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. Overall, V-Phaser achieved > 97\% sensitivity and > 97\% specificity on control read sets. On data derived from a patient after four years of HIV-1 infection, V-Phaser detected 2,015 variants across the -10 kb genome, including 603 rare variants (< 1\% frequency) detected only using phase information. V-Phaser identified variants at frequencies down to 0.2\%, comparable to the detection threshold of allele-specific PCR, a method that requires prior knowledge of the variants. The high sensitivity and specificity of V-Phaser enables identifying and tracking changes in low frequency variants in mixed populations such as RNA viruses.},
author = {Macalalad, Alexander R and Zody, Michael C and Charlebois, Patrick and Lennon, Niall J and Newman, Ruchi M and Malboeuf, Christine M and Ryan, Elizabeth M and Boutwell, Christian L and Power, Karen a and Brackney, Doug E and Pesko, Kendra N and Levin, Joshua Z and Ebel, Gregory D and Allen, Todd M and Birren, Bruce W and Henn, Matthew R},
doi = {10.1371/journal.pcbi.1002417},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Macalalad et al/PLoS computational biology/journal.pcbi.1002417.pdf:pdf},
issn = {1553-7358},
journal = {PLoS computational biology},
keywords = {Algorithms,Base Sequence,DNA, Viral,DNA, Viral: genetics,Genetic Variation,Genetic Variation: genetics,Molecular Sequence Data,Mutation,Mutation: genetics,Sensitivity and Specificity,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis, DNA,Sequence Analysis, DNA: methods},
month = jan,
number = {3},
pages = {e1002417},
pmid = {22438797},
title = {{Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3305335\&tool=pmcentrez\&rendertype=abstract},
volume = {8},
year = {2012}
}
@article{Resendis-Antonio2012,
abstract = {Modular organization in biological networks has been suggested as a natural mechanism by which a cell coordinates its metabolic strategies for evolving and responding to environmental perturbations. To understand how this occurs, there is a need for developing computational schemes that contribute to integration of genomic-scale information and assist investigators in formulating biological hypotheses in a quantitative and systematic fashion. In this work, we combined metabolome data and constraint-based modeling to elucidate the relationships among structural modules, functional organization, and the optimal metabolic phenotype of Rhizobium etli, a bacterium that fixes nitrogen in symbiosis with Phaseolus vulgaris. To experimentally characterize the metabolic phenotype of this microorganism, we obtained the metabolic profile of 220 metabolites at two physiological stages: under free-living conditions, and during nitrogen fixation with P. vulgaris. By integrating these data into a constraint-based model, we built a refined computational platform with the capability to survey the metabolic activity underlying nitrogen fixation in R. etli. Topological analysis of the metabolic reconstruction led us to identify modular structures with functional activities. Consistent with modular activity in metabolism, we found that most of the metabolites experimentally detected in each module simultaneously increased their relative abundances during nitrogen fixation. In this work, we explore the relationships among topology, biological function, and optimal activity in the metabolism of R. etli through an integrative analysis based on modeling and metabolome data. Our findings suggest that the metabolic activity during nitrogen fixation is supported by interacting structural modules that correlate with three functional classifications: nucleic acids, peptides, and lipids. More fundamentally, we supply evidence that such modular organization during functional nitrogen fixation is a robust property under different environmental conditions.},
author = {Resendis-Antonio, Osbaldo and Hern\'{a}ndez, Magdalena and Mora, Yolanda and Encarnaci\'{o}n, Sergio},
doi = {10.1371/journal.pcbi.1002720},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Resendis-Antonio et al/PLoS computational biology/journal.pcbi.1002720.pdf:pdf},
issn = {1553-7358},
journal = {PLoS computational biology},
keywords = {Carbon,Carbon: metabolism,Metabolic Networks and Pathways,Metabolic Networks and Pathways: physiology,Metabolome,Metabolome: physiology,Metabolomics,Metabolomics: methods,Models, Biological,Nitrogen Fixation,Nitrogen Fixation: physiology,Phaseolus,Phaseolus: microbiology,Phenotype,Proteome,Rhizobium etli,Rhizobium etli: genetics,Rhizobium etli: metabolism,Symbiosis,Symbiosis: physiology,Systems Biology,Systems Biology: methods},
month = jan,
number = {10},
pages = {e1002720},
pmid = {23071431},
title = {{Functional modules, structural topology, and optimal activity in metabolic networks.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3469419\&tool=pmcentrez\&rendertype=abstract},
volume = {8},
year = {2012}
}
@article{Prlic2012,
abstract = {BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality. RESULTS: BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model. AVAILABILITY: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.6 or higher. All inquiries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.},
author = {Prli\'{c}, Andreas and Yates, Andrew and Bliven, Spencer E and Rose, Peter W and Jacobsen, Julius and Troshin, Peter V and Chapman, Mark and Gao, Jianjiong and Koh, Chuan Hock and Foisy, Sylvain and Holland, Richard and Rimsa, Gediminas and Heuer, Michael L and Brandst\"{a}tter-M\"{u}ller, H and Bourne, Philip E and Willis, Scooter},
doi = {10.1093/bioinformatics/bts494},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Prli\'{c} et al/Bioinformatics (Oxford, England)/Prli\'{c} et al. - 2012 - BioJava an open-source framework for bioinformatics in 2012.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
month = oct,
number = {20},
pages = {2693--5},
pmid = {22877863},
title = {{BioJava: an open-source framework for bioinformatics in 2012.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3467744\&tool=pmcentrez\&rendertype=abstract},
volume = {28},
year = {2012}
}
@article{Grabherr2011,
abstract = {Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.},
author = {Grabherr, Manfred G and Haas, Brian J and Yassour, Moran and Levin, Joshua Z and Thompson, Dawn a and Amit, Ido and Adiconis, Xian and Fan, Lin and Raychowdhury, Raktima and Zeng, Qiandong and Chen, Zehua and Mauceli, Evan and Hacohen, Nir and Gnirke, Andreas and Rhind, Nicholas and di Palma, Federica and Birren, Bruce W and Nusbaum, Chad and Lindblad-Toh, Kerstin and Friedman, Nir and Regev, Aviv},
doi = {10.1038/nbt.1883},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Grabherr et al/Nature biotechnology/nbt.1883.pdf:pdf},
issn = {1546-1696},
journal = {Nature biotechnology},
keywords = {Algorithms,Base Sequence,Gene Expression Profiling,Gene Expression Profiling: methods,Molecular Sequence Data,RNA,RNA: chemistry,RNA: genetics,RNA: methods,RNA: standards,Reference Values,Sequence Analysis,Transcriptome},
month = jul,
number = {7},
pages = {644--52},
pmid = {21572440},
title = {{Full-length transcriptome assembly from RNA-Seq data without a reference genome.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3571712\&tool=pmcentrez\&rendertype=abstract},
volume = {29},
year = {2011}
}
@misc{TheMendeleySupportTeam2011c,
abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.},
address = {London},
author = {{The Mendeley Support Team}},
booktitle = {Mendeley Desktop},
file = {:Users/ramirezr/Documents/Mendeley Desktop/The Mendeley Support Team/Mendeley Desktop/The Mendeley Support Team - 2011 - Getting Started with Mendeley(2).pdf:pdf},
keywords = {Mendeley,how-to,user manual},
pages = {1--16},
publisher = {Mendeley Ltd.},
title = {{Getting Started with Mendeley}},
url = {http://www.mendeley.com},
year = {2011}
}
@article{Huang2011,
abstract = {Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, one of the most important diseases of wheat worldwide. cDNA libraries had been constructed from urediniospores, germinated urediniospores and haustoria. However, little is known about the expression patterns of the genes related to the infection process and sporulation of the pathogen. In this study, a custom oligonucleotide microarray was constructed using sequences of 442 gene transcripts selected from Pst cDNA libraries. The expression patterns of the genes were determined by hybridizing the microarray with cDNA from Pst in vitro and Pst-infected wheat leaves. The time course study identified 55 transcripts that were differentially expressed during the infection process in a compatible interaction. They were identified to have functions related to the following biological processes, including carbohydrate and lipid metabolism, energy, cell signaling, protein synthesis, cell structure and division. In an incompatible interaction, 17 transcripts of the pathogen were differentially expressed in resistant wheat leaves inoculated with an avirulent Pst race, ten of which had similar expression patterns to those in the compatible interaction. Several candidates for pathogenicity and virulence/avirulence related genes were also identified. The results of quantitative real-time PCR validated the expression patterns of some selected genes. The study demonstrates that the custom oligonucleotide microarray technology is useful to determine the expression patterns of the pathogen genes involved in different types of the host-pathogen interactions and stages of development.},
author = {Huang, Xueling and Chen, Xianming and Coram, Tristan and Wang, Meinan and Kang, Zhensheng},
doi = {10.1016/j.jgg.2011.07.004},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Huang et al/Journal of genetics and genomics = Yi chuan xue bao/1-s2.0-S1673852711001275-main.pdf:pdf},
issn = {1673-8527},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
keywords = {Basidiomycota,Basidiomycota: genetics,Basidiomycota: growth \& development,Carbohydrate Metabolism,Carbohydrate Metabolism: genetics,Gene Expression Profiling,Gene Expression Regulation, Developmental,Host-Pathogen Interactions,Lipid Metabolism,Lipid Metabolism: genetics,Oligonucleotide Array Sequence Analysis,Plant Diseases,Plant Diseases: microbiology,Triticum,Triticum: microbiology},
month = aug,
number = {8},
pages = {357--71},
pmid = {21867962},
publisher = {Elsevier Limited and Science Press},
title = {{Gene expression profiling of Puccinia striiformis f. sp. tritici during development reveals a highly dynamic transcriptome.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21867962},
volume = {38},
year = {2011}
}
@article{Merali2010,
author = {Merali, Z},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Merali/Nature/Unknown - Unknown - © 20 10 Macmillan Publishers Limited. All rights reserved 1 4.pdf:pdf},
journal = {Nature},
pages = {6--8},
title = {...why scientific programming does not compute},
url = {http://scholar.google.com/scholar?hl=en\&btnG=Search\&q=intitle:...why+scientific+programming+does+not+compute\#1},
year = {2010}
}
@article{Stone2010,
abstract = {Psychological well-being (WB) includes a person's overall appraisal of his or her life (Global WB) and affective state (Hedonic WB), and it is considered a key aspect of the health of individuals and groups. Several cross-sectional studies have documented a relation between Global WB and age. Little is known, however, about the age distribution of Hedonic WB. It may yield a different view of aging because it is less influenced by the cognitive reconstruction inherent in Global WB measures and because it includes both positive and negative components of WB. In this study we report on both Global and Hedonic WB assessed in a 2008 telephone survey of 340,847 people in the United States. Consistent with prior studies, Global WB and positive Hedonic WB generally had U-shaped age profiles showing increased WB after the age of 50 years. However, negative Hedonic WB variables showed distinctly different and stronger patterns: Stress and Anger steeply declined from the early 20s, Worry was elevated through middle age and then declined, and Sadness was essentially flat. Unlike a prior study, men and women had very similar age profiles of WB. Several measures that could plausibly covary with the age-WB association (e.g., having children at home) did not alter the age-WB patterns. Global and Hedonic WB measures appear to index different aspects of WB over the lifespan, and the postmidlife increase in WB, especially in Hedonic WB, deserves continued exploration.},
author = {Stone, Arthur a and Schwartz, Joseph E and Broderick, Joan E and Deaton, Angus},
doi = {10.1073/pnas.1003744107},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Stone et al/Proceedings of the National Academy of Sciences of the United States of America/Stone et al. - 2010 - A snapshot of the age distribution of psychological well-being in the United States.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
month = may,
number = {4},
pages = {1--6},
pmid = {20479218},
title = {{A snapshot of the age distribution of psychological well-being in the United States.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20479218},
year = {2010}
}
@article{Goto2010,
abstract = {SUMMARY: The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser.

AVAILABILITY: BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/.

CONTACT: katayama@bioruby.org},
author = {Goto, Naohisa and Prins, Pjotr and Nakao, Mitsuteru and Bonnal, Raoul and Aerts, Jan and Katayama, Toshiaki},
doi = {10.1093/bioinformatics/btq475},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Goto et al/Bioinformatics (Oxford, England)/Bioinformatics-2010-Goto-2617-9.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
keywords = {Computational Biology,Databases, Factual,MEDLINE,Phylogeny,Programming Languages,Sequence Analysis, Protein,Software},
month = oct,
number = {20},
pages = {2617--9},
pmid = {20739307},
title = {{BioRuby: bioinformatics software for the Ruby programming language.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2951089\&tool=pmcentrez\&rendertype=abstract},
volume = {26},
year = {2010}
}
@article{VanOoijen2008,
abstract = {Resistance (R) proteins in plants are involved in pathogen recognition and subsequent activation of innate immune responses. Most resistance proteins contain a central nucleotide-binding domain. This so-called NB-ARC domain consists of three subdomains: NB, ARC1, and ARC2. The NB-ARC domain is a functional ATPase domain, and its nucleotide-binding state is proposed to regulate activity of the R protein. A highly conserved methionine-histidine-aspartate (MHD) motif is present at the carboxy-terminus of ARC2. An extensive mutational analysis of the MHD motif in the R proteins I-2 and Mi-1 is reported. Several novel autoactivating mutations of the MHD invariant histidine and conserved aspartate were identified. The combination of MHD mutants with autoactivating hydrolysis mutants in the NB subdomain showed that the autoactivation phenotypes are not additive. This finding indicates an important regulatory role for the MHD motif in the control of R protein activity. To explain these observations, a three-dimensional model of the NB-ARC domain of I-2 was built, based on the APAF-1 template structure. The model was used to identify residues important for I-2 function. Substitution of the selected residues resulted in the expected distinct phenotypes. Based on the model, it is proposed that the MHD motif fulfils the same function as the sensor II motif found in AAA+ proteins (ATPases associated with diverse cellular activities)-co-ordination of the nucleotide and control of subdomain interactions. The presented 3D model provides a framework for the formulation of hypotheses on how mutations in the NB-ARC exert their effects.},
author = {van Ooijen, Gerben and Mayr, Gabriele and Kasiem, Mobien M a and Albrecht, Mario and Cornelissen, Ben J C and Takken, Frank L W},
doi = {10.1093/jxb/ern045},
file = {:Users/ramirezr/Documents/Mendeley Desktop/van Ooijen et al/Journal of experimental botany/171085353a7d6144129845ac3d46e22f45c4f81e.pdf:pdf},
issn = {1460-2431},
journal = {Journal of experimental botany},
keywords = {Amino Acid Motifs,Amino Acid Motifs: genetics,Amino Acid Sequence,Gene Expression Regulation, Plant,Immunity, Innate,Models, Molecular,Molecular Sequence Data,Mutation, Missense,Plant Proteins,Plant Proteins: chemistry,Plant Proteins: genetics,Plant Proteins: metabolism,Point Mutation,Protein Structure, Tertiary,Sequence Homology, Amino Acid,Structure-Activity Relationship,Tobacco,Tobacco: genetics,Tobacco: physiology},
month = jan,
number = {6},
pages = {1383--97},
pmid = {18390848},
title = {{Structure-function analysis of the NB-ARC domain of plant disease resistance proteins.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18390848},
volume = {59},
year = {2008}
}
@article{Chen2005,
author = {Chen, X.M.},
doi = {10.1080/07060660509507230},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Chen/Canadian Journal of Plant Pathology/Chen, 2005.pdf:pdf},
issn = {0706-0661},
journal = {Canadian Journal of Plant Pathology},
keywords = {disease control,epidemiology,formae speciales,puccinia striiformis,races,resistance,stripe rust,wheat},
month = sep,
number = {3},
pages = {314--337},
title = {{Epidemiology and control of stripe rust [ Puccinia striiformis f. sp. tritici ] on wheat}},
url = {http://www.tandfonline.com/doi/abs/10.1080/07060660509507230},
volume = {27},
year = {2005}
}
@article{Johnson1981,
author = {Johnson, Roy},
doi = {10.1094/Phyto-71-567},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Johnson/Phytopathology/Johnson, 1981.PDF:PDF},
issn = {0031949X},
journal = {Phytopathology},
number = {6},
pages = {567},
title = {{Durable Resistance: Definition of, Genetic Control, and Attainment in Plant Breeding}},
url = {http://www.apsnet.org/publications/phytopathology/backissues/Documents/1981Abstracts/Phyto71\_567.htm},
volume = {71},
year = {1981}
}
@article{RILEY1968,
author = {RILEY, RALPH and CHAPMAN, VICTOR and JOHNSON, ROY},
doi = {10.1038/217383a0},
issn = {0028-0836},
journal = {Nature},
month = jan,
number = {5126},
pages = {383--384},
shorttitle = {Nature},
title = {{Introduction of Yellow Rust Resistance of Aegilops comosa into Wheat by Genetically Induced Homoeologous Recombination}},
url = {http://dx.doi.org/10.1038/217383a0},
volume = {217},
year = {1968}
}
@article{Mayer2014,
author = {Mayer, K. F. X. and Rogers, J. and Dole el, J. and Pozniak, C. and Eversole, K. and Feuillet, C. and Gill, B. and Friebe, B. and Lukaszewski, a. J. and Sourdille, P. and Endo, T. R. and Kubalakova, M. and Ihalikova, J. and Dubska, Z. and Vrana, J. and Perkova, R. and Imkova, H. and Febrer, M. and Clissold, L. and McLay, K. and Singh, K. and Chhuneja, P. and Singh, N. K. and Khurana, J. and Akhunov, E. and Choulet, F. and Alberti, A. and Barbe, V. and Wincker, P. and Kanamori, H. and Kobayashi, F. and Itoh, T. and Matsumoto, T. and Sakai, H. and Tanaka, T. and Wu, J. and Ogihara, Y. and Handa, H. and Maclachlan, P. R. and Sharpe, A. and Klassen, D. and Edwards, D. and Batley, J. and Olsen, O.-a. and Sandve, S. R. and Lien, S. and Steuernagel, B. and Wulff, B. and Caccamo, M. and Ayling, S. and Ramirez-Gonzalez, R. H. and Clavijo, B. J. and Wright, J. and Pfeifer, M. and Spannagl, M. and Martis, M. M. and Mascher, M. and Chapman, J. and Poland, J. a. and Scholz, U. and Barry, K. and Waugh, R. and Rokhsar, D. S. and Muehlbauer, G. J. and Stein, N. and Gundlach, H. and Zytnicki, M. and Jamilloux, V. and Quesneville, H. and Wicker, T. and Faccioli, P. and Colaiacovo, M. and Stanca, a. M. and Budak, H. and Cattivelli, L. and Glover, N. and Pingault, L. and Paux, E. and Sharma, S. and Appels, R. and Bellgard, M. and Chapman, B. and Nussbaumer, T. and Bader, K. C. and Rimbert, H. and Wang, S. and Knox, R. and Kilian, A. and Alaux, M. and Alfama, F. and Couderc, L. and Guilhot, N. and Viseux, C. and Loaec, M. and Keller, B. and Praud, S.},
doi = {10.1126/science.1251788},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Mayer et al/Science/Science-2014--.pdf:pdf},
issn = {0036-8075},
journal = {Science},
month = jul,
number = {6194},
pages = {1251788--1251788},
title = {{A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1251788},
volume = {345},
year = {2014}
}
@article{Leggett2013a,
abstract = {The processes of quality assessment and control are an active area of research at The Genome Analysis Centre (TGAC). Unlike other sequencing centers that often concentrate on a certain species or technology, TGAC applies expertise in genomics and bioinformatics to a wide range of projects, often requiring bespoke wet lab and in silico workflows. TGAC is fortunate to have access to a diverse range of sequencing and analysis platforms, and we are at the forefront of investigations into library quality and sequence data assessment. We have developed and implemented a number of algorithms, tools, pipelines and packages to ascertain, store, and expose quality metrics across a number of next-generation sequencing platforms, allowing rapid and in-depth cross-platform Quality Control (QC) bioinformatics. In this review, we describe these tools as a vehicle for data-driven informatics, offering the potential to provide richer context for downstream analysis and to inform experimental design.},
author = {Leggett, Richard M and Ramirez-Gonzalez, Ricardo H and Clavijo, Bernardo J and Waite, Darren and Davey, Robert P},
doi = {10.3389/fgene.2013.00288},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Leggett et al/Frontiers in genetics/fgene-04-00288.pdf:pdf},
issn = {1664-8021},
journal = {Frontiers in genetics},
keywords = {Adult,Diagnosis,Differential,Female,Humans,Lichen Planus,Lichen Planus: pathology,Mouth Diseases,Mouth Diseases: pathology},
month = jan,
number = {5},
pages = {288},
pmid = {24381581},
title = {{Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics.}},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3865868/ http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3865868\&tool=pmcentrez\&rendertype=abstract},
volume = {4},
year = {2013}
}
@article{Ramirez-Gonzalez2013,
abstract = {High-throughput parallel sequencing is a powerful tool for the quantification of microbial diversity through the amplification of nuclear ribosomal gene regions. Recent work has extended this approach to the quantification of diversity within otherwise difficult-to-study metazoan groups. However, nuclear ribosomal genes present both analytical challenges and practical limitations that are a consequence of the mutational properties of nuclear ribosomal genes. Here we exploit useful properties of protein-coding genes for cross-species amplification and denoising of 454 flowgrams. We first use experimental mixtures of species from the class Collembola to amplify and pyrosequence the 5' region of the COI barcode, and we implement a new algorithm called PyroClean for the denoising of Roche GS FLX pyrosequences. Using parameter values from the analysis of experimental mixtures, we then analyse two communities sampled from field sites on the island of Tenerife. Cross-species amplification success of target mitochondrial sequences in experimental species mixtures is high; however, there is little relationship between template DNA concentrations and pyrosequencing read abundance. Homopolymer error correction and filtering against a consensus reference sequence reduced the volume of unique sequences to approximately 5\% of the original unique raw reads. Filtering of remaining non-target sequences attributed to PCR error, sequencing error, or numts further reduced unique sequence volume to 0.8\% of the original raw reads. PyroClean reduces or eliminates the need for an additional, time-consuming step to cluster reads into Operational Taxonomic Units, which facilitates the detection of intraspecific DNA sequence variation. PyroCleaned sequence data from field sites in Tenerife demonstrate the utility of our approach for quantifying evolutionary diversity and its spatial structure. Comparison of our sequence data to public databases reveals that we are able to successfully recover both interspecific and intraspecific sequence diversity.},
author = {Ramirez-Gonzalez, Ricardo and Yu, Douglas W and Bruce, Catharine and Heavens, Darren and Caccamo, Mario and Emerson, Brent C},
doi = {10.1371/journal.pone.0057615},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Ramirez-Gonzalez et al/PLoS ONE/journal.pone.0057615.pdf:pdf},
issn = {19326203},
journal = {PLoS ONE},
month = jan,
number = {3},
pages = {e57615},
pmid = {23469211},
title = {{PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23469211},
volume = {8},
year = {2013}
}
@misc{,
title = {{No Title}}
}
@article{Zhao2014,
abstract = {To demonstrate the benefits of RNA-Seq over microarray in transcriptome profiling, both RNA-Seq and microarray analyses were performed on RNA samples from a human T cell activation experiment. In contrast to other reports, our analyses focused on the difference, rather than similarity, between RNA-Seq and microarray technologies in transcriptome profiling. A comparison of data sets derived from RNA-Seq and Affymetrix platforms using the same set of samples showed a high correlation between gene expression profiles generated by the two platforms. However, it also demonstrated that RNA-Seq was superior in detecting low abundance transcripts, differentiating biologically critical isoforms, and allowing the identification of genetic variants. RNA-Seq also demonstrated a broader dynamic range than microarray, which allowed for the detection of more differentially expressed genes with higher fold-change. Analysis of the two datasets also showed the benefit derived from avoidance of technical issues inherent to microarray probe performance such as cross-hybridization, non-specific hybridization and limited detection range of individual probes. Because RNA-Seq does not rely on a pre-designed complement sequence detection probe, it is devoid of issues associated with probe redundancy and annotation, which simplified interpretation of the data. Despite the superior benefits of RNA-Seq, microarrays are still the more common choice of researchers when conducting transcriptional profiling experiments. This is likely because RNA-Seq sequencing technology is new to most researchers, more expensive than microarray, data storage is more challenging and analysis is more complex. We expect that once these barriers are overcome, the RNA-Seq platform will become the predominant tool for transcriptome analysis.},
author = {Zhao, Shanrong and Fung-Leung, Wai-Ping and Bittner, Anton and Ngo, Karen and Liu, Xuejun},
doi = {10.1371/journal.pone.0078644},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Zhao et al/PloS one/journal.pone.0078644.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
month = jan,
number = {1},
pages = {e78644},
pmid = {24454679},
title = {{Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3894192\&tool=pmcentrez\&rendertype=abstract},
volume = {9},
year = {2014}
}
@article{Galushko2014,
author = {Galushko, V. and Gray, R.},
doi = {10.1093/scipol/scu004},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Galushko, Gray/Science and Public Policy/scipol.scu004.full.pdf:pdf},
issn = {0302-3427},
journal = {Science and Public Policy},
keywords = {crop research and breeding,privatization,wheat innovation},
month = mar,
pages = {1--15},
title = {{Twenty five years of private wheat breeding in the UK: Lessons for other countries}},
url = {http://spp.oxfordjournals.org/cgi/doi/10.1093/scipol/scu004},
year = {2014}
}
@article{Shao2013,
abstract = {454 sequencing technology is a promising approach for characterizing HIV-1 populations and for identifying low frequency mutations. The utility of 454 technology for determining allele frequencies and linkage associations in HIV infected individuals has not been extensively investigated. We evaluated the performance of 454 sequencing for characterizing HIV populations with defined allele frequencies.},
author = {Shao, Wei and Boltz, Valerie F and Spindler, Jonathan E and Kearney, Mary F and Maldarelli, Frank and Mellors, John W and Stewart, Claudia and Volfovsky, Natalia and Levitsky, Alexander and Stephens, Robert M and Coffin, John M},
doi = {10.1186/1742-4690-10-18},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Shao et al/Retrovirology/834ee8108f8ec638803edc8204b5c8b1414d30c9.pdf:pdf},
issn = {1742-4690},
journal = {Retrovirology},
keywords = {454 pyrosequencing,correspondence,error rate,gov,hiv-1,mail,nih,pcr induced recombination,shaow},
month = jan,
number = {1},
pages = {18},
pmid = {23402264},
publisher = {Retrovirology},
title = {{Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3599717\&tool=pmcentrez\&rendertype=abstract},
volume = {10},
year = {2013}
}
@article{Jia2013,
author = {Jia, Jizeng and Zhao, Shancen and Kong, Xiuying and Li, Yingrui and Zhao, Guangyao and He, Weiming and Appels, Rudi and Pfeifer, Matthias and Tao, Yong and Zhang, Xueyong and Jing, Ruilian and Zhang, Chi and Ma, Youzhi and Gao, Lifeng and Gao, Chuan and Spannagl, Manuel and Mayer, Klaus F. X. and Li, Dong and Pan, Shengkai and Zheng, Fengya and Hu, Qun and Xia, Xianchun and Li, Jianwen and Liang, Qinsi and Chen, Jie and Wicker, Thomas and Gou, Caiyun and Kuang, Hanhui and He, Genyun and Luo, Yadan and Keller, Beat and Xia, Qiuju and Lu, Peng and Wang, Junyi and Zou, Hongfeng and Zhang, Rongzhi and Xu, Junyang and Gao, Jinlong and Middleton, Christopher and Quan, Zhiwu and Liu, Guangming and Wang, Jian and Yang, Huanming and Liu, Xu and He, Zhonghu and Mao, Long and Wang, Jun},
doi = {10.1038/nature12028},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Jia et al/Nature/2013-Nature-Draft sequencing of wheat D genome.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
month = mar,
pages = {1--5},
publisher = {Nature Publishing Group},
title = {{Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation}},
url = {http://www.nature.com/doifinder/10.1038/nature12028},
year = {2013}
}
@article{Hastie2013,
abstract = {Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far. Using two-color genome mapping of tiling bacterial artificial chromosomes (BAC) clones on nanochannel arrays, we completed high-confidence assembly of a 2.1-Mb, highly repetitive region in the large and complex genome of Aegilops tauschii, the D-genome donor of hexaploid wheat (Triticum aestivum). Genome mapping is based on direct visualization of sequence motifs on single DNA molecules hundreds of kilobases in length. With the genome map as a scaffold, we anchored unplaced sequence contigs, validated the initial draft assembly, and resolved instances of misassembly, some involving contigs <2 kb long, to dramatically improve the assembly from 75\% to 95\% complete.},
author = {Hastie, Alex R and Dong, Lingli and Smith, Alexis and Finklestein, Jeff and Lam, Ernest T and Huo, Naxin and Cao, Han and Kwok, Pui-Yan and Deal, Karin R and Dvorak, Jan and Luo, Ming-Cheng and Gu, Yong and Xiao, Ming},
doi = {10.1371/journal.pone.0055864},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Hastie et al/PloS one/Hastie et al. - 2013 - Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the comp.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Artificial,Bacterial,Chromosome Mapping,Chromosomes,DNA,Genes,Genome,High-Throughput Nucleotide Sequencing,Molecular Sequence Data,Nanotechnology,Nanotechnology: instrumentation,Plant,Plant: genetics,Sequence Analysis,Triticum,Triticum: genetics},
month = jan,
number = {2},
pages = {e55864},
pmid = {23405223},
title = {{Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3566107\&tool=pmcentrez\&rendertype=abstract},
volume = {8},
year = {2013}
}
@article{Katoh2013,
abstract = {We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.},
author = {Katoh, Kazutaka and Standley, Daron M},
doi = {10.1093/molbev/mst010},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Katoh, Standley/Molecular biology and evolution/Mol Biol Evol-2013-Katoh-772-80.pdf:pdf},
issn = {1537-1719},
journal = {Molecular biology and evolution},
keywords = {Algorithms,Amino Acid Sequence,Base Sequence,DNA, Fungal,DNA, Fungal: genetics,DNA, Ribosomal,DNA, Ribosomal Spacer,DNA, Ribosomal Spacer: genetics,DNA, Ribosomal: genetics,Fungi,Fungi: genetics,Humans,Models, Genetic,Molecular Sequence Data,Phylogeny,Protein Structure, Tertiary,Quality Improvement,RNA, Bacterial,RNA, Bacterial: genetics,Ribonucleases,Ribonucleases: chemistry,Ribonucleases: genetics,Ribosome Subunits, Small, Bacterial,Ribosome Subunits, Small, Bacterial: genetics,Sequence Alignment,Sequence Alignment: methods,Software},
month = apr,
number = {4},
pages = {772--80},
pmid = {23329690},
title = {{MAFFT multiple sequence alignment software version 7: improvements in performance and usability.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3603318\&tool=pmcentrez\&rendertype=abstract},
volume = {30},
year = {2013}
}
@article{Wilkinson2012,
abstract = {BACKGROUND: Food security is an issue that has come under renewed scrutiny amidst concerns that substantial yield increases in cereal crops are required to feed the world's booming population. Wheat is of fundamental importance in this regard being one of the three most important crops for both human consumption and livestock feed; however, increase in crop yields have not kept pace with the demands of a growing world population. In order to address this issue, plant breeders require new molecular tools to help them identify genes for important agronomic traits that can be introduced into elite varieties. Studies of the genome using next-generation sequencing enable the identification of molecular markers such as single nucleotide polymorphisms that may be used by breeders to identify and follow genes when breeding new varieties. The development and application of next-generation sequencing technologies has made the characterisation of SNP markers in wheat relatively cheap and straightforward. There is a growing need for the widespread dissemination of this information to plant breeders.

DESCRIPTION: CerealsDB is an online resource containing a range of genomic datasets for wheat (Triticum aestivum) that will assist plant breeders and scientists to select the most appropriate markers for marker assisted selection. CerealsDB includes a database which currently contains in excess of 100,000 putative varietal SNPs, of which several thousand have been experimentally validated. In addition, CerealsDB contains databases for DArT markers and EST sequences, and links to a draft genome sequence for the wheat variety Chinese Spring.

CONCLUSION: CerealsDB is an open access website that is rapidly becoming an invaluable resource within the wheat research and plant breeding communities.},
author = {Wilkinson, Paul a and Winfield, Mark O and Barker, Gary L a and Allen, Alexandra M and Burridge, Amanda and Coghill, Jane a and Edwards, Keith J},
doi = {10.1186/1471-2105-13-219},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Wilkinson et al/BMC bioinformatics/1471-2105-13-219.pdf:pdf},
issn = {1471-2105},
journal = {BMC bioinformatics},
keywords = {Breeding,Databases, Nucleic Acid,Expressed Sequence Tags,Genomics,Humans,Internet,Polymorphism, Single Nucleotide,Software,Triticum,Triticum: genetics,User-Computer Interface},
month = jan,
number = {1},
pages = {219},
pmid = {22943283},
publisher = {BMC Bioinformatics},
title = {{CerealsDB 2.0: an integrated resource for plant breeders and scientists.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3447715\&tool=pmcentrez\&rendertype=abstract},
volume = {13},
year = {2012}
}
@article{Fisher2012,
abstract = {The past two decades have seen an increasing number of virulent infectious diseases in natural populations and managed landscapes. In both animals and plants, an unprecedented number of fungal and fungal-like diseases have recently caused some of the most severe die-offs and extinctions ever witnessed in wild species, and are jeopardizing food security. Human activity is intensifying fungal disease dispersal by modifying natural environments and thus creating new opportunities for evolution. We argue that nascent fungal infections will cause increasing attrition of biodiversity, with wider implications for human and ecosystem health, unless steps are taken to tighten biosecurity worldwide.},
author = {Fisher, Matthew C and Henk, Daniel A and Briggs, Cheryl J and Brownstein, John S and Madoff, Lawrence C and McCraw, Sarah L and Gurr, Sarah J},
doi = {10.1038/nature10947},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Fisher et al/Nature/nihms514851.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Animals,Biological,Communicable Diseases,Ecosystem,Emerging,Emerging: epidemiology,Emerging: microbiology,Emerging: veterinary,Extinction,Food Supply,Fungi,Fungi: classification,Fungi: genetics,Fungi: isolation \& purification,Fungi: pathogenicity,Humans,Mycoses,Mycoses: epidemiology,Mycoses: microbiology,Mycoses: veterinary,Plants,Plants: microbiology,Virulence,Virulence: genetics},
month = apr,
number = {7393},
pages = {186--94},
pmid = {22498624},
title = {{Emerging fungal threats to animal, plant and ecosystem health.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3821985\&tool=pmcentrez\&rendertype=abstract},
volume = {484},
year = {2012}
}
@article{Kersey2012,
abstract = {Ensembl Genomes (http://www.Ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.},
author = {Kersey, Paul J and Staines, Daniel M and Lawson, Daniel and Kulesha, Eugene and Derwent, Paul and Humphrey, Jay C and Hughes, Daniel S T and Keenan, Stephan and Kerhornou, Arnaud and Koscielny, Gautier and Langridge, Nicholas and McDowall, Mark D and Megy, Karine and Maheswari, Uma and Nuhn, Michael and Paulini, Michael and Pedro, Helder and Toneva, Iliana and Wilson, Derek and Yates, Andrew and Birney, Ewan},
doi = {10.1093/nar/gkr895},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Kersey et al/Nucleic acids research/Nucl. Acids Res.-2012-Kersey-D91-7.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Animals,Databases, Genetic,Genome,Genome, Bacterial,Genome, Fungal,Genome, Plant,Genomics,Invertebrates,Invertebrates: genetics,Molecular Sequence Annotation,Systems Integration},
month = jan,
number = {Database issue},
pages = {D91--7},
pmid = {22067447},
title = {{Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3245118\&tool=pmcentrez\&rendertype=abstract},
volume = {40},
year = {2012}
}
@article{Liu2012,
abstract = {The explosive growth of next-generation sequencing datasets poses a challenge to the mapping of reads to reference genomes in terms of alignment quality and execution speed. With the continuing progress of high-throughput sequencing technologies, read length is constantly increasing and many existing aligners are becoming inefficient as generated reads grow larger.},
author = {Liu, Yongchao and Schmidt, Bertil},
doi = {10.1093/bioinformatics/bts414},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Liu, Schmidt/Bioinformatics (Oxford, England)/Liu, Schmidt - 2012 - Long read alignment based on maximal exact match seeds.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
month = sep,
number = {18},
pages = {i318--i324},
pmid = {22962447},
title = {{Long read alignment based on maximal exact match seeds.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3436841\&tool=pmcentrez\&rendertype=abstract},
volume = {28},
year = {2012}
}
@article{Resendis-Antonio2011,
abstract = {BACKGROUND: Bacterial nitrogen fixation is the biological process by which atmospheric nitrogen is uptaken by bacteroids located in plant root nodules and converted into ammonium through the enzymatic activity of nitrogenase. In practice, this biological process serves as a natural form of fertilization and its optimization has significant implications in sustainable agricultural programs. Currently, the advent of high-throughput technology supplies with valuable data that contribute to understanding the metabolic activity during bacterial nitrogen fixation. This undertaking is not trivial, and the development of computational methods useful in accomplishing an integrative, descriptive and predictive framework is a crucial issue to decoding the principles that regulated the metabolic activity of this biological process.

RESULTS: In this work we present a systems biology description of the metabolic activity in bacterial nitrogen fixation. This was accomplished by an integrative analysis involving high-throughput data and constraint-based modeling to characterize the metabolic activity in Rhizobium etli bacteroids located at the root nodules of Phaseolus vulgaris (bean plant). Proteome and transcriptome technologies led us to identify 415 proteins and 689 up-regulated genes that orchestrate this biological process. Taking into account these data, we: 1) extended the metabolic reconstruction reported for R. etli; 2) simulated the metabolic activity during symbiotic nitrogen fixation; and 3) evaluated the in silico results in terms of bacteria phenotype. Notably, constraint-based modeling simulated nitrogen fixation activity in such a way that 76.83\% of the enzymes and 69.48\% of the genes were experimentally justified. Finally, to further assess the predictive scope of the computational model, gene deletion analysis was carried out on nine metabolic enzymes. Our model concluded that an altered metabolic activity on these enzymes induced different effects in nitrogen fixation, all of these in qualitative agreement with observations made in R. etli and other Rhizobiaceas.

CONCLUSIONS: In this work we present a genome scale study of the metabolic activity in bacterial nitrogen fixation. This approach leads us to construct a computational model that serves as a guide for 1) integrating high-throughput data, 2) describing and predicting metabolic activity, and 3) designing experiments to explore the genotype-phenotype relationship in bacterial nitrogen fixation.},
author = {Resendis-Antonio, Osbaldo and Hern\'{a}ndez, Magdalena and Salazar, Emmanuel and Contreras, Sandra and Batallar, Gabriel Mart\'{\i}nez and Mora, Yolanda and Encarnaci\'{o}n, Sergio},
doi = {10.1186/1752-0509-5-120},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Resendis-Antonio et al/BMC systems biology/1752-0509-5-120.pdf:pdf},
issn = {1752-0509},
journal = {BMC systems biology},
keywords = {Gene Expression Regulation, Bacterial,Gene Expression Regulation, Bacterial: genetics,Gene Expression Regulation, Bacterial: physiology,Mass Spectrometry,Metabolic Networks and Pathways,Metabolic Networks and Pathways: genetics,Metabolic Networks and Pathways: physiology,Microarray Analysis,Models, Biological,Nitrogen Fixation,Nitrogen Fixation: genetics,Nitrogen Fixation: physiology,Phaseolus,Phaseolus: microbiology,Proteomics,Proteomics: methods,Rhizobium etli,Rhizobium etli: genetics,Rhizobium etli: metabolism,Rhizobium etli: physiology,Root Nodules, Plant,Root Nodules, Plant: microbiology,Systems Biology,Systems Biology: methods},
month = jan,
number = {1},
pages = {120},
pmid = {21801415},
publisher = {BioMed Central Ltd},
title = {{Systems biology of bacterial nitrogen fixation: high-throughput technology and its integrative description with constraint-based modeling.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3164627\&tool=pmcentrez\&rendertype=abstract},
volume = {5},
year = {2011}
}
@article{Cock2010,
abstract = {FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger standard, the Solexa/Illumina variants and conversion between them, based on publicly available information such as the MAQ documentation and conventions recently agreed by the Open Bioinformatics Foundation projects Biopython, BioPerl, BioRuby, BioJava and EMBOSS. Being an open access publication, it is hoped that this description, with the example files provided as Supplementary Data, will serve in future as a reference for this important file format.},
author = {Cock, Peter J a and Fields, Christopher J and Goto, Naohisa and Heuer, Michael L and Rice, Peter M},
doi = {10.1093/nar/gkp1137},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Cock et al/Nucleic acids research/dcd52b04af11a3976ff9c3ec5ae5744a00996a63.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Computational Biology,Computational Biology: history,History, 20th Century,History, 21st Century,Sequence Analysis, DNA,Sequence Analysis, DNA: history,Sequence Analysis, DNA: standards,Software},
month = apr,
number = {6},
pages = {1767--71},
pmid = {20015970},
title = {{The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2847217\&tool=pmcentrez\&rendertype=abstract},
volume = {38},
year = {2010}
}
@article{Gene2010,
author = {Gene, Resistance and Bread, I N and Line, Wheat and Ji, W Q and Hu, Y G and Baloch, G M and Zhong, H and Wang, C Y},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Gene et al/Unknown/Ali2010.pdf:pdf},
number = {1},
pages = {383--390},
title = {{MOLECULAR IMPLICATIONS FROM SSR MARKERS FOR STRIPE RUST ( PUCCINIA STRIIFORMIS F . SP . TRITICI )}},
volume = {42},
year = {2010}
}
@article{Mayer2009,
abstract = {Chromosome 1H (approximately 622 Mb) of barley (Hordeum vulgare) was isolated by flow sorting and shotgun sequenced by GSFLX pyrosequencing to 1.3-fold coverage. Fluorescence in situ hybridization and stringent sequence comparison against genetically mapped barley genes revealed 95\% purity of the sorted chromosome 1H fraction. Sequence comparison against the reference genomes of rice (Oryza sativa) and sorghum (Sorghum bicolor) and against wheat (Triticum aestivum) and barley expressed sequence tag datasets led to the estimation of 4,600 to 5,800 genes on chromosome 1H, and 38,000 to 48,000 genes in the whole barley genome. Conserved gene content between chromosome 1H and known syntenic regions of rice chromosomes 5 and 10, and of sorghum chromosomes 1 and 9 was detected on a per gene resolution. Informed by the syntenic relationships between the two reference genomes, genic barley sequence reads were integrated and ordered to deduce a virtual gene map of barley chromosome 1H. We demonstrate that synteny-based analysis of low-pass shotgun sequenced flow-sorted Triticeae chromosomes can deliver linearly ordered high-resolution gene inventories of individual chromosomes, which complement extensive Triticeae expressed sequence tag datasets. Thus, integration of genomic, transcriptomic, and synteny-derived information represents a major step toward developing reference sequences of chromosomes and complete genomes of the most important plant tribe for mankind.},
author = {Mayer, Klaus F X and Taudien, Stefan and Martis, Mihaela and Simkov\'{a}, Hana and Such\'{a}nkov\'{a}, Pavla and Gundlach, Heidrun and Wicker, Thomas and Petzold, Andreas and Felder, Marius and Steuernagel, Burkhard and Scholz, Uwe and Graner, Andreas and Platzer, Matthias and Dolezel, Jaroslav and Stein, Nils},
doi = {10.1104/pp.109.142612},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Mayer et al/Plant physiology/538c375266ccc66be2005b9038dde9743c43d7a6.pdf:pdf},
issn = {0032-0889},
journal = {Plant physiology},
keywords = {Base Sequence,Chromosome Mapping,Chromosomes, Plant,Chromosomes, Plant: genetics,Conserved Sequence,Databases, Nucleic Acid,Expressed Sequence Tags,Flow Cytometry,Gene Order,Gene Order: genetics,Genetic Engineering,Genetic Markers,Genome, Plant,Genome, Plant: genetics,Hordeum,Hordeum: genetics,Oryza sativa,Oryza sativa: genetics,Repetitive Sequences, Nucleic Acid,Repetitive Sequences, Nucleic Acid: genetics,Sequence Analysis, DNA,Sorghum,Sorghum: genetics,Synteny,Synteny: genetics},
month = oct,
number = {2},
pages = {496--505},
pmid = {19692534},
title = {{Gene content and virtual gene order of barley chromosome 1H.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2754631\&tool=pmcentrez\&rendertype=abstract},
volume = {151},
year = {2009}
}
@article{Cock2009,
abstract = {SUMMARY: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. AVAILABILITY: Biopython is freely available, with documentation and source code at (www.biopython.org) under the Biopython license.},
author = {Cock, Peter J A and Antao, Tiago and Chang, Jeffrey T and Chapman, Brad A and Cox, Cymon J and Dalke, Andrew and Friedberg, Iddo and Hamelryck, Thomas and Kauff, Frank and Wilczynski, Bartek and de Hoon, Michiel J L},
doi = {10.1093/bioinformatics/btp163},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Cock et al/Bioinformatics (Oxford, England)/Cock et al. - 2009 - Biopython freely available Python tools for computational molecular biology and bioinformatics.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
keywords = {Computational Biology,Computational Biology: methods,Databases, Factual,Internet,Programming Languages,Software},
month = jun,
number = {11},
pages = {1422--3},
pmid = {19304878},
title = {{Biopython: freely available Python tools for computational molecular biology and bioinformatics.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2682512\&tool=pmcentrez\&rendertype=abstract},
volume = {25},
year = {2009}
}
@article{Chao2008,
author = {Chao, Shiaoman and Zhang, Wenjun and Akhunov, Eduard and Sherman, Jamie and Ma, Yaqin and Luo, Ming-Cheng and Dubcovsky, Jorge},
doi = {10.1007/s11032-008-9210-6},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Chao et al/Molecular Breeding/chao2009.pdf:pdf},
issn = {1380-3743},
journal = {Molecular Breeding},
month = jul,
number = {1},
pages = {23--33},
title = {{Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars}},
url = {http://link.springer.com/10.1007/s11032-008-9210-6},
volume = {23},
year = {2008}
}
@article{Wangkumhang2007,
abstract = {BACKGROUND: Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results. RESULTS: This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end) base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG) draw that allow users to select SNPs and graphically visualize designed primers and their conditions. CONCLUSION: WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number), this tool facilitates the awkward process of getting flanking sequences and other related information from public SNP databases. It takes into account the underlying destabilizing effect to ensure the effectiveness of designed primers. With user-friendly SVG interface, WASP intuitively presents resulting designed primers, which assist users to export or to make further adjustment to the design. This software can be freely accessed at http://bioinfo.biotec.or.th/WASP.},
author = {Wangkumhang, Pongsakorn and Chaichoompu, Kridsadakorn and Ngamphiw, Chumpol and Ruangrit, Uttapong and Chanprasert, Juntima and Assawamakin, Anunchai and Tongsima, Sissades},
doi = {10.1186/1471-2164-8-275},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Wangkumhang et al/BMC genomics/a9e9cbfd58b968ba41947c034cbbdd54b3fe4474.pdf:pdf},
issn = {1471-2164},
journal = {BMC genomics},
keywords = {Alleles,Computer Graphics,Internet,Mutation,Polymerase Chain Reaction,Polymerase Chain Reaction: methods,Polymorphism,Single Nucleotide,User-Computer Interface},
month = jan,
pages = {275},
pmid = {17697334},
title = {{WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1976135\&tool=pmcentrez\&rendertype=abstract},
volume = {8},
year = {2007}
}
@article{Slater2005,
abstract = {BACKGROUND: Exhaustive methods of sequence alignment are accurate but slow, whereas heuristic approaches run quickly, but their complexity makes them more difficult to implement. We introduce bounded sparse dynamic programming (BSDP) to allow rapid approximation to exhaustive alignment. This is used within a framework whereby the alignment algorithms are described in terms of their underlying model, to allow automated development of efficient heuristic implementations which may be applied to a general set of sequence comparison problems.

RESULTS: The speed and accuracy of this approach compares favourably with existing methods. Examples of its use in the context of genome annotation are given.

CONCLUSIONS: This system allows rapid implementation of heuristics approximating to many complex alignment models, and has been incorporated into the freely available sequence alignment program, exonerate.},
author = {Slater, Guy St C and Birney, Ewan},
doi = {10.1186/1471-2105-6-31},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Slater, Birney/BMC bioinformatics/db7c5023458491a3a822c9d4fe0a4ff7b633534b.pdf:pdf},
issn = {1471-2105},
journal = {BMC bioinformatics},
keywords = {Algorithms,Artificial Intelligence,Automation,Computational Biology,Computational Biology: methods,Computer Simulation,DNA,DNA, Complementary,DNA, Complementary: metabolism,Databases, Factual,Genome,Humans,Information Storage and Retrieval,Mathematical Computing,Models, Biological,Models, Theoretical,RNA, Messenger,RNA, Messenger: metabolism,Sequence Alignment,Sequence Analysis, DNA,Software},
month = jan,
pages = {31},
pmid = {15713233},
title = {{Automated generation of heuristics for biological sequence comparison.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=553969\&tool=pmcentrez\&rendertype=abstract},
volume = {6},
year = {2005}
}
@article{Akhunov2003,
abstract = {Genes detected by wheat expressed sequence tags (ESTs) were mapped into chromosome bins delineated by breakpoints of 159 overlapping deletions. These data were used to assess the organizational and evolutionary aspects of wheat genomes. Relative gene density and recombination rate increased with the relative distance of a bin from the centromere. Single-gene loci present once in the wheat genomes were found predominantly in the proximal, low-recombination regions, while multigene loci tended to be more frequent in distal, high-recombination regions. One-quarter of all gene motifs within wheat genomes were represented by two or more duplicated loci (paralogous sets). For 40 such sets, ancestral loci and loci derived from them by duplication were identified. Loci derived by duplication were most frequently located in distal, high-recombination chromosome regions whereas ancestral loci were most frequently located proximal to them. It is suggested that recombination has played a central role in the evolution of wheat genome structure and that gradients of recombination rates along chromosome arms promote more rapid rates of genome evolution in distal, high-recombination regions than in proximal, low-recombination regions.},
author = {Akhunov, Eduard D and Goodyear, Andrew W and Geng, Shu and Qi, Li-Li and Echalier, Benjamin and Gill, Bikram S and Miftahudin and Gustafson, J Perry and Lazo, Gerard and Chao, Shiaoman and Anderson, Olin D and Linkiewicz, Anna M and Dubcovsky, Jorge and {La Rota}, Mauricio and Sorrells, Mark E and Zhang, Deshui and Nguyen, Henry T and Kalavacharla, Venugopal and Hossain, Khwaja and Kianian, Shahryar F and Peng, Junhua and Lapitan, Nora L V and Gonzalez-Hernandez, Jose L and Anderson, James a and Choi, Dong-Woog and Close, Timothy J and Dilbirligi, Muharrem and Gill, Kulvinder S and Walker-Simmons, M Kay and Steber, Camille and McGuire, Patrick E and Qualset, Calvin O and Dvorak, Jan},
doi = {10.1101/gr.808603},
issn = {1088-9051},
journal = {Genome research},
keywords = {Chromosome Mapping,Chromosome Mapping: methods,Chromosome Mapping: statistics \& numerical data,Chromosomes, Plant,Chromosomes, Plant: genetics,Evolution, Molecular,Genes, Duplicate,Genes, Duplicate: genetics,Genes, Plant,Genes, Plant: genetics,Genetic Markers,Genetic Markers: genetics,Genome, Plant,Multigene Family,Multigene Family: genetics,Oryza sativa,Oryza sativa: genetics,Recombination, Genetic,Recombination, Genetic: genetics,Sequence Homology, Nucleic Acid,Triticum,Triticum: genetics},
month = may,
number = {5},
pages = {753--63},
pmid = {12695326},
title = {{The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=430889\&tool=pmcentrez\&rendertype=abstract},
volume = {13},
year = {2003}
}
@article{Leggett2013,
author = {Leggett, Richard M. and Ramirez-Gonzalez, Ricardo H. and Verweij, Walter and Kawashima, Cintia G. and Iqbal, Zamin and Jones, Jonathan D. G. and Caccamo, Mario and MacLean, Daniel},
doi = {10.1371/journal.pone.0060058},
editor = {Hsu, Yi-Hsiang},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Leggett et al/PLoS ONE/journal.pone.0060058.pdf:pdf},
issn = {1932-6203},
journal = {PLoS ONE},
month = mar,
number = {3},
pages = {e60058},
title = {{Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs}},
url = {http://dx.plos.org/10.1371/journal.pone.0060058},
volume = {8},
year = {2013}
}
@article{Ariyadasa2014,
abstract = {Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96\% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.},
author = {Ariyadasa, Ruvini and Mascher, Martin and Nussbaumer, Thomas and Schulte, Daniela and Frenkel, Zeev and Poursarebani, Naser and Zhou, Ruonan and Steuernagel, Burkhard and Gundlach, Heidrun and Taudien, Stefan and Felder, Marius and Platzer, Matthias and Himmelbach, Axel and Schmutzer, Thomas and Hedley, Pete E and Muehlbauer, Gary J and Scholz, Uwe and Korol, Abraham and Mayer, Klaus F X and Waugh, Robbie and Langridge, Peter and Graner, Andreas and Stein, Nils},
doi = {10.1104/pp.113.228213},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Ariyadasa et al/Plant physiology/Plant Physiol.-2014-Ariyadasa-412-23.pdf:pdf},
issn = {1532-2548},
journal = {Plant physiology},
month = jan,
number = {1},
pages = {412--23},
pmid = {24243933},
title = {{A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3875818\&tool=pmcentrez\&rendertype=abstract},
volume = {164},
year = {2014}
}
@article{Avni2013,
abstract = {In wheat, monocarpic senescence is a tightly regulated process during which nitrogen (N) and micronutrients stored pre-anthesis are remobilized from vegetative tissues to the developing grains. Recently, a close connection between senescence and remobilization was shown through the map-based cloning of the GPC (grain protein content) gene in wheat. GPC-B1 encodes a NAC transcription factor associated with earlier senescence and increased grain protein, iron and zinc content, and is deleted or non-functional in most commercial wheat varieties. In the current research, we identified 'loss of function' ethyl methanesulfonate mutants for the two GPC-B1 homoeologous genes; GPC-A1 and GPC-D1, in a hexaploid wheat mutant population. The single gpc-a1 and gpc-d1 mutants, the double gpc-1 mutant and control lines were grown under field conditions at four locations and were characterized for senescence, GPC, micronutrients and yield parameters. Our results show a significant delay in senescence in both the gpc-a1 and gpc-d1 single mutants and an even stronger effect in the gpc-1 double mutant in all the environments tested in this study. The accumulation of total N in the developing grains showed a similar increase in the control and gpc-1 plants until 25 days after anthesis (DAA) but at 41 and 60 DAA the control plants had higher grain N content than the gpc-1 mutants. At maturity, GPC in all mutants was significantly lower than in control plants while grain weight was unaffected. These results demonstrate that the GPC-A1 and GPC-D1 genes have a redundant function and play a major role in the regulation of monocarpic senescence and nutrient remobilization in wheat.},
author = {Avni, Raz and Zhao, Rongrong and Pearce, Stephen and Jun, Yan and Uauy, Cristobal and Tabbita, Facundo and Fahima, Tzion and Slade, Ann and Dubcovsky, Jorge and Distelfeld, Assaf},
doi = {10.1007/s00425-013-1977-y},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Avni et al/Planta/art\%3A10.1007\%2Fs00425-013-1977-y.pdf:pdf},
issn = {1432-2048},
journal = {Planta},
keywords = {grain protein content,iron,nam,remobilization,senescence,transcription factor,zinc},
month = oct,
pmid = {24170335},
title = {{Functional characterization of GPC-1 genes in hexaploid wheat.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24170335},
year = {2013}
}
@article{Takagi2013a,
abstract = {Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole-genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions missing from the reference (gaps) cannot be identified by simple alignment. Here we report on a method called 'MutMap-Gap', which involves delineating a candidate region harboring a mutation of interest using the recently reported MutMap method, followed by de novo assembly, alignment, and identification of the mutation within genome gaps. We applied MutMap-Gap to isolate the blast resistant gene Pii from the rice cv Hitomebore using mutant lines that have lost Pii function. MutMap-Gap should prove useful for cloning genes that exhibit significant structural variations such as disease resistance genes of the nucleotide-binding site-leucine rich repeat (NBS-LRR) class.},
author = {Takagi, Hiroki and Uemura, Aiko and Yaegashi, Hiroki and Tamiru, Muluneh and Abe, Akira and Mitsuoka, Chikako and Utsushi, Hiroe and Natsume, Satoshi and Kanzaki, Hiroyuki and Matsumura, Hideo and Saitoh, Hiromasa and Yoshida, Kentaro and Cano, Liliana M and Kamoun, Sophien and Terauchi, Ryohei},
doi = {10.1111/nph.12369},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Takagi et al/The New phytologist/Mutmap rice R gene Pii.pdf:pdf},
issn = {1469-8137},
journal = {The New phytologist},
keywords = {de novo assembly,for mutant,identification of mutations responsible,mutmap,next-generation sequencing,next-generation sequencing allows the,r-gene,rice,whole-genome sequencing},
month = oct,
number = {1},
pages = {276--83},
pmid = {23790109},
title = {{MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23790109},
volume = {200},
year = {2013}
}
@article{DeSchrijver2010,
abstract = {Next-generation amplicon sequencing enables high-throughput genetic diagnostics, sequencing multiple genes in several patients together in one sequencing run. Currently, no open-source out-of-the-box software solution exists that reliably reports detected genetic variations and that can be used to improve future sequencing effectiveness by analyzing the PCR reactions.},
author = {{De Schrijver}, Joachim M and {De Leeneer}, Kim and Lefever, Steve and Sabbe, Nick and Pattyn, Filip and {Van Nieuwerburgh}, Filip and Coucke, Paul and Deforce, Dieter and Vandesompele, Jo and Bekaert, Sofie and Hellemans, Jan and {Van Criekinge}, Wim},
doi = {10.1186/1471-2105-11-269},
file = {:Users/ramirezr/Documents/Mendeley Desktop/De Schrijver et al/BMC bioinformatics/De Schrijver et al. - 2010 - Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identificat.pdf:pdf},
issn = {1471-2105},
journal = {BMC bioinformatics},
keywords = {Base Sequence,DNA,DNA: methods,Databases,Genetic,Molecular Sequence Data,Polymerase Chain Reaction,Polymerase Chain Reaction: methods,Sequence Alignment,Sequence Analysis,Software,User-Computer Interface},
month = jan,
number = {1},
pages = {269},
pmid = {20487544},
title = {{Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20487544 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2880033\&tool=pmcentrez\&rendertype=abstract},
volume = {11},
year = {2010}
}
@article{Murcia2010,
abstract = {Determining the evolutionary basis of cross-species transmission and immune evasion is key to understanding the mechanisms that control the emergence of either new viruses or novel antigenic variants with pandemic potential. The hemagglutinin glycoprotein of influenza A viruses is a critical host range determinant and a major target of neutralizing antibodies. Equine influenza virus (EIV) is a significant pathogen of the horse that causes periodical outbreaks of disease even in populations with high vaccination coverage. EIV has also jumped the species barrier and emerged as a novel respiratory pathogen in dogs, canine influenza virus. We studied the dynamics of equine influenza virus evolution in horses at the intrahost level and how this evolutionary process is affected by interhost transmission in a natural setting. To this end, we performed clonal sequencing of the hemagglutinin 1 gene derived from individual animals at different times postinfection. Our results show that despite the population consensus sequence remaining invariant, genetically distinct subpopulations persist during the course of infection and are also transmitted, with some variants likely to change antigenicity. We also detected a natural case of mixed infection in an animal infected during an outbreak of equine influenza, raising the possibility of reassortment between different strains of virus. In sum, our data suggest that transmission bottlenecks may not be as narrow as originally perceived and that the genetic diversity required to adapt to new host species may be partially present in the donor host and potentially transmitted to the recipient host.},
author = {Murcia, Pablo R and Baillie, Gregory J and Daly, Janet and Elton, Debra and Jervis, Carley and Mumford, Jennifer A and Newton, Richard and Parrish, Colin R and Hoelzer, Karin and Dougan, Gordon and Parkhill, Julian and Lennard, Nicola and Ormond, Doug and Moule, Sharon and Whitwham, Andrew and McCauley, John W and McKinley, Trevelyan J and Holmes, Edward C and Grenfell, Bryan T and Wood, James L N},
doi = {10.1128/JVI.00112-10},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Murcia et al/Journal of virology/6943.pdf:pdf},
issn = {1098-5514},
journal = {Journal of virology},
keywords = {Animals,Disease Outbreaks,Disease Outbreaks: veterinary,Dogs,Evolution,H3N8 Subtype,H3N8 Subtype: genetics,H3N8 Subtype: immunology,H3N8 Subtype: pathogenicity,Hemagglutinin Glycoproteins,Horse Diseases,Horse Diseases: epidemiology,Horse Diseases: genetics,Horse Diseases: transmission,Horse Diseases: virology,Horses,Human,Human: epidemiology,Human: genetics,Human: transmission,Human: virology,Humans,Immune Evasion,Influenza,Influenza A Virus,Influenza Virus,Influenza Virus: classification,Influenza Virus: genetics,Influenza Virus: immunology,Likelihood Functions,Molecular,Mutation,Orthomyxoviridae Infections,Orthomyxoviridae Infections: epidemiology,Orthomyxoviridae Infections: genetics,Orthomyxoviridae Infections: transmission,Orthomyxoviridae Infections: veterinary,Orthomyxoviridae Infections: virology,Phylogeny},
month = jul,
number = {14},
pages = {6943--54},
pmid = {20444896},
title = {{Intra- and interhost evolutionary dynamics of equine influenza virus.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2898244\&tool=pmcentrez\&rendertype=abstract},
volume = {84},
year = {2010}
}
@article{Stajich2002,
abstract = {The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as Ensembl, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.},
author = {Stajich, Jason E and Block, David and Boulez, Kris and Brenner, Steven E and Chervitz, Stephen A and Dagdigian, Chris and Fuellen, Georg and Gilbert, James G R and Korf, Ian and Lapp, Hilmar and Lehv\"{a}slaiho, Heikki and Matsalla, Chad and Mungall, Chris J and Osborne, Brian I and Pocock, Matthew R and Schattner, Peter and Senger, Martin and Stein, Lincoln D and Stupka, Elia and Wilkinson, Mark D and Birney, Ewan},
doi = {10.1101/gr.361602},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Stajich et al/Genome research/Stajich et al. - 2002 - The Bioperl toolkit Perl modules for the life sciences.pdf:pdf},
issn = {1088-9051},
journal = {Genome research},
keywords = {Algorithms,Animals,Biological Science Disciplines,Biological Science Disciplines: methods,Biological Science Disciplines: trends,Computational Biology,Computational Biology: methods,Computational Biology: trends,Computer Graphics,Database Management Systems,Databases, Genetic,Humans,Internet,Online Systems,Software,Software Design,Systems Integration},
month = oct,
number = {10},
pages = {1611--8},
pmid = {12368254},
title = {{The Bioperl toolkit: Perl modules for the life sciences.}},
url = {http://genome.cshlp.org/content/12/10/1611},
volume = {12},
year = {2002}
}
@article{Grama1997,
author = {Sun, G. L. and Fahima, T. and Korol, A. B. and Turpeinen, T. and Grama, A. and Ronin, Y. I. and Nevo, E.},
doi = {10.1007/s001220050604},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Sun et al/TAG Theoretical and Applied Genetics/Sun1997.pdf:pdf},
issn = {0040-5752},
journal = {TAG Theoretical and Applied Genetics},
keywords = {gene mapping,rapd,rflp,stripe rust,triticum durum,¹riticum dicoccoides},
month = sep,
number = {4},
pages = {622--628},
title = {{Identification of molecular markers linked to the Yr15 stripe rust resistance gene of wheat originated in wild emmer wheat, Triticum dicoccoides}},
url = {http://link.springer.com/10.1007/s001220050604},
volume = {95},
year = {1997}
}
@article{Krauss1966,
author = {Krauss, A.},
doi = {10.1002/jpln.19661120115},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Krauss/Zeitschrift f\"{u}r Pflanzenern\"{a}hrung, D\"{u}ngung, Bodenkunde/Hassebrauk, 1965.pdf:pdf},
issn = {03729702},
journal = {Zeitschrift f\"{u}r Pflanzenern\"{a}hrung, D\"{u}ngung, Bodenkunde},
number = {1},
pages = {53--53},
title = {{Hassebrauk, K.: Nomenklatur, geographische Verbreitung und Wirtsbereich des Gelbrostes, Puccinia striiformis West. Mitteilungen aus der Biologischen Bundesanstalt f\"{u}r Land- und Forstwirtschaft Berlin-Dahlem, Heft 116. Verlag Parey Berlin u. Hamburg 1965. }},
url = {http://doi.wiley.com/10.1002/jpln.19661120115},
volume = {112},
year = {1966}
}
@article{Ramirez-Gonzalez2013a,
author = {Ramirez-Gonzalez, Ricardo H. and Leggett, Richard M. and Waite, Darren and Thanki, Anil and Drou, Nizar and Caccamo, Mario and Davey, Robert},
doi = {10.12688/f1000research.2-248.v1},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Ramirez-Gonzalez et al/F1000Research/10.12688\_f1000research.2-248.v1\_20131115.pdf:pdf},
issn = {2046-1402},
journal = {F1000Research},
month = nov,
title = {{StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics}},
url = {http://f1000research.com/articles/2-248/v1},
year = {2013}
}
@article{Murcia2012,
abstract = {The latest human influenza pandemic highlights the ability of influenza viruses to jump species barriers and emerge in new hosts, as well as the role of pigs in generating viruses with pandemic potential. The mutational power of influenza virus, caused by intrinsically error-prone viral polymerases, has been directly linked to viral emergence, as adaptive mutations present in the reservoir host are likely to be key to the evolution of sustained transmission in new hosts. Hence, studying how mutations are generated, maintained and transmitted in and among pigs is critical to understanding how novel viruses could emerge. Here we characterized the evolution and mutational spectra of influenza virus populations within na\"{\i}ve and vaccinated pigs linked by natural transmission, by analyzing multiple viral sequences obtained at different times post-infection. We show that the genetic make-up of influenza viruses in pigs is highly dynamic: the frequency of particular mutations, including those that could potentially alter host specificity or result in vaccine escape, fluctuated markedly, including one rapid fixation event. We also show that co-infections are common and multiple viruses – even defective ones – were transmitted between pigs despite being vaccinated. Our results provide empirical evidence of the complex dynamics of influenza viral populations in pigs and provide insight on the evolutionary basis of RNA viral emergence.},
author = {Murcia, Pablo R and Hughes, Joseph and Battista, Patrizia and Lloyd, Lucy and Baillie, Gregory J and Ramirez-Gonzalez, Ricardo H and Ormond, Doug and Oliver, Karen and Elton, Debra and Mumford, Jennifer a and Caccamo, Mario and Kellam, Paul and Grenfell, Bryan T and Holmes, Edward C and Wood, James L N},
doi = {10.1371/journal.ppat.1002730},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Murcia et al/PLoS Pathogens/179de56384086d3d5b961c0878b921b686dc6a2b.pdf:pdf},
isbn = {1553-7374 (Electronic) 1553-7366 (Linking)},
issn = {15537366},
journal = {PLoS Pathogens},
keywords = {Animals,Antibodies,Aviadenovirus,Aviadenovirus: genetics,Aviadenovirus: immunology,Cloning,Evolution,Gene Expression Regulation,H1N1 Subtype,H1N1 Subtype: genetics,H1N1 Subtype: immunology,Host-Pathogen Interactions,Influenza A Virus,Influenza Vaccines,Molecular,Orthomyxoviridae Infections,Orthomyxoviridae Infections: immunology,Orthomyxoviridae Infections: virology,Swine,Swine Diseases,Swine Diseases: immunology,Swine Diseases: virology,Vaccination,Viral,Viral: immunology,Virus Shedding},
month = jan,
number = {5},
pages = {e1002730},
pmid = {22693449},
title = {{Evolution of an Eurasian avian-like influenza virus in na\"{\i}ve and vaccinated pigs}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3364949\&tool=pmcentrez\&rendertype=abstract},
volume = {8},
year = {2012}
}
@article{Bonnal2012,
abstract = {SUMMARY: Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. AVAILABILITY: Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html CONTACT: bonnal@ingm.org.},
author = {Bonnal, Raoul J P and Aerts, Jan and Githinji, George and Goto, Naohisa and Maclean, Dan and Miller, Chase a and Mishima, Hiroyuki and Pagani, Massimiliano and Ramirez-gonzalez, Ricardo and Smant, Geert and Strozzi, Francesco and Syme, Rob and Vos, Rutger and Wennblom, Trevor J and Woodcroft, Ben J and Katayama, Toshiaki and Prins, Pjotr},
doi = {10.1093/bioinformatics/bts080},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Bonnal et al/Bioinformatics/4524ef9e3ba6e6aa6ff6681358d484fd747200d1.pdf:pdf},
isbn = {1367-4811 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
keywords = {Computational Biology,Computational Biology: methods,Internet,Programming Languages,Software},
month = apr,
number = {7},
pages = {1035--1037},
pmid = {22332238},
title = {{Biogem: An effective tool-based approach for scaling up open source software development in bioinformatics}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3315718\&tool=pmcentrez\&rendertype=abstract},
volume = {28},
year = {2012}
}
@article{Groenen2012a,
abstract = {For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.},
author = {Groenen, Martien a M and Archibald, Alan L and Uenishi, Hirohide and Tuggle, Christopher K and Takeuchi, Yasuhiro and Rothschild, Max F and Rogel-Gaillard, Claire and Park, Chankyu and Milan, Denis and Megens, Hendrik-Jan and Li, Shengting and Larkin, Denis M and Kim, Heebal and Frantz, Laurent a F and Caccamo, Mario and Ahn, Hyeonju and Aken, Bronwen L and Anselmo, Anna and Anthon, Christian and Auvil, Loretta and Badaoui, Bouabid and Beattie, Craig W and Bendixen, Christian and Berman, Daniel and Blecha, Frank and Blomberg, Jonas and Bolund, Lars and Bosse, Mirte and Botti, Sara and Bujie, Zhan and Bystrom, Megan and Capitanu, Boris and Carvalho-Silva, Denise and Chardon, Patrick and Chen, Celine and Cheng, Ryan and Choi, Sang-Haeng and Chow, William and Clark, Richard C and Clee, Christopher and Crooijmans, Richard P M a and Dawson, Harry D and Dehais, Patrice and {De Sapio}, Fioravante and Dibbits, Bert and Drou, Nizar and Du, Zhi-Qiang and Eversole, Kellye and Fadista, Jo\~{a}o and Fairley, Susan and Faraut, Thomas and Faulkner, Geoffrey J and Fowler, Katie E and Fredholm, Merete and Fritz, Eric and Gilbert, James G R and Giuffra, Elisabetta and Gorodkin, Jan and Griffin, Darren K and Harrow, Jennifer L and Hayward, Alexander and Howe, Kerstin and Hu, Zhi-Liang and Humphray, Sean J and Hunt, Toby and Hornsh\o j, Henrik and Jeon, Jin-Tae and Jern, Patric and Jones, Matthew and Jurka, Jerzy and Kanamori, Hiroyuki and Kapetanovic, Ronan and Kim, Jaebum and Kim, Jae-Hwan and Kim, Kyu-Won and Kim, Tae-Hun and Larson, Greger and Lee, Kyooyeol and Lee, Kyung-Tai and Leggett, Richard and Lewin, Harris a and Li, Yingrui and Liu, Wansheng and Loveland, Jane E and Lu, Yao and Lunney, Joan K and Ma, Jian and Madsen, Ole and Mann, Katherine and Matthews, Lucy and McLaren, Stuart and Morozumi, Takeya and Murtaugh, Michael P and Narayan, Jitendra and Nguyen, Dinh Truong and Ni, Peixiang and Oh, Song-Jung and Onteru, Suneel and Panitz, Frank and Park, Eung-Woo and Park, Hong-Seog and Pascal, Geraldine and Paudel, Yogesh and Perez-Enciso, Miguel and Ramirez-Gonzalez, Ricardo and Reecy, James M and Rodriguez-Zas, Sandra and Rohrer, Gary a and Rund, Lauretta and Sang, Yongming and Schachtschneider, Kyle and Schraiber, Joshua G and Schwartz, John and Scobie, Linda and Scott, Carol and Searle, Stephen and Servin, Bertrand and Southey, Bruce R and Sperber, Goran and Stadler, Peter and Sweedler, Jonathan V and Tafer, Hakim and Thomsen, Bo and Wali, Rashmi and Wang, Jian and Wang, Jun and White, Simon and Xu, Xun and Yerle, Martine and Zhang, Guojie and Zhang, Jianguo and Zhang, Jie and Zhao, Shuhong and Rogers, Jane and Churcher, Carol and Schook, Lawrence B},
doi = {10.1038/nature11622},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Groenen et al/Nature/Groenen et al. - 2012 - Analyses of pig genomes provide insight into porcine demography and evolution.pdf:pdf;:Users/ramirezr/Documents/Mendeley Desktop/Groenen et al/Nature/NIHMS51611-supplement-1\_Supplementary\_Information.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Animal,Animals,Demography,Genome,Genome: genetics,Models,Molecular Sequence Data,Phylogeny,Population Dynamics,Sus scrofa,Sus scrofa: classification,Sus scrofa: genetics},
month = nov,
number = {7424},
pages = {393--8},
pmid = {23151582},
title = {{Analyses of pig genomes provide insight into porcine demography and evolution.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3566564\&tool=pmcentrez\&rendertype=abstract},
volume = {491},
year = {2012}
}
@article{Uddin2014,
author = {Uddin, Mohammed and Tammimies, Kristiina and Pellecchia, Giovanna and Alipanahi, Babak and Hu, Pingzhao and Wang, Zhuozhi and Pinto, Dalila and Lau, Lynette and Nalpathamkalam, Thomas and Marshall, Christian R and Blencowe, Benjamin J and Frey, Brendan J and Merico, Daniele and Yuen, Ryan K C and Scherer, Stephen W},
doi = {10.1038/ng.2980},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Uddin et al/Nature Genetics/Unknown - Unknown - No Title.pdf:pdf},
issn = {1061-4036},
journal = {Nature Genetics},
month = may,
title = {{Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder}},
url = {http://www.nature.com/doifinder/10.1038/ng.2980},
year = {2014}
}
@article{Kuchaiev2011,
abstract = {High-throughput methods for detecting molecular interactions have produced large sets of biological network data with much more yet to come. Analogous to sequence alignment, efficient and reliable network alignment methods are expected to improve our understanding of biological systems. Unlike sequence alignment, network alignment is computationally intractable. Hence, devising efficient network alignment heuristics is currently a foremost challenge in computational biology.},
author = {Kuchaiev, Oleksii and Przulj, Natasa},
doi = {10.1093/bioinformatics/btr127},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Kuchaiev, Przulj/Bioinformatics (Oxford, England)/Kuchaiev, Przulj - 2011 - Integrative network alignment reveals large regions of global network similarity in yeast and human.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
month = may,
number = {10},
pages = {1390--6},
pmid = {21414992},
title = {{Integrative network alignment reveals large regions of global network similarity in yeast and human.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21608112},
volume = {27},
year = {2011}
}
@article{International2010,
abstract = {Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.},
author = {International, The and Initiative, Brachypodium},
doi = {10.1038/nature08747},
file = {:Users/ramirezr/Documents/Mendeley Desktop/International, Initiative/Nature/898697084c90c356be25f0f31d47b7498f08a4e8.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Chromosomes, Plant,Chromosomes, Plant: genetics,Crops, Agricultural,Crops, Agricultural: genetics,DNA Transposable Elements,DNA Transposable Elements: genetics,Evolution, Molecular,Gene Fusion,Gene Fusion: genetics,Genes, Plant,Genes, Plant: genetics,Genome, Plant,Genome, Plant: genetics,Genomics,Molecular Sequence Data,Oryza sativa,Oryza sativa: genetics,Poaceae,Poaceae: classification,Poaceae: genetics,RNA, Plant,RNA, Plant: analysis,RNA, Plant: genetics,Sequence Analysis, DNA,Sorghum,Sorghum: genetics,Synteny,Synteny: genetics,Transcription, Genetic,Transcription, Genetic: genetics},
month = feb,
number = {7282},
pages = {763--8},
pmid = {20148030},
title = {{Genome sequencing and analysis of the model grass Brachypodium distachyon.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20148030},
volume = {463},
year = {2010}
}
@article{Li2009,
abstract = {The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals.},
author = {Li, Heng and Durbin, Richard},
doi = {10.1093/bioinformatics/btp324},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Li, Durbin/Bioinformatics (Oxford, England)/Li, Durbin - 2009 - Fast and accurate short read alignment with Burrows-Wheeler transform.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
keywords = {Algorithms,Genomics,Genomics: methods,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Software},
month = jul,
number = {14},
pages = {1754--60},
pmid = {19451168},
title = {{Fast and accurate short read alignment with Burrows-Wheeler transform.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2705234\&tool=pmcentrez\&rendertype=abstract},
volume = {25},
year = {2009}
}
@misc{Zhu2008a,
abstract = {There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances in genomic technology, impetus to exploit natural diversity, and development of robust statistical analysis methods make association mapping appealing and affordable to plant research programs. Association mapping identifies quantitative trait loci (QTLs) by examining the marker-trait associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. General understanding of association mapping has increased significantly since its debut in plants. We have seen a more concerted effort in assembling various association-mapping populations and initiating experiments through either candidate-gene or genome-wide approaches in different plant species. In this review, we describe the current status of association mapping in plants and outline opportunities and challenges in complex trait dissection and genomics-assisted crop improvement.},
author = {Zhu, Chengsong and Gore, Michael and Buckler, Edward S. and Yu, Jianming},
booktitle = {The Plant Genome Journal},
doi = {10.3835/plantgenome2008.02.0089},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Zhu et al/The Plant Genome Journal/Zhu et al. 2008 The Plant Genome.pdf:pdf},
isbn = {1940-3372},
issn = {1940-3372},
number = {1},
pages = {5},
pmid = {20083210373},
title = {{Status and Prospects of Association Mapping in Plants}},
volume = {1},
year = {2008}
}
@article{Hutchison2007,
abstract = {Fifteen years elapsed between the discovery of the double helix (1953) and the first DNA sequencing (1968). Modern DNA sequencing began in 1977, with development of the chemical method of Maxam and Gilbert and the dideoxy method of Sanger, Nicklen and Coulson, and with the first complete DNA sequence (phage X174), which demonstrated that sequence could give profound insights into genetic organization. Incremental improvements allowed sequencing of molecules >200 kb (human cytomegalovirus) leading to an avalanche of data that demanded computational analysis and spawned the field of bioinformatics. The US Human Genome Project spurred sequencing activity. By 1992 the first 'sequencing factory' was established, and others soon followed. The first complete cellular genome sequences, from bacteria, appeared in 1995 and other eubacterial, archaebacterial and eukaryotic genomes were soon sequenced. Competition between the public Human Genome Project and Celera Genomics produced working drafts of the human genome sequence, published in 2001, but refinement and analysis of the human genome sequence will continue for the foreseeable future. New 'massively parallel' sequencing methods are greatly increasing sequencing capacity, but further innovations are needed to achieve the 'thousand dollar genome' that many feel is prerequisite to personalized genomic medicine. These advances will also allow new approaches to a variety of problems in biology, evolution and the environment.},
author = {Hutchison, Clyde a},
doi = {10.1093/nar/gkm688},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Hutchison/Nucleic acids research/3cc09d670a96749a6cd3e5892e612112df04c6de.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Computational Biology,Computational Biology: history,Databases, Nucleic Acid,Databases, Nucleic Acid: history,Electrophoresis, Polyacrylamide Gel,Electrophoresis, Polyacrylamide Gel: history,Genomics,Genomics: history,History, 20th Century,History, 21st Century,Human Genome Project,Human Genome Project: history,Humans,Sequence Analysis, DNA,Sequence Analysis, DNA: history,Sequence Analysis, DNA: trends},
month = jan,
number = {18},
pages = {6227--37},
pmid = {17855400},
title = {{DNA sequencing: bench to bedside and beyond.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2094077\&tool=pmcentrez\&rendertype=abstract},
volume = {35},
year = {2007}
}
@article{William2006,
abstract = {Leaf (brown) and stripe (yellow) rusts, caused by Puccinia triticina and Puccinia striiformis, respectively, are fungal diseases of wheat (Triticum aestivum) that cause significant yield losses annually in many wheat-growing regions of the world. The objectives of our study were to characterize genetic loci associated with resistance to leaf and stripe rusts using molecular markers in a population derived from a cross between the rust-susceptible cultivar 'Avocet S' and the resistant cultivar 'Pavon76'. Using bulked segregant analysis and partial linkage mapping with AFLPs, SSRs and RFLPs, we identified 6 independent loci that contributed to slow rusting or adult plant resistance (APR) to the 2 rust diseases. Using marker information available from existing linkage maps, we have identified additional markers associated with resistance to these 2 diseases and established several linkage groups in the 'Avocet S' x 'Pavon76' population. The putative loci identified on chromosomes 1BL, 4BL, and 6AL influenced resistance to both stripe and leaf rust. The loci on chromosomes 3BS and 6BL had significant effects only on stripe rust, whereas another locus, characterized by AFLP markers, had minor effects on leaf rust only. Data derived from Interval mapping indicated that the loci identified explained 53\% of the total phenotypic variation (R2) for stripe rust and 57\% for leaf rust averaged across 3 sets of field data. A single chromosome recombinant line population segregating for chromosome 1B was used to map Lr46/Yr29 as a single Mendelian locus. Characterization of slow-rusting genes for leaf and stripe rust in improved wheat germplasm would enable wheat breeders to combine these additional loci with known slow-rusting loci to generate wheat cultivars with higher levels of slow-rusting resistance.},
author = {William, H M and Singh, R P and Huerta-Espino, J and Palacios, G and Suenaga, K},
doi = {10.1139/g06-052},
file = {:Users/ramirezr/Documents/Mendeley Desktop/William et al/Genome National Research Council Canada = G\'{e}nome Conseil national de recherches Canada/74b8515f364f708d30aec80fb74bc6f7e59fdf3e.pdf:pdf},
issn = {0831-2796},
journal = {Genome / National Research Council Canada = G\'{e}nome / Conseil national de recherches Canada},
keywords = {Basidiomycota,Basidiomycota: pathogenicity,Chromosome Mapping,Chromosomes,Crosses,Genes,Genetic,Genetic Markers,Lod Score,Phenotype,Plant,Plant Diseases,Plant Diseases: genetics,Plant Diseases: microbiology,Plant: genetics,Quantitative Trait Loci,Triticum,Triticum: genetics,Triticum: microbiology},
month = aug,
number = {8},
pages = {977--90},
pmid = {17036073},
title = {{Characterization of genetic loci conferring adult plant resistance to leaf rust and stripe rust in spring wheat.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17036073},
volume = {49},
year = {2006}
}
@article{Pond2005,
abstract = {The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution. AVAILABILITY: http://www.hyphy.org CONTACT: muse@stat.ncsu.edu SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org.},
author = {Pond, Sergei L Kosakovsky and Frost, Simon D W and Muse, Spencer V},
doi = {10.1093/bioinformatics/bti079},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Pond, Frost, Muse/Bioinformatics (Oxford, England)/Bioinformatics-2005-Pond-676-9.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics (Oxford, England)},
keywords = {Algorithms,Computer Simulation,Evolution, Molecular,Models, Genetic,Phylogeny,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis, Protein,Sequence Analysis, Protein: methods,Software,User-Computer Interface},
month = mar,
number = {5},
pages = {676--9},
pmid = {15509596},
title = {{HyPhy: hypothesis testing using phylogenies.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15509596},
volume = {21},
year = {2005}
}
@book{Roelfs1992,
author = {Roelfs, AP and Singh, RP and Saari, EE},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Roelfs, Singh, Saari/Unknown/Rust Deseases of Wheat.pdf:pdf},
isbn = {968612747X},
title = {{Rust Diseases of Wheat: Concepts \& Methods of Disease Management}},
url = {http://books.google.com/books?hl=en\&lr=\&id=GHOD3FOZRfAC\&oi=fnd\&pg=PR6\&dq=Rust+Diseases+of+Wheat,+Concepts+and+methods+of+disease+management\&ots=iYvii\_82Eu\&sig=GzQS4hQZnYkUULUipAi7MfKLjjY},
year = {1992}
}
@article{Gill1991,
author = {Gill, B. S. and Friebe, B. and Endo, T. R.},
doi = {10.1139/g91-128},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Gill, Friebe, Endo/Genome/64d59c3b1d352f8484ede82e974c620d27af1608.pdf:pdf},
issn = {0831-2796},
journal = {Genome},
month = oct,
number = {5},
pages = {830--839},
title = {{Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat ( Triticum aestivum )}},
url = {http://www.nrcresearchpress.com/doi/abs/10.1139/g91-128},
volume = {34},
year = {1991}
}
@article{Ramirez-Gonzalez2012,
abstract = {BACKGROUND: The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses. The SAMtools utilities are implemented in C and provide an API for programmatic access, to help make this functionality available to programmers wishing to develop in the high level Ruby language we have developed bio-samtools, a Ruby binding to the SAMtools library. RESULTS: The utility of SAMtools is encapsulated in 3 main classes, Bio::DB::Sam, representing the alignment files and providing access to the data in them, Bio::DB::Alignment, representing the individual read alignments inside the files and Bio::DB::Pileup, representing the summarised nucleotides of reads over a single point in the nucleotide sequence to which the reads are aligned. CONCLUSIONS: Bio-samtools is a flexible and easy to use interface that programmers of many levels of experience can use to access information in the popular and common SAM/BAM format.},
author = {Ramirez-Gonzalez, Ricardo H and Bonnal, Raoul and Caccamo, Mario and Maclean, Daniel},
doi = {10.1186/1751-0473-7-6},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Ramirez-Gonzalez et al/Source code for biology and medicine/5254ce7cb8357508f27c41f58275e32e36ba0687.pdf:pdf},
issn = {1751-0473},
journal = {Source code for biology and medicine},
keywords = {bam,bio,dna,high,next-generation sequencing,ruby,sam,throughput},
month = jan,
number = {1},
pages = {6},
pmid = {22640879},
title = {{Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3473260\&tool=pmcentrez\&rendertype=abstract},
volume = {7},
year = {2012}
}
@article{Earl2011,
abstract = {Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.},
author = {Earl, Dent and Bradnam, Keith and {St John}, John and Darling, Aaron and Lin, Dawei and Fass, Joseph and Yu, Hung On Ken and Buffalo, Vince and Zerbino, Daniel R and Diekhans, Mark and Nguyen, Ngan and Ariyaratne, Pramila Nuwantha and Sung, Wing-kin and Ning, Zemin and Haimel, Matthias and Simpson, Jared T and Fonseca, Nuno A and Birol, İnan\c{c} and Docking, T Roderick and Ho, Isaac Y and Rokhsar, Daniel S and Chikhi, Rayan and Lavenier, Dominique and Chapuis, Guillaume and Naquin, Delphine and Maillet, Nicolas and Schatz, Michael C and Kelley, David R and Phillippy, Adam M and Koren, Sergey and Yang, Shiaw-pyng and Wu, Wei and Chou, Wen-chi and Srivastava, Anuj and Shaw, Timothy I and Ruby, J Graham and Skewes-Cox, Peter and Betegon, Miguel and Dimon, Michelle T and Solovyev, Victor and Seledtsov, Igor and Kosarev, Petr and Vorobyev, Denis and Ramirez-Gonzalez, Ricardo and Leggett, Richard and MacLean, Dan and Xia, Fangfang and Luo, Ruibang and Li, Zhenyu and Xie, Yinlong and Liu, Binghang and Gnerre, Sante and MacCallum, Iain and Przybylski, Dariusz and Ribeiro, Filipe J and Yin, Shuangye and Sharpe, Ted and Hall, Giles and Kersey, Paul J and Durbin, Richard and Jackman, Shaun D and Chapman, Jarrod A and Huang, Xiaoqiu and DeRisi, Joseph L and Caccamo, Mario and Li, Yingrui and Jaffe, David B and Green, Richard E and Haussler, David and Korf, Ian and Paten, Benedict},
doi = {10.1101/gr.126599.111},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Earl et al/Genome research/d15069f4400a7a1e14b2ef8f8c83ad6328ae55e4.pdf:pdf},
issn = {1549-5469},
journal = {Genome research},
keywords = {DNA,DNA: methods,Genome,Genome: physiology,Genomics,Genomics: methods,Sequence Analysis},
month = dec,
number = {12},
pages = {2224--41},
pmid = {21926179},
title = {{Assemblathon 1: a competitive assessment of de novo short read assembly methods.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3227110\&tool=pmcentrez\&rendertype=abstract},
volume = {21},
year = {2011}
}
@article{Ramirez-Gonzalez2011,
abstract = {SUMMARY: Scientists now use high-throughput sequencing technologies and short-read assembly methods to create draft genome assemblies in just days. Tools and pipelines like the assembler, and the workflow management environments make it easy for a non-specialist to implement complicated pipelines to produce genome assemblies and annotations very quickly. Such accessibility results in a proliferation of assemblies and associated files, often for many organisms. These assemblies get used as a working reference by lots of different workers, from a bioinformatician doing gene prediction or a bench scientist designing primers for PCR. Here we describe Gee Fu, a database tool for genomic assembly and feature data, including next-generation sequence alignments. Gee Fu is an instance of a Ruby-On-Rails web application on a feature database that provides web and console interfaces for input, visualization of feature data via AnnoJ, access to data through a web-service interface, an API for direct data access by Ruby scripts and access to feature data stored in BAM files. Gee Fu provides a platform for storing and sharing different versions of an assembly and associated features that can be accessed and updated by bench biologists and bioinformaticians in ways that are easy and useful for each.$\backslash$n$\backslash$nAVAILABILITY: http://tinyurl.com/geefu$\backslash$n$\backslash$nCONTACT: dan.maclean@tsl.ac.uk.},
author = {Ramirez-Gonzalez, Ricardo and Caccamo, Mario and Maclean, Daniel},
doi = {10.1093/bioinformatics/btr442},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Ramirez-Gonzalez, Caccamo, MacLean/Bioinformatics/9b6d8bdd488044728efa3e9b0e8feb770cf279ae.pdf:pdf},
isbn = {1367-4811 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
keywords = {Animals,Automatic Data Processing,Base Sequence,Databases,Genetic,Genome,Genomics,Humans,Information Storage and Retrieval,Information Storage and Retrieval: methods,Internet,Microarray Analysis,Sequence Alignment,Software},
month = oct,
number = {19},
pages = {2754--2755},
pmid = {21803806},
title = {{Gee Fu: A sequence version and web-services database tool for genomic assembly, genome feature and NGS data}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21803806},
volume = {27},
year = {2011}
}
@misc{,
title = {{No Title}}
}
@article{Trick2012a,
abstract = {BACKGROUND: Next generation sequencing (NGS) technologies are providing new ways to accelerate fine-mapping and gene isolation in many species. To date, the majority of these efforts have focused on diploid organisms with readily available whole genome sequence information. In this study, as a proof of concept, we tested the use of NGS for SNP discovery in tetraploid wheat lines differing for the previously cloned grain protein content (GPC) gene GPC-B1. Bulked segregant analysis (BSA) was used to define a subset of putative SNPs within the candidate gene region, which were then used to fine-map GPC-B1.

RESULTS: We used Illumina paired end technology to sequence mRNA (RNAseq) from near isogenic lines differing across a \~{}30-cM interval including the GPC-B1 locus. After discriminating for SNPs between the two homoeologous wheat genomes and additional quality filtering, we identified inter-varietal SNPs in wheat unigenes between the parental lines. The relative frequency of these SNPs was examined by RNAseq in two bulked samples made up of homozygous recombinant lines differing for their GPC phenotype. SNPs that were enriched at least 3-fold in the corresponding pool (6.5\% of all SNPs) were further evaluated. Marker assays were designed for a subset of the enriched SNPs and mapped using DNA from individuals of each bulk. Thirty nine new SNP markers, corresponding to 67\% of the validated SNPs, mapped across a 12.2-cM interval including GPC-B1. This translated to 1 SNP marker per 0.31 cM defining the GPC-B1 gene to within 13-18 genes in syntenic cereal genomes and to a 0.4 cM interval in wheat.

CONCLUSIONS: This study exemplifies the use of RNAseq for SNP discovery in polyploid species and supports the use of BSA as an effective way to target SNPs to specific genetic intervals to fine-map genes in unsequenced genomes.},
author = {Trick, Martin and Adamski, Nikolai Maria and Mugford, Sarah G and Jiang, Cong-Cong and Febrer, Melanie and Uauy, Cristobal},
doi = {10.1186/1471-2229-12-14},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Trick et al/BMC plant biology/Trick et al. - 2012 - Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map gene.pdf:pdf},
issn = {1471-2229},
journal = {BMC plant biology},
keywords = {Chromosome Mapping,Computational Biology,DNA, Plant,DNA, Plant: genetics,Gene Library,Genome, Plant,Molecular Sequence Data,Polymorphism, Single Nucleotide,Polyploidy,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Synteny,Triticum,Triticum: genetics},
month = jan,
number = {1},
pages = {14},
pmid = {22280551},
publisher = {BioMed Central Ltd},
title = {{Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3296661\&tool=pmcentrez\&rendertype=abstract},
volume = {12},
year = {2012}
}
@article{Elliot2010,
abstract = {In many nonhuman species of vertebrates, females are attracted to red on male conspecifics. Red is also a signal of male status in many nonhuman vertebrate species, and females show a mating preference for high-status males. These red-attraction and red-status links have been found even when red is displayed on males artificially. In the present research, we document parallels between human and nonhuman females' response to male red. Specifically, in a series of 7 experiments we demonstrate that women perceive men to be more attractive and sexually desirable when seen on a red background and in red clothing, and we additionally show that status perceptions are responsible for this red effect. The influence of red appears to be specific to women's romantic attraction to men: Red did not influence men's perceptions of other men, nor did it influence women's perceptions of men's overall likability, agreeableness, or extraversion. Participants showed no awareness that the research focused on the influence of color. These findings indicate that color not only has aesthetic value but can carry meaning and impact psychological functioning in subtle, important, and provocative ways. (PsycINFO Database Record (c) 2010 APA, all rights reserved).},
author = {Elliot, Andrew J and {Niesta Kayser}, Daniela and Greitemeyer, Tobias and Lichtenfeld, Stephanie and Gramzow, Richard H and Maier, Markus a and Liu, Huijun},
doi = {10.1037/a0019689},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Elliot et al/Journal of experimental psychology. General/Elliot et al. - 2010 - Red, rank, and romance in women viewing men.pdf:pdf},
issn = {1939-2222},
journal = {Journal of experimental psychology. General},
keywords = {and although the popular,attraction,attractiveness,color,general public and,great interest to the,media,men,red,romantic preferences are of,s,s physical attraction to,status,the scientific community alike,what influences women,women},
month = aug,
number = {3},
pages = {399--417},
pmid = {20677892},
title = {{Red, rank, and romance in women viewing men.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20677892},
volume = {139},
year = {2010}
}
@article{Mortazavi2008,
abstract = {We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41-52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript prevalence and to test the linear range of transcript detection, which spanned five orders of magnitude. Although >90\% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3' untranscribed regions, as well as new candidate microRNA precursors. RNA splice events, which are not readily measured by standard gene expression microarray or serial analysis of gene expression methods, were detected directly by mapping splice-crossing sequence reads. We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices.},
author = {Mortazavi, Ali and Williams, Brian A and McCue, Kenneth and Schaeffer, Lorian and Wold, Barbara},
doi = {10.1038/nmeth.1226},
issn = {1548-7105},
journal = {Nature methods},
keywords = {3' Untranslated Regions,Algorithms,Alternative Splicing,Animals,Brain,Brain: metabolism,Chromosome Mapping,Chromosome Mapping: methods,Databases, Nucleic Acid,Exons,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Expression Profiling: statistics \& numerical,Liver,Liver: metabolism,Mice,Mice, Inbred C57BL,Muscle, Skeletal,Muscle, Skeletal: metabolism,Oligonucleotide Array Sequence Analysis,Promoter Regions, Genetic,RNA,RNA Splicing,RNA, Messenger,RNA, Messenger: genetics,RNA, Messenger: metabolism,RNA: genetics,RNASeq,Sensitivity and Specificity,Sequence Analysis, RNA,Sequence Analysis, RNA: methods,Sequence Analysis, RNA: statistics \& numerical dat,Software},
mendeley-tags = {RNASeq},
month = jul,
number = {7},
pages = {621--8},
pmid = {18516045},
publisher = {Nature Publishing Group},
shorttitle = {Nat Meth},
title = {{Mapping and quantifying mammalian transcriptomes by RNA-Seq.}},
url = {http://dx.doi.org/10.1038/nmeth.1226},
volume = {5},
year = {2008}
}
@article{,
file = {:Users/ramirezr/Documents/Mendeley Desktop/Unknown/Unknown/Wheat Growth Guide HGCA 2009.pdf:pdf},
title = {{The wheat growth guide}},
year = {2008}
}
@article{Uauy2006,
abstract = {High grain protein content (GPC) is a frequent target of wheat breeding programmes because of its positive effect on bread and pasta quality. A wild wheat allele at the Gpc-B1 locus with a significant impact on this trait was identified previously. The precise mapping of several senescence-related traits in a set of tetraploid recombinant substitution lines (RSLs) segregating for Gpc-B1 is reported here. Flag leaf chlorophyll degradation, change in peduncle colour, and spike water content were completely linked to the Gpc-B1 locus and to the differences in GPC within a 0.3 cM interval corresponding to a physical distance of only 250 kb. The effect of Gpc-B1 was also examined in different environments and genetic backgrounds using a set of tetraploid and hexaploid pairs of isogenic lines. The results were consistent with those observed in the RSLs. The high GPC allele conferred a shorter duration of grain fill due to earlier flag leaf senescence and increased GPC in all four genetic backgrounds. The effect on grain size was more variable, depending on the genotype-environment combinations. These results are consistent with a model in which the wild-type allele of Gpc-B1 accelerates senescence in flag leaves producing pleiotropic effects on nitrogen remobilization, total GPC, and grain size.},
author = {Uauy, Cristobal and Brevis, Juan Carlos and Dubcovsky, Jorge},
doi = {10.1093/jxb/erl047},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Uauy, Brevis, Dubcovsky/Journal of experimental botany/Uauy, Brevis, Dubcovsky - 2006 - The high grain protein content gene Gpc-B1 accelerates senescence and has pleiotropic effects on protei.pdf:pdf},
issn = {0022-0957},
journal = {Journal of experimental botany},
keywords = {Alleles,Cell Aging,Chlorophyll,Chlorophyll: metabolism,Genes, Plant,Genes, Plant: physiology,Physical Chromosome Mapping,Plant Proteins,Plant Proteins: genetics,Plant Proteins: metabolism,Plant Proteins: physiology,Polyploidy,Triticum,Triticum: genetics,Triticum: growth \& development,Triticum: metabolism,Water,Water: metabolism},
month = jan,
number = {11},
pages = {2785--94},
pmid = {16831844},
title = {{The high grain protein content gene Gpc-B1 accelerates senescence and has pleiotropic effects on protein content in wheat.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16831844},
volume = {57},
year = {2006}
}
@article{Uauy2006a,
abstract = {Enhancing the nutritional value of food crops is a means of improving human nutrition and health. We report here the positional cloning of Gpc-B1, a wheat quantitative trait locus associated with increased grain protein, zinc, and iron content. The ancestral wild wheat allele encodes a NAC transcription factor (NAM-B1) that accelerates senescence and increases nutrient remobilization from leaves to developing grains, whereas modern wheat varieties carry a nonfunctional NAM-B1 allele. Reduction in RNA levels of the multiple NAM homologs by RNA interference delayed senescence by more than 3 weeks and reduced wheat grain protein, zinc, and iron content by more than 30\%.},
author = {Uauy, Cristobal and Distelfeld, Assaf and Fahima, Tzion and Blechl, Ann and Dubcovsky, Jorge},
doi = {10.1126/science.1133649},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Uauy et al/Science (New York, N.Y.)/Uauy et al. - 2006 - A NAC Gene regulating senescence improves grain protein, zinc, and iron content in wheat.pdf:pdf},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Amino Acid Sequence,Base Sequence,Cloning, Molecular,Frameshift Mutation,Genes, Plant,Iron,Iron: metabolism,Molecular Sequence Data,Plant Leaves,Plant Leaves: chemistry,Plant Proteins,Plant Proteins: metabolism,Plants, Genetically Modified,Protein Structure, Tertiary,Quantitative Trait Loci,RNA Interference,RNA, Plant,RNA, Plant: genetics,RNA, Plant: metabolism,Transcription Factors,Transcription Factors: chemistry,Transcription Factors: genetics,Transcription Factors: physiology,Triticum,Triticum: chemistry,Triticum: genetics,Triticum: metabolism,Triticum: physiology,Zinc,Zinc: metabolism},
month = nov,
number = {5803},
pages = {1298--301},
pmid = {17124321},
title = {{A NAC Gene regulating senescence improves grain protein, zinc, and iron content in wheat.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17124321},
volume = {314},
year = {2006}
}
@article{Lander2001,
abstract = {The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.},
author = {Lander, E S and Linton, L M and Birren, B and Nusbaum, C and Zody, M C and Baldwin, J and Devon, K and Dewar, K and Doyle, M and FitzHugh, W and Funke, R and Gage, D and Harris, K and Heaford, a and Howland, J and Kann, L and Lehoczky, J and LeVine, R and McEwan, P and McKernan, K and Meldrim, J and Mesirov, J P and Miranda, C and Morris, W and Naylor, J and Raymond, C and Rosetti, M and Santos, R and Sheridan, a and Sougnez, C and Stange-Thomann, N and Stojanovic, N and Subramanian, a and Wyman, D and Rogers, J and Sulston, J and Ainscough, R and Beck, S and Bentley, D and Burton, J and Clee, C and Carter, N and Coulson, a and Deadman, R and Deloukas, P and Dunham, a and Dunham, I and Durbin, R and French, L and Grafham, D and Gregory, S and Hubbard, T and Humphray, S and Hunt, a and Jones, M and Lloyd, C and McMurray, a and Matthews, L and Mercer, S and Milne, S and Mullikin, J C and Mungall, a and Plumb, R and Ross, M and Shownkeen, R and Sims, S and Waterston, R H and Wilson, R K and Hillier, L W and McPherson, J D and Marra, M a and Mardis, E R and Fulton, L a and Chinwalla, a T and Pepin, K H and Gish, W R and Chissoe, S L and Wendl, M C and Delehaunty, K D and Miner, T L and Delehaunty, a and Kramer, J B and Cook, L L and Fulton, R S and Johnson, D L and Minx, P J and Clifton, S W and Hawkins, T and Branscomb, E and Predki, P and Richardson, P and Wenning, S and Slezak, T and Doggett, N and Cheng, J F and Olsen, a and Lucas, S and Elkin, C and Uberbacher, E and Frazier, M and Gibbs, R a and Muzny, D M and Scherer, S E and Bouck, J B and Sodergren, E J and Worley, K C and Rives, C M and Gorrell, J H and Metzker, M L and Naylor, S L and Kucherlapati, R S and Nelson, D L and Weinstock, G M and Sakaki, Y and Fujiyama, a and Hattori, M and Yada, T and Toyoda, a and Itoh, T and Kawagoe, C and Watanabe, H and Totoki, Y and Taylor, T and Weissenbach, J and Heilig, R and Saurin, W and Artiguenave, F and Brottier, P and Bruls, T and Pelletier, E and Robert, C and Wincker, P and Smith, D R and Doucette-Stamm, L and Rubenfield, M and Weinstock, K and Lee, H M and Dubois, J and Rosenthal, a and Platzer, M and Nyakatura, G and Taudien, S and Rump, a and Yang, H and Yu, J and Wang, J and Huang, G and Gu, J and Hood, L and Rowen, L and Madan, a and Qin, S and Davis, R W and Federspiel, N a and Abola, a P and Proctor, M J and Myers, R M and Schmutz, J and Dickson, M and Grimwood, J and Cox, D R and Olson, M V and Kaul, R and Shimizu, N and Kawasaki, K and Minoshima, S and Evans, G a and Athanasiou, M and Schultz, R and Roe, B a and Chen, F and Pan, H and Ramser, J and Lehrach, H and Reinhardt, R and McCombie, W R and de la Bastide, M and Dedhia, N and Bl\"{o}cker, H and Hornischer, K and Nordsiek, G and Agarwala, R and Aravind, L and Bailey, J a and Bateman, a and Batzoglou, S and Birney, E and Bork, P and Brown, D G and Burge, C B and Cerutti, L and Chen, H C and Church, D and Clamp, M and Copley, R R and Doerks, T and Eddy, S R and Eichler, E E and Furey, T S and Galagan, J and Gilbert, J G and Harmon, C and Hayashizaki, Y and Haussler, D and Hermjakob, H and Hokamp, K and Jang, W and Johnson, L S and Jones, T a and Kasif, S and Kaspryzk, a and Kennedy, S and Kent, W J and Kitts, P and Koonin, E V and Korf, I and Kulp, D and Lancet, D and Lowe, T M and McLysaght, a and Mikkelsen, T and Moran, J V and Mulder, N and Pollara, V J and Ponting, C P and Schuler, G and Schultz, J and Slater, G and Smit, a F and Stupka, E and Szustakowski, J and Thierry-Mieg, D and Thierry-Mieg, J and Wagner, L and Wallis, J and Wheeler, R and Williams, a and Wolf, Y I and Wolfe, K H and Yang, S P and Yeh, R F and Collins, F and Guyer, M S and Peterson, J and Felsenfeld, a and Wetterstrand, K a and Patrinos, a and Morgan, M J and de Jong, P and Catanese, J J and Osoegawa, K and Shizuya, H and Choi, S and Chen, Y J and Szustakowki, J},
doi = {10.1038/35057062},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Lander et al/Nature/ccc1cf5da8ade433c740ba0eec13538fd81e89a0.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
keywords = {Animals,Chromosome Mapping,Conserved Sequence,CpG Islands,DNA Transposable Elements,Databases, Factual,Drug Industry,Evolution, Molecular,Forecasting,GC Rich Sequence,Gene Duplication,Genes,Genetic Diseases, Inborn,Genetics, Medical,Genome, Human,Human Genome Project,Humans,Mutation,Private Sector,Proteins,Proteins: genetics,Proteome,Public Sector,RNA,RNA: genetics,Repetitive Sequences, Nucleic Acid,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Species Specificity},
month = feb,
number = {6822},
pages = {860--921},
pmid = {11237011},
title = {{Initial sequencing and analysis of the human genome.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11237011},
volume = {409},
year = {2001}
}
@article{Korber2001,
abstract = {Evolutionary modelling studies indicate less than a century has passed since the most recent common ancestor of the HIV-1 pandemic strains and, in that time frame, an extraordinarily diverse viral population has developed. HIV-1 employs a multitude of schemes to generate variants: accumulation of base substitutions, insertions and deletions, addition and loss of glycosylation sites in the envelope protein, and recombination. A comparison between HIV and influenza virus illustrates the extraordinary scale of HIV variation, and underscores the importance of exploring innovative HIV vaccine strategies. Deeper understanding of the implications of variation for both antibody and T-cell responses may help in the effort to rationally design vaccines that stimulate broad cross-reactivity. The impact of HIV-1 variation on host immune response is reviewed in this context.},
author = {Korber, B and Gaschen, B and Yusim, K and Thakallapally, R and Kesmir, C and Detours, V},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Korber et al/British medical bulletin/496ba2a6ea75e71bdbb511d5066a69e6c375942b.pdf:pdf},
issn = {0007-1420},
journal = {British medical bulletin},
keywords = {AIDS Vaccines,AIDS Vaccines: immunology,Animals,Antigenic Variation,Antigenic Variation: genetics,Cross Reactions,Cross Reactions: immunology,Drug Design,Epitope Mapping,Epitope Mapping: methods,Epitopes,Epitopes: genetics,Evolution, Molecular,Genetic Variation,Genetic Variation: genetics,Genetic Variation: immunology,HIV-1,HIV-1: genetics,HIV-1: immunology,HIV-1: pathogenicity,Haemophilus Vaccines,Haemophilus Vaccines: pharmacology,Humans,Influenza A virus,Influenza A virus: genetics,Mutation,Mutation: genetics,Phylogeny,T-Lymphocytes, Cytotoxic,T-Lymphocytes, Cytotoxic: drug effects,World Health},
month = jan,
pages = {19--42},
pmid = {11714622},
title = {{Evolutionary and immunological implications of contemporary HIV-1 variation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11714622},
volume = {58},
year = {2001}
}
@book{GriffithsAJFMillerJHSuzukiDT2000,
abstract = {True to its title, the theme of this book is genetic analysis. This theme emphasizes our belief that the best way to understand genetics is by learning how genetic inference is made. On almost every page, we recreate the landmark experiments in genetics and have the students analyze the data and draw conclusions as if they had done the research themselves. This proactive process teaches students how to think like scientists. The modes of inference and the techniques of analysis are the keys to future exploration. Similarly, quantitative analysis is central to the book because many of the new ideas in genetics, from the original conception of the gene to such modern techniques as SSLP mapping, are based on quantitative analysis. The problems at the end of each chapter provide students with the opportunity to test their understanding in quantitative analyses that effectively simulate the act of doing genetics.},
address = {New York, NY},
author = {Griffiths, Anthony and Jeffrey, Miller and David, Suzuki and Richard, Lewontin and William and Gelbart},
edition = {7th},
isbn = {0-7167-3520-2},
language = {en},
publisher = {W. H. Freeman},
title = {{An Introduction to Genetic Analysis}},
url = {http://www.ncbi.nlm.nih.gov/books/NBK21766/},
year = {2000}
}
@misc{Durbin,
author = {Durbin, James},
title = {csvsql},
url = {https://github.com/jdurbin/durbinlib/wiki/csvsql}
}
@article{Hu2013,
abstract = {Reprogramming of cellular metabolism is an emerging hallmark of neoplastic transformation. However, it is not known how the expression of metabolic genes in tumors differs from that in normal tissues, or whether different tumor types exhibit similar metabolic changes. Here we compare expression patterns of metabolic genes across 22 diverse types of human tumors. Overall, the metabolic gene expression program in tumors is similar to that in the corresponding normal tissues. Although expression changes of some metabolic pathways (e.g., upregulation of nucleotide biosynthesis and glycolysis) are frequently observed across tumors, expression changes of other pathways (e.g., oxidative phosphorylation) are very heterogeneous. Our analysis also suggests that the expression changes of some metabolic genes (e.g., isocitrate dehydrogenase and fumarate hydratase) may enhance or mimic the effects of recurrent mutations in tumors. On the level of individual biochemical reactions, many hundreds of metabolic isoenzymes show significant and tumor-specific expression changes. These isoenzymes are potential targets for anticancer therapy.},
author = {Hu, Jie and Locasale, Jason W and Bielas, Jason H and O'Sullivan, Jacintha and Sheahan, Kieran and Cantley, Lewis C and {Vander Heiden}, Matthew G and Vitkup, Dennis},
doi = {10.1038/nbt.2530},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Hu et al/Nature biotechnology/nbt.2530.pdf:pdf},
issn = {1546-1696},
journal = {Nature biotechnology},
keywords = {Cell Transformation, Neoplastic,Cell Transformation, Neoplastic: genetics,Cell Transformation, Neoplastic: metabolism,Computational Biology,Gene Expression Regulation, Neoplastic,Glycolysis,Glycolysis: genetics,Humans,Isocitrate Dehydrogenase,Isocitrate Dehydrogenase: genetics,Isocitrate Dehydrogenase: metabolism,Isoenzymes,Metabolic Networks and Pathways,Metabolic Networks and Pathways: genetics,Molecular Targeted Therapy,Mutation,Neoplasms,Neoplasms: genetics,Neoplasms: metabolism,Oligonucleotide Array Sequence Analysis,Oxidative Phosphorylation},
month = jun,
number = {6},
pages = {522--9},
pmid = {23604282},
publisher = {Nature Publishing Group},
title = {{Heterogeneity of tumor-induced gene expression changes in the human metabolic network.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3681899\&tool=pmcentrez\&rendertype=abstract},
volume = {31},
year = {2013}
}
@article{Allen2013,
abstract = {Globally, wheat is the most widely grown crop and one of the three most important crops for human and livestock feed. However, the complex nature of the wheat genome has, until recently, resulted in a lack of single nucleotide polymorphism (SNP)-based molecular markers of practical use to wheat breeders. Recently, large numbers of SNP-based wheat markers have been made available via the use of next-generation sequencing combined with a variety of genotyping platforms. However, many of these markers and platforms have difficulty distinguishing between heterozygote and homozygote individuals and are therefore of limited use to wheat breeders carrying out commercial-scale breeding programmes. To identify exome-based co-dominant SNP-based assays, which are capable of distinguishing between heterozygotes and homozygotes, we have used targeted re-sequencing of the wheat exome to generate large amounts of genomic sequences from eight varieties. Using a bioinformatics approach, these sequences have been used to identify 95 266 putative single nucleotide polymorphisms, of which 10 251 were classified as being putatively co-dominant. Validation of a subset of these putative co-dominant markers confirmed that 96\% were true polymorphisms and 65\% were co-dominant SNP assays. The new co-dominant markers described here are capable of genotypic classification of a segregating locus in polyploid wheat and can be used on a variety of genotyping platforms; as such, they represent a powerful tool for wheat breeders. These markers and related information have been made publically available on an interactive web-based database to facilitate their use on genotyping programmes worldwide.},
author = {Allen, Alexandra M and Barker, Gary L a and Wilkinson, Paul and Burridge, Amanda and Winfield, Mark and Coghill, Jane and Uauy, Cristobal and Griffiths, Simon and Jack, Peter and Berry, Simon and Werner, Peter and Melichar, James P E and McDougall, Jane and Gwilliam, Rhian and Robinson, Phil and Edwards, Keith J},
doi = {10.1111/pbi.12009},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Allen et al/Plant biotechnology journal/pbi12009.pdf:pdf},
issn = {1467-7652},
journal = {Plant biotechnology journal},
keywords = {kaspar genotyping,next-generation,nucleotide polymorphism,sequencing,single,wheat},
month = apr,
number = {3},
pages = {279--95},
pmid = {23279710},
title = {{Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.).}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23279710},
volume = {11},
year = {2013}
}
@article{Takagi2013,
abstract = {The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time-consuming and labor-intensive. Here we report the rapid identification of plant QTLs by whole-genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines and F2 populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps.},
author = {Takagi, Hiroki and Abe, Akira and Yoshida, Kentaro and Kosugi, Shunichi and Natsume, Satoshi and Mitsuoka, Chikako and Uemura, Aiko and Utsushi, Hiroe and Tamiru, Muluneh and Takuno, Shohei and Innan, Hideki and Cano, Liliana M and Kamoun, Sophien and Terauchi, Ryohei},
doi = {10.1111/tpj.12105},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Takagi et al/The Plant journal for cell and molecular biology/QTL-Seq.pdf:pdf},
issn = {1365-313X},
journal = {The Plant journal : for cell and molecular biology},
keywords = {Chromosome Mapping,DNA, Plant,DNA, Plant: genetics,Genome, Plant,Oryza sativa,Oryza sativa: genetics,Phenotype,Polymorphism, Single Nucleotide,Quantitative Trait Loci,Sequence Alignment},
month = may,
number = {1},
pages = {174--83},
pmid = {23289725},
title = {{QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23289725},
volume = {74},
year = {2013}
}
@article{Crespo2012,
abstract = {BACKGROUND: The activation of immune cells in the brain is believed to be one of the earliest events in prion disease development, where misfolded PrionSc protein deposits are thought to act as irritants leading to a series of events that culminate in neuronal cell dysfunction and death. The role of these events in prion disease though is still a matter of debate. To elucidate the mechanisms leading from abnormal protein deposition to neuronal injury, we have performed a detailed network analysis of genes differentially expressed in several mouse prion models.

RESULTS: We found a master regulatory core of genes related to immune response controlling other genes involved in prion protein replication and accumulation, and neuronal cell death. This regulatory core determines the existence of two stable states that are consistent with the transcriptome analysis comparing prion infected versus uninfected mouse brain. An in silico perturbation analysis demonstrates that core genes are individually capable of triggering the transition and that the network remains locked once the diseased state is reached.

CONCLUSIONS: We hypothesize that this locking may be the cause of the sustained immune response observed in prion disease. Our analysis supports the hypothesis that sustained brain inflammation is the main pathogenic process leading to neuronal dysfunction and loss, which, in turn, leads to clinical symptoms in prion disease.},
author = {Crespo, Isaac and Roomp, Kirsten and Jurkowski, Wiktor and Kitano, Hiroaki and del Sol, Antonio},
doi = {10.1186/1752-0509-6-132},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Crespo et al/BMC systems biology/1752-0509-6-132.pdf:pdf},
issn = {1752-0509},
journal = {BMC systems biology},
keywords = {Animals,Cell Death,Cell Death: genetics,Disease Progression,Gene Regulatory Networks,Inflammation,Inflammation: genetics,Inflammation: pathology,Mice,Neurons,Neurons: pathology,Prion Diseases,Prion Diseases: genetics,Prion Diseases: pathology,Systems Biology},
month = jan,
pages = {132},
pmid = {23068602},
title = {{Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3607922\&tool=pmcentrez\&rendertype=abstract},
volume = {6},
year = {2012}
}
@article{Feuillet2011,
abstract = {2010 marks the 10th anniversary of the completion of the first plant genome sequence (Arabidopsis thaliana). Triggered by advancements in sequencing technologies, many crop genome sequences have been produced, with eight published since 2008. To date, however, only the rice (Oryza sativa) genome sequence has been finished to a quality level similar to that of the Arabidopsis sequence. This trend to produce draft genomes could affect the ability of researchers to address biological questions of speciation and recent evolution or to link sequence variation accurately to phenotypes. Here, we review the current crop genome sequencing activities, discuss how variability in sequence quality impacts utility for different studies and provide a perspective for a paradigm shift in selecting crops for sequencing in the future.},
author = {Feuillet, Catherine and Leach, Jan E and Rogers, Jane and Schnable, Patrick S and Eversole, Kellye},
doi = {10.1016/j.tplants.2010.10.005},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Feuillet et al/Trends in plant science/Trends\_Plant\_Sci\_vol16(2)pp77-88.pdf:pdf},
issn = {1878-4372},
journal = {Trends in plant science},
keywords = {Crops, Agricultural,Crops, Agricultural: genetics,Genome, Plant,Genomics,Genomics: methods,Genomics: trends,Plants,Plants: genetics,Sequence Analysis, DNA},
month = feb,
number = {2},
pages = {77--88},
pmid = {21081278},
publisher = {Elsevier Ltd},
title = {{Crop genome sequencing: lessons and rationales.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21081278},
volume = {16},
year = {2011}
}
@article{Quince2009,
abstract = {We present an algorithm, PyroNoise, that clusters the flowgrams of 454 pyrosequencing reads using a distance measure that models sequencing noise. This infers the true sequences in a collection of amplicons. We pyrosequenced a known mixture of microbial 16S rDNA sequences extracted from a lake and found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated.},
author = {Quince, Christopher and Lanz\'{e}n, Anders and Curtis, Thomas P and Davenport, Russell J and Hall, Neil and Head, Ian M and Read, L Fiona and Sloan, William T},
doi = {10.1038/nmeth.1361},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Quince et al/Nature methods/Quince et al. - 2009 - Accurate determination of microbial diversity from 454 pyrosequencing data.pdf:pdf},
issn = {1548-7105},
journal = {Nature methods},
keywords = {Algorithms,Bacteria,Bacteria: genetics,Genetic Variation,Models, Genetic,Polymerase Chain Reaction,RNA, Bacterial,RNA, Bacterial: genetics,RNA, Ribosomal, 16S,RNA, Ribosomal, 16S: genetics,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Software},
month = sep,
number = {9},
pages = {639--41},
pmid = {19668203},
publisher = {Nature Publishing Group},
title = {{Accurate determination of microbial diversity from 454 pyrosequencing data.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19668203},
volume = {6},
year = {2009}
}

@article{Eddy2004,
author = {Eddy, Sean R},
doi = {10.1038/nbt1004-1315},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Eddy/Nature biotechnology/Eddy - 2004 - What is a hidden Markov model.pdf:pdf},
issn = {1087-0156},
journal = {Nature biotechnology},
keywords = {Algorithms,Computational Biology,Computational Biology: methods,Data Interpretation, Statistical,Markov Chains,Models, Biological,Models, Statistical,Sequence Analysis,Sequence Analysis: methods},
month = oct,
number = {10},
pages = {1315--6},
pmid = {15470472},
title = {{What is a hidden Markov model?}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2931519\&tool=pmcentrez\&rendertype=abstract},
volume = {22},
year = {2004}
}
@article{Kent2002,
abstract = {Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT's speed stems from an index of all nonoverlapping K-mers in the genome. This index fits inside the RAM of inexpensive computers, and need only be computed once for each genome assembly. BLAT has several major stages. It uses the index to find regions in the genome likely to be homologous to the query sequence. It performs an alignment between homologous regions. It stitches together these aligned regions (often exons) into larger alignments (typically genes). Finally, BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible. This paper describes how BLAT was optimized. Effects on speed and sensitivity are explored for various K-mer sizes, mismatch schemes, and number of required index matches. BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome.},
author = {Kent, W. J.},
doi = {10.1101/gr.229202},
issn = {1088-9051},
journal = {Genome Research},
month = mar,
number = {4},
pages = {656--664},
title = {{BLAT---The BLAST-Like Alignment Tool}},
url = {http://genome.cshlp.org/content/12/4/656.abstract http://www.genome.org/cgi/doi/10.1101/gr.229202},
volume = {12},
year = {2002}
}
@article{Mauricio2001,
abstract = {Gregor Mendel was either clever or lucky enough to study traits of simple inheritance in his pea plants; however, many plant characters of interest to modern geneticists are decidedly complex. Understanding the genetic basis of such complex, or quantitative, traits requires a combination of modern molecular genetic techniques and powerful statistical methods. These approaches have begun to give us insight into understanding the evolution of complex traits both in crops and in wild plants.},
author = {Mauricio, R},
doi = {10.1038/35072085},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Mauricio/Nature reviews. Genetics/e30e1d8a6bafb5584d1aeaf92ee1b64c93048cdd.pdf:pdf},
issn = {1471-0056},
journal = {Nature reviews. Genetics},
keywords = {Genome, Plant,Genotype,Gossypium,Gossypium: genetics,Lycopersicon esculentum,Lycopersicon esculentum: genetics,Models, Genetic,Plants,Plants: genetics,Polyploidy,Quantitative Trait, Heritable,Zea mays,Zea mays: genetics},
month = may,
number = {5},
pages = {370--81},
pmid = {11331903},
title = {{Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11331903},
volume = {2},
year = {2001}
}
@article{Peng2000,
author = {Peng, JH and Fahima, T and R\"{o}der, MS and Huang, QY},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Peng et al/Genetica/34ed15b5e86c87b37fddde5d61d923bebb4f0aa8.pdf:pdf},
journal = {Genetica},
keywords = {aflp,microsatellite,molecular mapping,stripe-rust resistance gene,triticum dicoccoides},
pages = {199--210},
title = {{High-density molecular map of chromosome region harboring stripe-rust resistance genes YrH52 and Yr15 derived from wild emmer wheat, Triticum dicoccoides}},
url = {http://link.springer.com/article/10.1023/A\%3A1017573726512},
year = {2000}
}
@article{Nystedt2013,
author = {Nystedt, Bj\"{o}rn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and H\"{a}llman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and K\"{a}ller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittyl\"{a}, Totte and Olson, \AA ke and Rilakovic, Nemanja and Ritland, Carol and Rossell\'{o}, Josep a. and Sena, Juliana and Svensson, Thomas and Talavera-L\'{o}pez, Carlos and Thei\ss en, G\"{u}nter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh and Bohlmann, Joerg and Bousquet, Jean and {Garcia Gil}, Rosario and Hvidsten, Torgeir R. and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Bj\"{o}rn and {Lee Thompson}, Stacey and {Van de Peer}, Yves and Andersson, Bj\"{o}rn and Nilsson, Ove and Ingvarsson, P\"{a}r K. and Lundeberg, Joakim and Jansson, Stefan},
doi = {10.1038/nature12211},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Nystedt et al/Nature/Nature 2013 Nystedt.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
month = may,
number = {Table 1},
publisher = {Nature Publishing Group},
title = {{The Norway spruce genome sequence and conifer genome evolution}},
url = {http://www.nature.com/doifinder/10.1038/nature12211},
year = {2013}
}
@article{Aguiar2012,
author = {Aguiar, Derek and Istrail, Sorin},
doi = {10.1089/cmb.2012.0084},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Aguiar, Istrail/Journal of Computational Biology/cmb.2012.0084.pdf:pdf},
issn = {1066-5277},
journal = {Journal of Computational Biology},
keywords = {algorithms,graph theory,haplotypes,next generation sequencing,sequence analysis},
month = jun,
number = {6},
pages = {577--590},
title = {{HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data}},
url = {http://online.liebertpub.com/doi/abs/10.1089/cmb.2012.0084},
volume = {19},
year = {2012}
}
@article{Chen2011,
abstract = {Some plant terpenes such as sterols and carotenes are part of primary metabolism and found essentially in all plants. However, the majority of the terpenes found in plants are classified as 'secondary' compounds, those chemicals whose synthesis has evolved in plants as a result of selection for increased fitness via better adaptation to the local ecological niche of each species. Thousands of such terpenes have been found in the plant kingdom, but each species is capable of synthesizing only a small fraction of this total. In plants, a family of terpene synthases (TPSs) is responsible for the synthesis of the various terpene molecules from two isomeric 5-carbon precursor 'building blocks', leading to 5-carbon isoprene, 10-carbon monoterpenes, 15-carbon sesquiterpenes and 20-carbon diterpenes. The bryophyte Physcomitrella patens has a single TPS gene, copalyl synthase/kaurene synthase (CPS/KS), encoding a bifunctional enzyme producing ent-kaurene, which is a precursor of gibberellins. The genome of the lycophyte Selaginella moellendorffii contains 18 TPS genes, and the genomes of some model angiosperms and gymnosperms contain 40-152 TPS genes, not all of them functional and most of the functional ones having lost activity in either the CPS- or KS-type domains. TPS genes are generally divided into seven clades, with some plant lineages having a majority of their TPS genes in one or two clades, indicating lineage-specific expansion of specific types of genes. Evolutionary plasticity is evident in the TPS family, with closely related enzymes differing in their product profiles, subcellular localization, or the in planta substrates they use.},
author = {Chen, Feng and Tholl, Dorothea and Bohlmann, J\"{o}rg and Pichersky, Eran},
doi = {10.1111/j.1365-313X.2011.04520.x},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Chen et al/The Plant journal for cell and molecular biology/j.1365-313X.2011.04520.x.pdf:pdf},
issn = {1365-313X},
journal = {The Plant journal : for cell and molecular biology},
keywords = {Alkyl and Aryl Transferases,Alkyl and Aryl Transferases: genetics,Alkyl and Aryl Transferases: metabolism,Comparative Genomic Hybridization,Evolution, Molecular,Gene Duplication,Genes, Plant,Genetic Variation,Genome, Plant,Multigene Family,Phylogeny,Plants,Plants: enzymology,Plants: genetics,Substrate Specificity,Terpenes,Terpenes: metabolism},
month = apr,
number = {1},
pages = {212--29},
pmid = {21443633},
title = {{The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21443633},
volume = {66},
year = {2011}
}
@online{LGC,
author = {LGC{\ }Genomics},
title={{KASP Genotyping}},
year = {2014},
url = {http://www.lgcgroup.com/LGCGroup/media/PDFs/Products/Genotyping/kasp-explanation-fact-sheet.pdf},
urldate = {2016-09-13}
}
@article{Allen2011,
abstract = {Food security is a global concern and substantial yield increases in cereal crops are required to feed the growing world population. Wheat is one of the three most important crops for human and livestock feed. However, the complexity of the genome coupled with a decline in genetic diversity within modern elite cultivars has hindered the application of marker-assisted selection (MAS) in breeding programmes. A crucial step in the successful application of MAS in breeding programmes is the development of cheap and easy to use molecular markers, such as single-nucleotide polymorphisms. To mine selected elite wheat germplasm for intervarietal single-nucleotide polymorphisms, we have used expressed sequence tags derived from public sequencing programmes and next-generation sequencing of normalized wheat complementary DNA libraries, in combination with a novel sequence alignment and assembly approach. Here, we describe the development and validation of a panel of 1114 single-nucleotide polymorphisms in hexaploid bread wheat using competitive allele-specific polymerase chain reaction genotyping technology. We report the genotyping results of these markers on 23 wheat varieties, selected to represent a broad cross-section of wheat germplasm including a number of elite UK varieties. Finally, we show that, using relatively simple technology, it is possible to rapidly generate a linkage map containing several hundred single-nucleotide polymorphism markers in the doubled haploid mapping population of Avalon × Cadenza.},
author = {Allen, Alexandra M and Barker, Gary L a and Berry, Simon T and Coghill, Jane a and Gwilliam, Rhian and Kirby, Susan and Robinson, Phil and Brenchley, Rachel C and D'Amore, Rosalinda and McKenzie, Neil and Waite, Darren and Hall, Anthony and Bevan, Michael and Hall, Neil and Edwards, Keith J},
doi = {10.1111/j.1467-7652.2011.00628.x},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Allen et al/Plant biotechnology journal/0fb88346e1f67f7131bade74b565293343fffcac.pdf:pdf},
issn = {1467-7652},
journal = {Plant biotechnology journal},
keywords = {Alleles,Biological Markers,Biological Markers: analysis,Chromosome Mapping,Databases, Genetic,Expressed Sequence Tags,Gene Library,Genetic Linkage,Genotype,Polymerase Chain Reaction,Polymerase Chain Reaction: methods,Polymorphism, Single Nucleotide,Polyploidy,Sequence Alignment,Triticum,Triticum: genetics},
month = dec,
number = {9},
pages = {1086--99},
pmid = {21627760},
title = {{Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.).}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21627760},
volume = {9},
year = {2011}
}
@article{Mallery2010,
author = {Mallery, D. L. and McEwan, W. a. and Bidgood, S. R. and Towers, G. J. and Johnson, C. M. and James, L. C.},
doi = {10.1073/pnas.1014074107},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Mallery et al/Proceedings of the National Academy of Sciences/Mallery et al. - 2010 - Antibodies mediate intracellular immunity through tripartite motif-containing 21 (TRIM21).pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
month = nov,
pages = {6--11},
title = {{Antibodies mediate intracellular immunity through tripartite motif-containing 21 (TRIM21)}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1014074107},
volume = {21},
year = {2010}
}
@article{Resendis-Antonio2009,
abstract = {BACKGROUND: Integrative analysis between dynamical modeling of metabolic networks and data obtained from high throughput technology represents a worthy effort toward a holistic understanding of the link among phenotype and dynamical response. Even though the theoretical foundation for modeling metabolic network has been extensively treated elsewhere, the lack of kinetic information has limited the analysis in most of the cases. To overcome this constraint, we present and illustrate a new statistical approach that has two purposes: integrate high throughput data and survey the general dynamical mechanisms emerging for a slightly perturbed metabolic network.

METHODOLOGY/PRINCIPAL FINDINGS: This paper presents a statistic framework capable to study how and how fast the metabolites participating in a perturbed metabolic network reach a steady-state. Instead of requiring accurate kinetic information, this approach uses high throughput metabolome technology to define a feasible kinetic library, which constitutes the base for identifying, statistical and dynamical properties during the relaxation. For the sake of illustration we have applied this approach to the human Red blood cell metabolism (hRBC) and its capacity to predict temporal phenomena was evaluated. Remarkable, the main dynamical properties obtained from a detailed kinetic model in hRBC were recovered by our statistical approach. Furthermore, robust properties in time scale and metabolite organization were identify and one concluded that they are a consequence of the combined performance of redundancies and variability in metabolite participation.

CONCLUSIONS/SIGNIFICANCE: In this work we present an approach that integrates high throughput metabolome data to define the dynamic behavior of a slightly perturbed metabolic network where kinetic information is lacking. Having information of metabolite concentrations at steady-state, this method has significant relevance due its potential scope to analyze others genome scale metabolic reconstructions. Thus, I expect this approach will significantly contribute to explore the relationship between dynamic and physiology in other metabolic reconstructions, particularly those whose kinetic information is practically nulls. For instances, I envisage that this approach can be useful in genomic medicine or pharmacogenomics, where the estimation of time scales and the identification of metabolite organization may be crucial to characterize and identify (dis)functional stages.},
author = {Resendis-Antonio, Osbaldo},
doi = {10.1371/journal.pone.0004967},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Resendis-Antonio/PloS one/journal.pone.0004967.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Algorithms,Cluster Analysis,Computational Biology,Computational Biology: methods,Erythrocytes,Erythrocytes: metabolism,Humans,Metabolic Networks and Pathways,Models, Biological},
month = jan,
number = {3},
pages = {e4967},
pmid = {19305506},
title = {{Filling kinetic gaps: dynamic modeling of metabolism where detailed kinetic information is lacking.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2654918\&tool=pmcentrez\&rendertype=abstract},
volume = {4},
year = {2009}
}

@article{Borrill2016,
doi = {10.1104/pp.15.01667},
url = {http://dx.doi.org/10.1104/pp.15.01667},
year  = {2016},
month = {feb},
publisher = {American Society of Plant Biologists ({ASPB})},
volume = {170},
number = {4},
pages = {2172--2186},
author = {Philippa Borrill and Ricardo Ramirez-Gonzalez and Cristobal Uauy},
title = {{expVIP}: a Customizable {RNA}-seq Data Analysis and Visualization Platform},
journal = {Plant Physiology}
}

@article{Ma2015,
doi = {10.1186/s13007-015-0082-6},
url = {http://dx.doi.org/10.1186/s13007-015-0082-6},
year  = {2015},
month = {aug},
publisher = {Springer Science $\mathplus$ Business Media},
volume = {11},
number = {1},
author = {Jian Ma and Jiri Stiller and Zhi Zheng and Ya-Xi Liu and Yuming Wei and You-Liang Zheng and Chunji Liu},
title = {A high-throughput pipeline for detecting locus-specific polymorphism in hexaploid wheat (Triticum aestivum L.)},
journal = {Plant Methods}
}

@article{Wang2016,
doi = {10.1093/bioinformatics/btw134},
url = {http://dx.doi.org/10.1093/bioinformatics/btw134},
year  = {2016},
month = {mar},
publisher = {Oxford University Press ({OUP})},
pages = {btw134},
author = {Yi Wang and Vijay K. Tiwari and Nidhi Rawat and Bikram S. Gill and Naxin Huo and Frank M. You and Devin Coleman-Derr and Yong Q. Gu},
title = {{GSP}: a web-based platform for designing genome-specific primers in polyploids},
journal = {Bioinformatics}
}

@article{Krasileva2016,
year = {\noop{3001}submitted 2016},
author = {Ksenia Krasileva and Hans Vasquez-Gross and Tyson Howell1 and Paul Bailey and Francine Paraiso and Leah Clissold and James Simmonds and  Ricardo Ramirez-Gonzalez and X Wang and Philippa Borrill and  Christine Fosker and Sarah Ayling and Andy Phillips and Cristobal Uauy and Jorge Dubcovsky},
title = {Uncovering hidden variation in young polyploid wheat genomes},
journal = {}
}

@Article{Burt2015,
author="Burt, C.
and Steed, A.
and Gosman, N.
and Lemmens, M.
and Bird, N.
and Ramirez-Gonzalez, R.
and Holdgate, S.
and Nicholson, P.",
title="Mapping a Type 1 FHB resistance on chromosome 4AS of Triticum macha and deployment in combination with two Type 2 resistances",
journal="Theoretical and Applied Genetics",
year="2015",
volume="128",
number="9",
pages="1725--1738",
abstract="Markers closely flanking a Type 1 FHB resistance have been produced and the potential of combining this with Type 2 resistances to improve control of FHB has been demonstrated.                ",
issn="1432-2242",
doi="10.1007/s00122-015-2542-9",
url="http://dx.doi.org/10.1007/s00122-015-2542-9"
}

@article{Cantu2011,
author = {Cantu, Dario AND Govindarajulu, Manjula AND Kozik, Alex AND Wang, Meinan AND Chen, Xianming AND Kojima, Kenji K. AND Jurka, Jerzy AND Michelmore, Richard W. AND Dubcovsky, Jorge},
journal = {PLoS ONE},
publisher = {Public Library of Science},
title = {Next Generation Sequencing Provides Rapid Access to the Genome of \textit{Puccinia striiformis} f. sp. \textit{tritici}, the Causal Agent of Wheat Stripe Rust},
year = {2011},
month = {08},
volume = {6},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0024230},
pages = {1-8},
abstract = {
<p>(XLSX)</p>
},
number = {8},
doi = {10.1371/journal.pone.0024230}
}

@article{King2015,
author = {King, Robert AND Bird, Nicholas AND Ramirez-Gonzalez, Ricardo AND Coghill, Jane A. AND Patil, Archana AND Hassani-Pak, Keywan AND Uauy, Cristobal AND Phillips, Andrew L.},
journal = {PLoS ONE},
publisher = {Public Library of Science},
title = {Mutation Scanning in Wheat by Exon Capture and Next-Generation Sequencing},
year = {2015},
month = {09},
volume = {10},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0137549},
pages = {1-18},
abstract = {<p>Targeted Induced Local Lesions in Genomes (TILLING) is a reverse genetics approach to identify novel sequence variation in genomes, with the aims of investigating gene function and/or developing useful alleles for breeding. Despite recent advances in wheat genomics, most current TILLING methods are low to medium in throughput, being based on PCR amplification of the target genes. We performed a pilot-scale evaluation of TILLING in wheat by next-generation sequencing through exon capture. An oligonucleotide-based enrichment array covering ~2 Mbp of wheat coding sequence was used to carry out exon capture and sequencing on three mutagenised lines of wheat containing previously-identified mutations in the <italic>TaGA20ox1</italic> homoeologous genes. After testing different mapping algorithms and settings, candidate SNPs were identified by mapping to the IWGSC wheat Chromosome Survey Sequences. Where sequence data for all three homoeologues were found in the reference, mutant calls were unambiguous; however, where the reference lacked one or two of the homoeologues, captured reads from these genes were mis-mapped to other homoeologues, resulting either in dilution of the variant allele frequency or assignment of mutations to the wrong homoeologue. Competitive PCR assays were used to validate the putative SNPs and estimate cut-off levels for SNP filtering. At least 464 high-confidence SNPs were detected across the three mutagenized lines, including the three known alleles in <italic>TaGA20ox1</italic>, indicating a mutation rate of ~35 SNPs per Mb, similar to that estimated by PCR-based TILLING. This demonstrates the feasibility of using exon capture for genome re-sequencing as a method of mutation detection in polyploid wheat, but accurate mutation calling will require an improved genomic reference with more comprehensive coverage of homoeologues.</p>},
number = {9},
doi = {10.1371/journal.pone.0137549}
}


@incollection{Wellings1998,
author = {Wellings, C.R. and McIntosh, Robert A. },
booktitle = {Proceedings 9th International Wheat Genetics Symposium},
language = {en},
publisher = {University of Saskatchewan},
address={Saskatoon, SK, Canada},
title = {Host-pathogen studies of wheat stripe rust in Australia.},
pages={336--338},
editor={Slinkard, A.E},
year = {1998}
}

@Article{Gerechter-Amitai1989,
author="Gerechter-Amitai, Z. K.
and van Silfhout, C. H.
and Grama, Adriana
and Kleitman, Frida",
title="Yr15 --- a new gene for resistance to Puccinia striiformis in Triticum dicoccoides sel. G-25",
journal="Euphytica",
year="1989",
volume="43",
number="1",
pages="187--190",
abstract="In a comparative study of reaction patterns and by analysis of segregation ratios in cross progenies, Triticum dicoccoides Koern. sel. G-25 was shown to possess a yet unknown gene for resistance to yellow rust. It is suggested to assign provisionally the symbol Yr15 to this gene.",
issn="1573-5060",
doi="10.1007/BF00037912",
url="http://dx.doi.org/10.1007/BF00037912"
}

@Article{Hodges2007,
author={Hodges, Emily
and Xuan, Zhenyu
and Balija, Vivekanand
and Kramer, Melissa
and Molla, Michael N.
and Smith, Steven W.
and Middle, Christina M.
and Rodesch, Matthew J.
and Albert, Thomas J.
and Hannon, Gregory J.
and McCombie, W. Richard},
title={Genome-wide in situ exon capture for selective resequencing},
journal={Nat Genet},
year={2007},
month={Dec},
publisher={Nature Publishing Group},
volume={39},
number={12},
pages={1522-1527},
issn={1061-4036},
doi={10.1038/ng.2007.42},
url={http://dx.doi.org/10.1038/ng.2007.42}
}

@Article{Pickrell2010,
author={Pickrell, Joseph K.
and Marioni, John C.
and Pai, Athma A.
and Degner, Jacob F.
and Engelhardt, Barbara E.
and Nkadori, Everlyne
and Veyrieras, Jean-Baptiste
and Stephens, Matthew
and Gilad, Yoav
and Pritchard, Jonathan K.},
title={Understanding mechanisms underlying human gene expression variation with RNA sequencing},
journal={Nature},
year={2010},
month={Apr},
day={01},
publisher={Macmillan Publishers Limited. All rights reserved},
volume={464},
number={7289},
pages={768-772},
issn={0028-0836},
doi={10.1038/nature08872},
url={http://dx.doi.org/10.1038/nature08872}
}

@Article{Schneeberger2009,
author={Schneeberger, Korbinian
and Ossowski, Stephan
and Lanz, Christa
and Juul, Trine
and Petersen, Annabeth Hogh
and Nielsen, Kare Lehmann
and Jorgensen, Jan-Elo
and Weigel, Detlef
and Andersen, Stig Uggerho},
title={SHOREmap: simultaneous mapping and mutation identification by deep sequencing},
journal={Nat Meth},
year={2009},
month={Aug},
publisher={Nature Publishing Group},
volume={6},
number={8},
pages={550-551},
issn={1548-7091},
doi={10.1038/nmeth0809-550},
url={http://dx.doi.org/10.1038/nmeth0809-550}
}

@online{MASWheat2013,
author={{MAS Wheat}},
year={2013},
title={MAS Wheat Transcriptome. Supplemental File 17.},
url={http://maswheat.ucdavis.edu/Transcriptome/index.htm}
}

@Article{Tang2015,
author="Tang, Haibao
and Zhang, Xingtan
and Miao, Chenyong
and Zhang, Jisen
and Ming, Ray
and Schnable, James C.
and Schnable, Patrick S.
and Lyons, Eric
and Lu, Jianguo",
title="ALLMAPS: robust scaffold ordering based on multiple maps",
journal="Genome Biology",
year="2015",
volume="16",
number="1",
pages="1--15",
abstract="The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at:                   https://github.com/tanghaibao/jcvi/wiki/ALLMAPS                                  .",
issn="1465-6906",
doi="10.1186/s13059-014-0573-1",
url="http://dx.doi.org/10.1186/s13059-014-0573-1"
}


@book{mcintosh1995,
author = {McIntosh, {R.A.} and {Wellings, C.R.} and {Park, R.F.}},
title = {{Wheat Rusts: an Atlas of Resistance Genes}},
year = {1995}, 
address={East Melbourne, Victoria, Australia}, 
publisher={CSIRO Publishing}
}



@Article{Ng2009,
author={Ng, Sarah B.
and Turner, Emily H.
and Robertson, Peggy D.
and Flygare, Steven D.
and Bigham, Abigail W.
and Lee, Choli
and Shaffer, Tristan
and Wong, Michelle
and Bhattacharjee, Arindam
and Eichler, Evan E.
and Bamshad, Michael
and Nickerson, Deborah A.
and Shendure, Jay},
title={Targeted capture and massively parallel sequencing of 12 human exomes},
journal={Nature},
year={2009},
month={Sep},
day={10},
publisher={Macmillan Publishers Limited. All rights reserved},
volume={461},
number={7261},
pages={272-276},
issn={0028-0836},
doi={10.1038/nature08250},
url={http://dx.doi.org/10.1038/nature08250}
}

@article {Winfield2012,
author = {Winfield, Mark O. and Wilkinson, Paul A. and Allen, Alexandra M. and Barker, Gary L. A. and Coghill, Jane A. and Burridge, Amanda and Hall, Anthony and Brenchley, Rachael C. and D’Amore, Rosalinda and Hall, Neil and Bevan, Michael W. and Richmond, Todd and Gerhardt, Daniel J. and Jeddeloh, Jeffrey A. and Edwards, Keith J.},
title = {Targeted re-sequencing of the allohexaploid wheat exome},
journal = {Plant Biotechnology Journal},
volume = {10},
number = {6},
publisher = {Blackwell Publishing Ltd},
issn = {1467-7652},
url = {http://dx.doi.org/10.1111/j.1467-7652.2012.00713.x},
doi = {10.1111/j.1467-7652.2012.00713.x},
pages = {733--742},
keywords = {next-generation sequencing, single-nucleotide polymorphisms, NimbleGen Array, wheat, bioinformatics, exome capture},
year = {2012},
}
@article{Henry01042014,
author = {Henry, Isabelle M. and Nagalakshmi, Ugrappa and Lieberman, Meric C. and Ngo, Kathie J. and Krasileva, Ksenia V. and Vasquez-Gross, Hans and Akhunova, Alina and Akhunov, Eduard and Dubcovsky, Jorge and Tai, Thomas H. and Comai, Luca}, 
title = {Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing},
volume = {26}, 
number = {4}, 
pages = {1382-1397}, 
year = {2014}, 
doi = {10.1105/tpc.113.121590}, 
abstract ={Chemical mutagenesis efficiently generates phenotypic variation in otherwise homogeneous genetic backgrounds, enabling functional analysis of genes. Advances in mutation detection have brought the utility of induced mutant populations on par with those produced by insertional mutagenesis, but systematic cataloguing of mutations would further increase their utility. We examined the suitability of multiplexed global exome capture and sequencing coupled with custom-developed bioinformatics tools to identify mutations in well-characterized mutant populations of rice (Oryza sativa) and wheat (Triticum aestivum). In rice, we identified ∼18,000 induced mutations from 72 independent M2 individuals. Functional evaluation indicated the recovery of potentially deleterious mutations for >2600 genes. We further observed that specific sequence and cytosine methylation patterns surrounding the targeted guanine residues strongly affect their probability to be alkylated by ethyl methanesulfonate. Application of these methods to six independent M2 lines of tetraploid wheat demonstrated that our bioinformatics pipeline is applicable to polyploids. In conclusion, we provide a method for developing large-scale induced mutation resources with relatively small investments that is applicable to resource-poor organisms. Furthermore, our results demonstrate that large libraries of sequenced mutations can be readily generated, providing enhanced opportunities to study gene function and assess the effect of sequence and chromatin context on mutations.}, 
URL = {http://www.plantcell.org/content/26/4/1382.abstract}, 
eprint = {http://www.plantcell.org/content/26/4/1382.full.pdf+html}, 
journal = {The Plant Cell} 
}

@Article{Brenchley2012,
author={Brenchley, Rachel
and Spannagl, Manuel
and Pfeifer, Matthias
and Barker, Gary L. A.
and D/'Amore, Rosalinda
and Allen, Alexandra M.
and McKenzie, Neil
and Kramer, Melissa
and Kerhornou, Arnaud
and Bolser, Dan
and Kay, Suzanne
and Waite, Darren
and Trick, Martin
and Bancroft, Ian
and Gu, Yong
and Huo, Naxin
and Luo, Ming-Cheng
and Sehgal, Sunish
and Gill, Bikram
and Kianian, Sharyar
and Anderson, Olin
and Kersey, Paul
and Dvorak, Jan
and McCombie, W. Richard
and Hall, Anthony
and Mayer, Klaus F. X.
and Edwards, Keith J.
and Bevan, Michael W.
and Hall, Neil},
title={Analysis of the bread wheat genome using whole-genome shotgun sequencing},
journal={Nature},
year={2012},
month={Nov},
day={29},
publisher={Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
volume={491},
number={7426},
pages={705-710},
issn={0028-0836},
doi={10.1038/nature11650},
url={http://dx.doi.org/10.1038/nature11650}
}

@Misc{Pozniak2016,
author =       {Pozniak, Curtis J},
title =        {{IWGSC} whole genome shotgun sequencing of Chinese Spring:  Towards a Reference Sequence of Wheat},
year =         {2016},
month =        {1},
url ={https://pag.confex.com/pag/xxiv/webprogram/Paper22378.html}
}

@Misc{Clark2016,
author={Clark, Matthew},
title={Unlocking bread wheat genomes diversity with new sequencing and assembly approaches},
year =         {2016},
month =        {1},
url = {https://pag.confex.com/pag/xxiv/webprogram/Paper20198.html}
}

@Misc{Venturini2016,
author={Venturini, L and Caimm S and Mapleson, D L and  Kaithakottil G G and Swarbreck, D},
title={Integrating multiple transcript assemblies for improved gene structure annotation with Mikado},
year =         {2016},
journal = {Genome Science}
}

@Misc{vanOoijen2002,
author={{van Ooijen}, J.W. and Voorrips, R.},
year={2002},
title={JoinMap: Version 3.0: Software for the Calculation of Genetic Linkage Maps},
address={Wageningen, the Netherlands},
publisher={Wageningen University and Research Center}
}

@article{Marcussen2014,
abstract = {The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor {\~{}}7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic.},
author = {Marcussen, Thomas and Sandve, Simen R. and Heier, Lise and Spannagl, Manuel and Pfeifer, Matthias and Jakobsen, Kjetill S. and Wulff, Brande B. H. and Steuernagel, Burkhard and Mayer, Klaus F. X. and Olsen, O.-A. and Rogers, Jane and Dole el, J. and Pozniak, Curtis and Eversole, Kellye and Feuillet, Catherine and Gill, Bikram and Friebe, Bernd and Lukaszewski, Adam J. and Sourdille, Pierre and Endo, Takashi R. and Kubalakova, M. and Ihalikova, J. and Dubska, Z. and Vrana, J. and Perkova, R. and Imkova, H. and Febrer, Melanie and Clissold, Leah and McLay, Kirsten and Singh, K. and Chhuneja, Parveen and Singh, Nagendra K. and Khurana, Jitendra and Akhunov, Eduard and Choulet, Fr{\'{e}}d{\'{e}}ric and Alberti, Adriana and Barbe, Val{\'{e}}rie and Wincker, Patrick and Kanamori, Hiroyuki and Kobayashi, Fuminori and Itoh, Takeshi and Matsumoto, Takashi and Sakai, Hiroaki and Tanaka, Tsuyoshi and Wu, Jianzhong and Ogihara, Yasunari and Handa, Hirokazu and Maclachlan, P. Ron and Sharpe, Andrew and Klassen, Darrin and Edwards, David and Batley, Jacqueline and Lien, Sigbj{\o}rn and Caccamo, Mario and Ayling, Sarah and Ramirez-Gonzalez, Ricardo H. and Clavijo, Bernardo J. and Wright, Jonathan and Martis, Mihaela M. and Mascher, Martin and Chapman, J. and Poland, Jesse A. and Scholz, Uwe and Barry, Kerrie and Waugh, Robbie and Rokhsar, Daniel S. and Muehlbauer, Gary J. and Stein, Nils and Gundlach, Heidrun and Zytnicki, Matthias and Jamilloux, V{\'{e}}ronique and Quesneville, Hadi and Wicker, Thomas and Faccioli, Primetta and Colaiacovo, Moreno and Stanca, Antonio Michele and Budak, Hikmet and Cattivelli, Luigi and Glover, Natasha and Pingault, Lise and Paux, Etienne and Sharma, Sapna and Appels, Rudi and Bellgard, Matthew and Chapman, Brett and Nussbaumer, Thomas and Bader, Kai Christian and Rimbert, H{\'{e}}l{\`{e}}ne and Wang, Shichen and Knox, Ron and Kilian, Andrzej and Alaux, Michael and Alfama, Fran{\c{c}}oise and Couderc, Lo{\"{i}}c and Guilhot, Nicolas and Viseux, Claire and Loaec, Mika{\"{e}}l and Keller, Beat and Praud, Sebastien},
doi = {10.1126/science.1250092},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Marcussen et al/Science/Ancient{\_}hybridizations{\_}among{\_}the{\_}ancestr.pdf:pdf},
isbn = {9781597452519},
issn = {0036-8075},
journal = {Science},
month = {jul},
number = {6194},
pages = {1250092--1250092},
pmid = {25035499},
title = {{Ancient hybridizations among the ancestral genomes of bread wheat}},
url = {http://www.sciencemag.org/content/345/6194/1250092$\backslash$nhttp://www.ncbi.nlm.nih.gov/pubmed/25035499$\backslash$nhttp://www.sciencemag.org/content/345/6194/1250092.abstract http://www.sciencemag.org/cgi/doi/10.1126/science.1250092},
volume = {345},
year = {2014}
}

@Article{Huang2010,
author="Huang, Xiu-Qiang
and Br{\^u}l{\'e}-Babel, Anita",
title="Development of genome-specific primers for homoeologous genes in allopolyploid species: the waxy and starch synthase II genes in allohexaploid wheat (Triticum aestivum L.) as examples",
journal="BMC Research Notes",
year="2010",
volume="3",
number="1",
pages="1--11",
abstract="In allopolypoid crops, homoeologous genes in different genomes exhibit a very high sequence similarity, especially in the coding regions of genes. This makes it difficult to design genome-specific primers to amplify individual genes from different genomes. Development of genome-specific primers for agronomically important genes in allopolypoid crops is very important and useful not only for the study of sequence diversity and association mapping of genes in natural populations, but also for the development of gene-based functional markers for marker-assisted breeding. Here we report on a useful approach for the development of genome-specific primers in allohexaploid wheat.",
issn="1756-0500",
doi="10.1186/1756-0500-3-140",
url="http://dx.doi.org/10.1186/1756-0500-3-140"
}

@Misc{Curry2016,
author={Curry, Jonathan  and  Kietzmann, Markus,  Smith, Steve and Kirby, Susan },
title={MAGIC BOX – Automated Primer Assay Design for Haploid, Diploid and Polyploid Species},
year =         {2016},
month =        {1},
url = {https://pag.confex.com/pag/xxiv/webprogram/Paper20323.html}
}

@article{Higgins1988,
abstract = {An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. Then the multiple alignment is achieved from a series of pairwise alignments of clusters of sequences, following the order of branching in the tree. The method is sufficiently fast and economical with memory to be easily implemented on a microcomputer, and yet the results obtained are comparable to those from packages requiring mainframe computer facilities. ?? 1988.},
author = {Higgins, Desmond G. and Sharp, Paul M.},
doi = {10.1016/0378-1119(88)90330-7},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Higgins, Sharp/Gene/higgins1988.pdf:pdf},
isbn = {0378-1119 (Print)$\backslash$r0378-1119 (Linking)},
issn = {03781119},
journal = {Gene},
keywords = {5S RNA,Cluster analysis,RNA secondary structure,dendrogram,globin,phylogenetic tree,protein secondary structure},
mendeley-groups = {Alignments},
month = {dec},
number = {1},
pages = {237--244},
pmid = {3243435},
title = {{CLUSTAL: a package for performing multiple sequence alignment on a microcomputer}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0378111988903307},
volume = {73},
year = {1988}
}


@article{Yachdav2016,
author = {Yachdav, Guy and Wilzbach, Sebastian and Rauscher, Benedikt and Sheridan, Robert and Sillitoe, Ian and Procter, James and Lewis, Suzanna E. and Rost, Burkhard and Goldberg, Tatyana},
doi = {10.1093/bioinformatics/btw474},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Yachdav et al/Bioinformatics/Bioinformatics-2016-Yachdav-bioinformatics{\_}btw474.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
mendeley-groups = {Phylogeny},
month = {jul},
title = {{MSAViewer: interactive JavaScript visualization of multiple sequence alignments}},
url = {http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/bioinformatics/btw474},
year = {2016}
}

@article {Winfield2016,
author = {Winfield, Mark O. and Allen, Alexandra M. and Burridge, Amanda J. and Barker, Gary L. A. and Benbow, Harriet R. and Wilkinson, Paul A. and Coghill, Jane and Waterfall, Christy and Davassi, Alessandro and Scopes, Geoff and Pirani, Ali and Webster, Teresa and Brew, Fiona and Bloor, Claire and King, Julie and West, Claire and Griffiths, Simon and King, Ian and Bentley, Alison R. and Edwards, Keith J.},
title = {High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool},
journal = {Plant Biotechnology Journal},
volume = {14},
number = {5},
issn = {1467-7652},
url = {http://dx.doi.org/10.1111/pbi.12485},
doi = {10.1111/pbi.12485},
pages = {1195--1206},
keywords = {wheat, secondary and tertiary gene pools, wheat progenitors, next-generation sequencing, genotyping array, single nucleotide polymorphism},
year = {2016},
}


@article{Pfeifer2014,
doi = {10.1126/science.1250091},
url = {http://dx.doi.org/10.1126/science.1250091},
year  = {2014},
month = {jul},
publisher = {American Association for the Advancement of Science ({AAAS})},
volume = {345},
number = {6194},
pages = {1250091--1250091},
author = {M. Pfeifer and K. G. Kugler and S. R. Sandve and B. Zhan and H. Rudi and T. R. Hvidsten and K. F. X. Mayer and O.-A. Olsen},
title = {Genome interplay in the grain transcriptome of hexaploid bread wheat},
journal = {Science}
}

@article{Bottley2006,
abstract = {The vast majority of angiosperms are (or were once) polyploid, and as hexaploid bread wheat has undergone two ploidy events separated by approximately 0.5 million years, it represents an elegant model to study gene silencing over time in polyploids. Using an SSCP platform, we have analysed patterns of transcriptional silencing (frequency, genome identity and organ specificity) within 236 single-copy genes, each mapping to one locus on one of the three homoeologous chromosomes within groups 1, 2, 3 and 7 of wheat. In about 27{\%} of unigenes expressed in leaf, and about 26{\%} of those in root, one (rarely two) members of a gene set (homoeoalleles) were not present in the cDNA template. Organ-specific regulation is commonplace, with many homoeoalleles transcribed in leaf but not root (and vice versa). There was little indication of extensive bias towards selective silencing of a particular genome copy. Expression of some of the silenced homoeoalleles was restored in certain aneuploid lines and varieties, and these displayed a significant degree of genetic variation for the silencing of a given homoeoallele. We propose that a substantial proportion of this phenomenon is effected by an epigenetic mechanism, and suggest that this form of genetic variation may be a significant player in the determination of phenotypic diversity in breeding populations.},
author = {Bottley, A. and Xia, G. M. and Koebner, R. M D},
doi = {10.1111/j.1365-313X.2006.02841.x},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Bottley, Xia, Koebner/The Plant Journal/Bottley{\_}et{\_}al-2006-The{\_}Plant{\_}Journal.pdf:pdf},
isbn = {0960-7412 (Print)},
issn = {09607412},
journal = {The Plant Journal},
keywords = {Epigenesis,Gene silencing,Polyploidy,SSCP,Wheat},
mendeley-groups = {expVIP},
month = {sep},
number = {6},
pages = {897--906},
pmid = {16899084},
title = {{Homoeologous gene silencing in hexaploid wheat}},
url = {http://doi.wiley.com/10.1111/j.1365-313X.2006.02841.x},
volume = {47},
year = {2006}
}

@article{Codd1970,
abstract = {Future users of large data banks must be protected from having to know how the data is organized in the machine (the internal representation). A prompting service which supplies such information is not a satisfactory solution. Activities of users at terminals and most application programs should remain unaffected when the internal representation of data is changed and even when some aspects of the external representation are changed. Changes in data representation will often be needed as a result of changes in query, update, and report traffic and natural growth in the types of stored information. Existing noninferential, formatted data systems provide users with tree-structured files or slightly more general network models of the data. In Section 1, inadequacies of these models are discussed. A model based on n -ary relations, a normal form for data base relations, and the concept of a universal data sublanguage are introduced. In Section 2, certain operations on relations (other than logical inference) are discussed and applied to the problems of redundancy and consistency in the user's model.},
author = {Codd, Edgar Frank},
doi = {10.1145/362384.362685},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Codd/Communications of the ACM/codd1970.pdf:pdf},
isbn = {3623843626},
issn = {00010782},
journal = {Communications of the ACM},
keywords = {and phrases,calculus,composition,consistency,data,data bank,data base,data integrity,data structure,derivability,hierarchies of data,join,networks of data,organization,predicate,redundancy,relations,retrieval language,security},
mendeley-groups = {Computing},
month = {jun},
number = {6},
pages = {377--387},
pmid = {9617087},
title = {{A relational model of data for large shared data banks}},
url = {http://portal.acm.org/citation.cfm?doid=362384.362685},
volume = {13},
year = {1970}
}

@manual{Oracle2014,
author = {Oracle},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Oracle/Unknown/refman-5.7-en.a4.pdf:pdf},
mendeley-groups = {Computing},
title = {{MySQL 5.7 Reference Manual}},
url = {http://downloads.mysql.com/docs/refman-5.7-en.a4.pdf},
year = {2014}
}

@article{Bray2016,
archivePrefix = {arXiv},
arxivId = {1505.02710},
author = {Bray, Nicolas L and Pimentel, Harold and Melsted, P{\'{a}}ll and Pachter, Lior},
doi = {10.1038/nbt.3519},
eprint = {1505.02710},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Bray et al/Nature Biotechnology/nbt.3519.pdf:pdf},
isbn = {1546-1696 (Electronic) 1087-0156 (Linking)},
issn = {1087-0156},
journal = {Nature Biotechnology},
mendeley-groups = {expVIP},
month = {apr},
number = {5},
pages = {525--527},
pmid = {27043002},
title = {{Near-optimal probabilistic RNA-seq quantification}},
url = {http://www.nature.com/doifinder/10.1038/nbt.3519},
volume = {34},
year = {2016}
}

@article{Krasner1988,
abstract = {This essay describes the Model-View-Controller (MVC) programming paradigm and methodology used in the Smalltalk-80TM programming system. MVC programming is the application of a three-way factoring, whereby objects of different classes take over the operations related to the application domain, the display of the application's state, and the user interaction with the model and the view. We present several extended examples of MVC implementations and of the layout of composite application views. The Appendices provide reference materials for the Smalltalk-80 programmer wishing to understand and use MVC better within the Smalltalk-80 system.},
author = {Krasner, Glenn E and Pope, Stephen T},
doi = {10.1.1.47.366},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Krasner, Pope/Joop Journal Of Object Oriented Programming/Krasner-JOOP88.pdf:pdf},
isbn = {0896-8438},
issn = {0896-8438},
journal = {Joop Journal Of Object Oriented Programming},
mendeley-groups = {Computing},
pages = {26--49},
title = {{A Cookbook for Using the Model- View-Controller User Interface Paradigm in Smalltalk-80}},
volume = {1},
year = {1988}
}

@online{RailsGuide2016,
author = {{Rails Guide}},
title = {Getting Started with Rails},
year = 2016,
url = {http://guides.rubyonrails.org/getting_started.html},
urldate = {2016-09-18}
}

@article{Yachdav2015,
abstract = {BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.},
author = {Yachdav, Guy and Goldberg, Tatyana and Wilzbach, Sebastian and Dao, David and Shih, Iris and Choudhary, Saket and Crouch, Steve and Franz, Max and Garc{\'{i}}a, Alexander and Garc{\'{i}}a, Leyla J. and Gr{\"{u}}ning, Bj{\"{o}}rn A. and Inupakutika, Devasena and Sillitoe, Ian and Thanki, Anil S. and Vieira, Bruno and Villaveces, Jos{\'{e}} M. and Schneider, Maria V. and Lewis, Suzanna and Pettifer, Steve and Rost, Burkhard and Corpas, Manuel},
doi = {10.7554/eLife.07009.001},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Yachdav et al/Unknown/e07009-download.pdf:pdf},
isbn = {2050084X (Electronic)},
issn = {2050084X},
journal = {eLife},
mendeley-groups = {Computing},
number = {JULY 2015},
pages = {1--7},
pmid = {26153621},
title = {{Anatomy of BioJS, an open source community for the life sciences}},
volume = {4},
year = {2015}
}

@article{Haerder1983,
abstract = {In this paper, a terminological framework is provided for describing different transaction- oriented recovery schemes for database systems in a conceptual rather than an implementation-dependent way. By introducing the terms materialized database, propagation strategy, and checkpoint, we obtain a means for classifying arbitrary implementations from a unified viewpoint. This is complemented by a classification scheme for logging techniques, which are precisely defined by using the other terms. It is shown that these criteria are related to all relevant questions such as speed and scope of recovery and amount of redundant information required. The primary purpose of this paper, however, is to establish an adequate and precise terminology for a topic in which the confusion of concepts and implementational aspects still imposes a lot of problems. [ABSTRACT FROM AUTHOR]},
author = {Haerder, Theo and Reuter, Andreas},
doi = {10.1145/289.291},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Haerder, Reuter/ACM Computing Surveys/haerder1983.pdf:pdf},
issn = {03600300},
journal = {ACM Computing Surveys},
keywords = {DATA libraries,DATABASE design,DATABASES,FAULT tolerance (Engineering),REAL-time computing,TRANSACTION systems (Computer systems)},
mendeley-groups = {Computing},
month = {dec},
number = {4},
pages = {287--317},
title = {{Principles of transaction-oriented database recovery}},
url = {http://search.ebscohost.com/login.aspx?direct=true{\&}db=bth{\&}AN=12126326{\&}site=eds-live http://portal.acm.org/citation.cfm?doid=289.291},
volume = {15},
year = {1983}
}

@book{Myatt2011,
  Author = {Glenn J. Myatt and Wayne P. Johnson},
  Title = {Making Sense of Data III: A Practical Guide to Designing Interactive Data Visualizations},
  Publisher = {Wiley},
  Year = {2011},
  ISBN = {0470536497}
}

@misc{Bostock2015,
author = {Bostock, Mike},
mendeley-groups = {expVIP},
title = {{D3: Data Driven Documents}},
url = {https://d3js.org},
year = {2015}
}

@article{Bostock2011,
  title = {D3: Data-Driven Documents},
  author = {Michael Bostock AND Vadim Ogievetsky AND Jeffrey Heer},
  journal = {IEEE Trans. Visualization \& Comp. Graphics (Proc. InfoVis)},
  year = {2011},
  url = {http://vis.stanford.edu/papers/d3}
}

@article{Oono2013,
abstract = {BACKGROUND: Phosphorus (P) is an essential macronutrient for plant growth and development. To modulate their P homeostasis, plants must balance P uptake, mobilisation, and partitioning to various organs. Despite the worldwide importance of wheat as a cultivated food crop, molecular mechanisms associated with phosphate (Pi) starvation in wheat remain unclear. To elucidate these mechanisms, we used RNA-Seq methods to generate transcriptome profiles of the wheat variety 'Chinese Spring' responding to 10 days of Pi starvation.$\backslash$n$\backslash$nRESULTS: We carried out de novo assembly on 73.8 million high-quality reads generated from RNA-Seq libraries. We then constructed a transcript dataset containing 29,617 non-redundant wheat transcripts, comprising 15,047 contigs and 14,570 non-redundant full-length cDNAs from the TriFLDB database. When compared with barley full-length cDNAs, 10,656 of the 15,047 contigs were unalignable, suggesting that many might be distinct from barley transcripts. The average expression level of the contigs was lower than that of the known cDNAs, implying that these contigs included transcripts that were rarely represented in the full-length cDNA library. Within the non-redundant transcript set, we identified 892-2,833 responsive transcripts in roots and shoots, corresponding on average to 23.4{\%} of the contigs not covered by cDNAs in TriFLDB under Pi starvation. The relative expression level of the wheat IPS1 (Induced by Phosphate Starvation 1) homologue, TaIPS1, was 341-fold higher in roots and 13-fold higher in shoots; this finding was further confirmed by qRT-PCR analysis. A comparative analysis of the wheat- and rice-responsive transcripts for orthologous genes under Pi-starvation revealed commonly upregulated transcripts, most of which appeared to be involved in a general response to Pi starvation, namely, an IPS1-mediated signalling cascade and its downstream functions such as Pi remobilisation, Pi uptake, and changes in Pi metabolism.$\backslash$n$\backslash$nCONCLUSIONS: Our transcriptome profiles demonstrated the impact of Pi starvation on global gene expression in wheat. This study revealed that enhancement of the Pi-mediated signalling cascade using IPS1 is a potent adaptation mechanism to Pi starvation that is conserved in both wheat and rice and validated the effectiveness of using short-read next-generation sequencing data for wheat transcriptome analysis in the absence of reference genome information.},
author = {Oono, Youko and Kobayashi, Fuminori and Kawahara, Yoshihiro and Yazawa, Takayuki and Handa, Hirokazu and Itoh, Takeshi and Matsumoto, Takashi},
doi = {10.1186/1471-2164-14-77},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Oono et al/Unknown/art{\%}3A10.1186{\%}2F1471-2164-14-77.pdf:pdf},
isbn = {1471-2164 (Electronic)$\backslash$r1471-2164 (Linking)},
issn = {1471-2164},
journal = {BMC genomics},
keywords = {Chromosome Mapping,Conserved Sequence,Databases, Genetic,Gene Expression Profiling,Gene Expression Regulation, Plant,Gene Expression Regulation, Plant: drug effects,Genes, Plant,Genes, Plant: genetics,MicroRNAs,MicroRNAs: genetics,MicroRNAs: metabolism,Phosphates,Phosphates: deficiency,Phosphates: pharmacology,Plant Proteins,Plant Proteins: genetics,RNA, Messenger,RNA, Messenger: genetics,RNA, Messenger: metabolism,Seedling,Seedling: drug effects,Seedling: genetics,Sequence Analysis, RNA,Signal Transduction,Signal Transduction: drug effects,Signal Transduction: genetics,Stress, Physiological,Stress, Physiological: drug effects,Stress, Physiological: genetics,Triticum,Triticum: drug effects,Triticum: genetics,Triticum: metabolism,Triticum: physiology},
mendeley-groups = {expVIP},
number = {1},
pages = {77},
pmid = {23379779},
title = {{Characterisation of the wheat (Triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3598684{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {14},
year = {2013}
}

@article{Kugler2013,
abstract = {BACKGROUND: Fusarium head blight (FHB) caused by Fusarium graminearum Schwabe is one of the most prevalent diseases of wheat (Triticum aestivum L.) and other small grain cereals. Resistance against the fungus is quantitative and more than 100 quantitative trait loci (QTL) have been described. Two well-validated and highly reproducible QTL, Fhb1 and Qfhs.ifa-5A have been widely investigated, but to date the underlying genes have not been identified.$\backslash$n$\backslash$nRESULTS: We have investigated a gene co-expression network activated in response to F. graminearum using RNA-seq data from near-isogenic lines, harboring either the resistant or the susceptible allele for Fhb1 and Qfhs.ifa-5A. The network identified pathogen-responsive modules, which were enriched for differentially expressed genes between genotypes or different time points after inoculation with the pathogen. Central gene analysis identified transcripts associated with either QTL within the network. Moreover, we present a detailed gene expression analysis of four gene families (glucanases, NBS-LRR, WRKY transcription factors and UDP-glycosyltransferases), which take prominent roles in the pathogen response.$\backslash$n$\backslash$nCONCLUSIONS: A combination of a network-driven approach and differential gene expression analysis identified genes and pathways associated with Fhb1 and Qfhs.ifa-5A. We find G-protein coupled receptor kinases and biosynthesis genes for jasmonate and ethylene earlier induced for Fhb1. Similarly, we find genes involved in the biosynthesis and metabolism of riboflavin more abundant for Qfhs.ifa-5A.},
author = {Kugler, Karl G and Siegwart, Gerald and Nussbaumer, Thomas and Ametz, Christian and Spannagl, Manuel and Steiner, Barbara and Lemmens, Marc and Mayer, Klaus FX and Buerstmayr, Hermann and Schweiger, Wolfgang},
doi = {10.1186/1471-2164-14-728},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Kugler et al/BMC Genomics/art{\%}3A10.1186{\%}2F1471-2164-14-728.pdf:pdf},
isbn = {1471216414728},
issn = {1471-2164},
journal = {BMC Genomics},
keywords = {Bread wheat,Fhb1,Fusarium graminearum,Fusarium head blight,Gene co-expression network,Qfhs.ifa-5A,RNA-seq,Transcriptome,Triticum aestivum,bread wheat,fhb1,fusarium graminearum,fusarium head blight,gene co-expression network,ifa-5a,qfhs,rna-seq,transcriptome,triticum aestivum},
mendeley-groups = {expVIP},
number = {1},
pages = {728},
pmid = {24152241},
title = {{Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivum L.)}},
url = {http://www.biomedcentral.com/1471-2164/14/728 http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-728},
volume = {14},
year = {2013}
}

@article{Cantu2011b,
abstract = {BACKGROUND: Increasing the nutrient concentration of wheat grains is important to ameliorate nutritional deficiencies in many parts of the world. Proteins and nutrients in the wheat grain are largely derived from the remobilization of degraded leaf molecules during monocarpic senescence. The down-regulation of the NAC transcription factor Grain Protein Content (GPC) in transgenic wheat plants delays senescence ({\textgreater}3 weeks) and reduces the concentration of protein, Zn and Fe in the grain ({\textgreater}30{\%}), linking senescence and nutrient remobilization.Based on the early and rapid up-regulation of GPC in wheat flag leaves after anthesis, we hypothesized that this transcription factor is an early regulator of monocarpic senescence. To test this hypothesis, we used high-throughput mRNA-seq technologies to characterize the effect of the GPC down-regulation on the wheat flag-leaf transcriptome 12 days after anthesis. At this early stage of senescence GPC transcript levels are significantly lower in transgenic GPC-RNAi plants than in the wild type, but there are still no visible phenotypic differences between genotypes.$\backslash$n$\backslash$nRESULTS: We generated 1.4 million 454 reads from early senescing flag leaves (average {\~{}}350 nt) and assembled 1.2 million into 30,497 contigs that were used as a reference to map 145 million Illumina reads from three wild type and four GPC-RNAi plants. Following normalization and statistical testing, we identified a set of 691 genes differentially regulated by GPC (431 ≥ 2-fold change). Transcript level ratios between transgenic and wild type plants showed a high correlation (R = 0.83) between qRT-PCR and Illumina results, providing independent validation of the mRNA-seq approach. A set of differentially expressed genes were analyzed across an early senescence time-course.$\backslash$n$\backslash$nCONCLUSIONS: Monocarpic senescence is an active process characterized by large-scale changes in gene expression which begins considerably before the appearance of visual symptoms of senescence. The mRNA-seq approach used here was able to detect small differences in transcript levels during the early stages of senescence. This resulted in an extensive list of GPC-regulated genes, which includes transporters, hormone regulated genes, and transcription factors. These GPC-regulated genes, particularly those up-regulated during senescence, provide valuable entry points to dissect the early stages of monocarpic senescence and nutrient remobilization in wheat.},
author = {Cantu, Dario and Pearce, Stephen P and Distelfeld, Assaf and Christiansen, Michael W and Uauy, Cristobal and Akhunov, Eduard and Fahima, Tzion and Dubcovsky, Jorge},
doi = {10.1186/1471-2164-12-492},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Cantu et al/Unknown/art{\%}3A10.1186{\%}2F1471-2164-12-492.pdf:pdf},
isbn = {1471-2164 (Electronic)$\backslash$r1471-2164 (Linking)},
issn = {1471-2164},
journal = {BMC Genomics},
mendeley-groups = {expVIP},
number = {1},
pages = {492},
pmid = {21981858},
title = {{Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence}},
url = {http://www.biomedcentral.com/1471-2164/12/492},
volume = {12},
year = {2011}
}

@article{Gillies2012,
abstract = {Wheat is a critical food source globally. Food security is an increasing concern; current production levels are not expected to keep pace with global demand. New technologies have provided a vast array of wheat genetic data; however, best use of this data requires placing it within a framework in which the various genes, pathways and interactions can be examined. Here we present the first systematic comparison of the global transcriptomes of the aleurone and starchy endosperm of the developing wheat seed (Triticum aestivum), at time points critical to the development of the aleurone layer; 6-, 9- and 14-day post-anthesis. Illumina sequencing gave 25-55 million sequence reads per tissue, of the trimmed reads, 70{\%}-81{\%} mapped to reference expressed sequence transcripts. Transcript abundance was analysed by performing RNA-Seq normalization to generate reads per kilobase of exon model per million mapped reads values, and these were used in comparative analyses between the tissues at each time point using Kal's Z-test. This identified 9414-13 202 highly differentially expressed transcripts that were categorized on the basis of tissue and time point expression and functionally analysed revealing two very distinct tissues. The results demonstrate the fundamental biological reprogramming of the two major biologically and economically significant tissues of the wheat seed over this time course. Understanding these changes in gene expression profiles is essential to mining the potential these tissues hold for human nutrition and contributing to the systems biology of this important crop plant.},
author = {Gillies, Susan A. and Futardo, Agnelo and Henry, Robert J.},
doi = {10.1111/j.1467-7652.2012.00705.x},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Gillies, Futardo, Henry/Plant biotechnology journal/Gillies{\_}et{\_}al-2012-Plant{\_}Biotechnology{\_}Journal.pdf:pdf},
isbn = {1467-7644},
issn = {1467-7652},
journal = {Plant biotechnology journal},
keywords = {Aleurone,Endosperm,Grain,Next generation sequencing,Transcriptome,Triticum aestivum},
mendeley-groups = {expVIP},
month = {aug},
number = {6},
pages = {668--79},
pmid = {22672716},
title = {{Gene expression in the developing aleurone and starchy endosperm of wheat.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22672716},
volume = {10},
year = {2012}
}

@article{Cantu2013,
abstract = {BACKGROUND: Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the molecular basis of PST pathogenicity. In particular, the characterisation of the structure, function and evolutionary dynamics of secreted effector proteins that are detected by host immune receptors can help guide and prioritize breeding efforts. However, to date, our knowledge of the effector repertoire of cereal rust pathogens is limited. RESULTS: We re-sequenced genomes of four PST isolates from the US and UK to identify effector candidates and relate them to their distinct virulence profiles. First, we assessed SNP frequencies between all isolates, with heterokaryotic SNPs being over tenfold more frequent (5.29 +/- 2.23 SNPs/kb) than homokaryotic SNPs (0.41 +/- 0.28 SNPs/kb). Next, we implemented a bioinformatics pipeline to integrate genomics, transcriptomics, and effector-focused annotations to identify and classify effector candidates in PST. RNAseq analysis highlighted transcripts encoding secreted proteins that were significantly enriched in haustoria compared to infected tissue. The expression of 22 candidate effector genes was characterised using qRT-PCR, revealing distinct temporal expression patterns during infection in wheat. Lastly, we identified proteins that displayed non-synonymous substitutions specifically between the two UK isolates PST-87/7 and PST-08/21, which differ in virulence to two wheat varieties. By focusing on polymorphic variants enriched in haustoria, we identified five polymorphic effector candidates between PST-87/7 and PST-08/21 among 2,999 secreted proteins. These allelic variants are now a priority for functional validation as virulence/avirulence effectors in the corresponding wheat varieties. CONCLUSIONS: Integration of genomics, transcriptomics, and effector-directed annotation of PST isolates has enabled us to move beyond the single isolate-directed catalogues of effector proteins and develop a framework for mining effector proteins in closely related isolates and relate these back to their defined virulence profiles. This should ultimately lead to more comprehensive understanding of the PST pathogenesis system, an important first step towards developing more effective surveillance and management strategies for one of the most devastating pathogens of wheat.},
author = {Cantu, D and Segovia, V and MacLean, D and Bayles, R and Chen, X and Kamoun, S and Dubcovsky, J and Saunders, D G and Uauy, C},
doi = {10.1186/1471-2164-14-270\n1471-2164-14-270 [pii]},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Cantu et al/Unknown/art{\%}3A10.1186{\%}2F1471-2164-14-270.pdf:pdf},
isbn = {1471-2164 (Electronic)$\backslash$n1471-2164 (Linking)},
issn = {1471-2164},
journal = {BMC Genomics},
keywords = {*Genome, Fungal,Basidiomycota/*genetics/*pathogenicity,Fungal Proteins/genetics/*secretion,Plant Diseases/genetics,Polymorphism, Genetic,Triticum/*microbiology,Virulence},
mendeley-groups = {expVIP},
pages = {270},
pmid = {23607900},
title = {{Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23607900$\backslash$nhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640902/pdf/1471-2164-14-270.pdf},
volume = {14},
year = {2013}
}

@article{Yang2013,
abstract = {The disease septoria leaf blotch of wheat, caused by fungal pathogen Septoria tritici, is of worldwide concern. The fungus exhibits a hemibiotrophic lifestyle, with a long symptomless, biotrophic phase followed by a sudden transition to necrotrophy associated with host necrosis. Little is known about the systematic interaction between fungal pathogenicity and host responses at specific growth stages and the factors triggering the transition. In order to gain some insights into global transcriptome alterations in both host and pathogen during the two phases of the compatible interaction, disease transition was monitored using pathogenesis-related gene markers and H2O2 signature prior to RNA-Seq. Transcriptome analysis revealed that the slow symptomless growth was accompanied by minor metabolic responses and slightly suppressed defences in the host, whereas necrotrophic growth was associated with enhanced host responses involving energy metabolism, transport, signalling, defence and oxidative stress as well as a decrease in photosynthesis. The fungus expresses distinct classes of stage-specific genes encoding potential effectors, probably first suppressing plant defence responses/facilitating the symptomless growth and later triggering life style transition and inducing host necrosis/facilitating the necrotrophic growth. Transport, signalling, anti-oxidative stress mechanisms and apoplastic nutrient acquisition play important roles in the entire infection process of S. tritici. Our findings uncover systematic S. tritici-induced expression profiles of wheat related to specific fungal infection strategies and provide a transcriptome resource for studying both hosts and pathogens in plant-Dothideomycete interactions.},
author = {Yang, Fen and Li, Wanshun and J{\o}rgensen, Hans J. L.},
doi = {10.1371/journal.pone.0081606},
editor = {Lee, Yong-Hwan},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Yang, Li, Jrgensen/PLoS ONE/journal.pone.0081606.PDF:PDF},
issn = {1932-6203},
journal = {PLoS ONE},
mendeley-groups = {expVIP},
month = {nov},
number = {11},
pages = {e81606},
pmid = {24303057},
title = {{Transcriptional Reprogramming of Wheat and the Hemibiotrophic Pathogen Septoria tritici during Two Phases of the Compatible Interaction}},
url = {http://dx.plos.org/10.1371/journal.pone.0081606},
volume = {8},
year = {2013}
}

@article{Leach2014,
abstract = {BACKGROUND: Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoloci, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution 'nullisomic-tetrasomic' lines) with next generation deep sequencing of gene transcripts (RNA-Seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative contribution of individual homoeoloci to gene expression.$\backslash$n$\backslash$nRESULTS: We discover, based on a sample comprising {\~{}}5-10{\%} of the total wheat gene content, that at least 45{\%} of wheat genes are expressed from all three distinct homoeoloci. Most of these genes show strikingly biased expression patterns in which expression is dominated by a single homoeolocus. The remaining {\~{}}55{\%} of wheat genes are expressed from either one or two homoeoloci only, through a combination of extensive transcriptional silencing and homoeolocus loss.$\backslash$n$\backslash$nCONCLUSIONS: We conclude that wheat is tending towards functional diploidy, through a variety of mechanisms causing single homoeoloci to become the predominant source of gene transcripts. This discovery has profound consequences for wheat breeding and our understanding of wheat evolution.},
author = {Leach, Lindsey J and Belfield, Eric J and Jiang, Caifu and Brown, Carly and Mithani, Aziz and Harberd, Nicholas P},
doi = {10.1186/1471-2164-15-276},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Leach et al/Unknown/art{\%}3A10.1186{\%}2F1471-2164-15-276.pdf:pdf},
isbn = {1471-2164},
issn = {1471-2164},
journal = {BMC genomics},
keywords = {Base Sequence,Chromosomes, Plant,Expressed Sequence Tags,Gene Deletion,Gene Expression Profiling,Gene Expression Regulation, Plant,Gene Library,Gene Silencing,Genes, Plant,Genome, Plant,Haplotypes,Organ Specificity,Organ Specificity: genetics,Polyploidy,Quantitative Trait Loci,Reproducibility of Results,Sequence Alignment,Sequence Analysis, RNA,Transcriptome,Triticum,Triticum: genetics},
mendeley-groups = {expVIP},
number = {1},
pages = {276},
pmid = {24726045},
title = {{Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat.}},
url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-276},
volume = {15},
year = {2014}
}

@article{Li2013,
abstract = {Wheat (Triticum aestivum L.) is one of the most important crops cultivated worldwide. Identifying the complete transcriptome of wheat grain could serve as foundation for further study of wheat seed development. However, the relatively large size and the polyploid complexity of the genome have been substantial barriers to molecular genetics and transcriptome analysis of wheat. Alternatively, RNA sequencing has provided some useful information about wheat genes. However, because of the large number of short reads generated by RNA sequencing, factors that are crucial to transcriptome assembly, including software, candidate parameters and assembly strategies, need to be optimized and evaluated for wheat data. In the present study, four cDNA libraries associated with wheat grain development were constructed and sequenced. A total of 14.17 Gb of high-quality reads were obtained and used to assess different assembly strategies. The most successful approach was to filter the reads with Q30 prior to de novo assembly using Trinity, merge the assembled contigs with genes available in wheat cDNA reference data sets, and combine the resulting assembly with an assembly from a reference-based strategy. Using this approach, a relatively accurate and nearly complete transcriptome associated with wheat grain development was obtained, suggesting that this is an effective strategy for generation of a high-quality transcriptome from RNA sequencing data.},
author = {Li, Huai-Zhu and Gao, Xiang and Li, Xiao-Yan and Chen, Qi-Jiao and Dong, Jian and Zhao, Wan-Chun},
doi = {10.1371/journal.pone.0083530},
editor = {Wu, Qiong},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Li et al/PLoS ONE/journal.pone.0083530.PDF:PDF},
issn = {1932-6203},
journal = {PLoS ONE},
mendeley-groups = {expVIP},
month = {dec},
number = {12},
pages = {e83530},
pmid = {24349528},
title = {{Evaluation of Assembly Strategies Using RNA-Seq Data Associated with Grain Development of Wheat (Triticum aestivum L.)}},
url = {http://dx.plos.org/10.1371/journal.pone.0083530},
volume = {8},
year = {2013}
}


@article{Yang2015,
author = {Yang, Zaijun and Peng, Zhengsong and Wei, Shuhong and Liao, Mingli and Yu, Yan and Jang, Zeyan},
doi = {10.1186/s12864-015-1453-0},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Yang et al/Unknown/art{\%}3A10.1186{\%}2Fs12864-015-1453-0.pdf:pdf},
isbn = {1286401514530},
issn = {1471-2164},
journal = {BMC Genomics},
keywords = {pistil,pistillody,rna sequencing,stamen,wheat},
mendeley-groups = {expVIP},
number = {1},
pages = {1--11},
title = {{Pistillody mutant reveals key insights into stamen and pistil development in wheat (Triticum aestivum L.)}},
url = {http://www.biomedcentral.com/1471-2164/16/211},
volume = {16},
year = {2015}
}

@article{Zhang2014,
abstract = {BACKGROUND: Stripe rust (Puccinia striiformis f. sp. tritici; Pst) and powdery mildew (Blumeria graminis f. sp. tritici; Bgt) are important diseases of wheat (Triticum aestivum) worldwide. Similar mechanisms and gene transcripts are assumed to be involved in the host defense response because both pathogens are biotrophic fungi. The main objective of our study was to identify co-regulated mRNAs that show a change in expression pattern after inoculation with Pst or Bgt, and to identify mRNAs specific to the fungal stress response.$\backslash$n$\backslash$nRESULTS: The transcriptome of the hexaploid wheat line N9134 inoculated with the Chinese Pst race CYR 31 was compared with that of the same line inoculated with Bgt race E09 at 1, 2, and 3 days post-inoculation. Infection by Pst and Bgt affected transcription of 23.8{\%} of all T. aestivum genes. Infection by Bgt triggered a more robust alteration in gene expression in N9134 compared with the response to Pst infection. An array of overlapping gene clusters with distinctive expression patterns provided insight into the regulatory differences in the responses to Bgt and Pst infection. The differentially expressed genes were grouped into seven enriched Kyoto Encyclopedia of Genes and Genomes pathways in Bgt-infected leaves and four pathways in Pst-infected leaves, while only two pathways overlapped. In the plant-pathogen interaction pathway, N9134 activated a higher number of genes and pathways in response to Bgt infection than in response to Pst invasion. Genomic analysis revealed that the wheat genome shared some microbial genetic fragments, which were specifically induced in response to Bgt and Pst infection.$\backslash$n$\backslash$nCONCLUSIONS: Taken together, our findings indicate that the responses of wheat N9134 to infection by Bgt and Pst shows differences in the pathways and genes activated. The mass sequence data for wheat-fungus interaction generated in this study provides a powerful platform for future functional and molecular research on wheat-fungus interactions.},
author = {Zhang, Hong and Yang, Yongzheng and Wang, Changyou and Liu, Min and Li, Hao and Fu, Ying and Wang, Yajuan and Nie, Yingbin and Liu, Xinlun and Ji, Wanquan},
doi = {10.1186/1471-2164-15-898},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Zhang et al/BMC Genomics/art{\%}3A10.1186{\%}2F1471-2164-15-898.pdf:pdf},
isbn = {1471-2164},
issn = {1471-2164},
journal = {BMC Genomics},
keywords = {Bread wheat,Gene expression,Powdery mildew,RNA-Seq,Stripe rust,bread wheat,gene expression,powdery mildew,rna-seq,stripe rust},
mendeley-groups = {expVIP},
number = {1},
pages = {898},
pmid = {25318379},
title = {{Large-scale transcriptome comparison reveals distinct gene activations in wheat responding to stripe rust and powdery mildew}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25318379 http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-898},
volume = {15},
year = {2014}
}

@article{Li2014,
abstract = {Nascent allohexaploid wheat may represent the initial genetic state of common wheat (Triticum aestivum), which arose as a hybrid between Triticum turgidum (AABB) and Aegilops tauschii (DD) and by chromosome doubling and outcompeted its parents in growth vigor and adaptability. To better understand the molecular basis for this success, we performed mRNA and small RNA transcriptome analyses in nascent allohexaploid wheat and its following generations, their progenitors, and the natural allohexaploid cultivar Chinese Spring, with the assistance of recently published A and D genome sequences. We found that nonadditively expressed protein-coding genes were rare but relevant to growth vigor. Moreover, a high proportion of protein-coding genes exhibited parental expression level dominance, with genes for which the total homoeolog expression level in the progeny was similar to that in T. turgidum potentially participating in development and those with similar expression to that in Ae. tauschii involved in adaptation. In addition, a high proportion of microRNAs showed nonadditive expression upon polyploidization, potentially leading to differential expression of important target genes. Furthermore, increased small interfering RNA density was observed for transposable element-associated D homoeologs in the allohexaploid progeny, which may account for biased repression of D homoeologs. Together, our data provide insights into small RNA-mediated dynamic homoeolog regulation mechanisms that may contribute to heterosis in nascent hexaploid wheat.},
author = {Li, A and Liu, D and Wu, J. and Zhao, X and Hao, M and Geng, S and Yan, J and Jiang, X and Zhang, L. and Wu, J. and Yin, L and Zhang, R and Wu, L and Zheng, Y and Mao, L},
doi = {10.1105/tpc.114.124388},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Li et al/The Plant Cell/Plant Cell-2014-Li-1878-900.pdf:pdf},
isbn = {0000000233774},
issn = {1040-4651},
journal = {The Plant Cell},
mendeley-groups = {expVIP},
month = {may},
number = {5},
pages = {1878--1900},
pmid = {24838975},
title = {{mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat}},
url = {http://www.plantcell.org/cgi/doi/10.1105/tpc.114.124388$\backslash$npapers3://publication/doi/10.1105/tpc.114.124388 http://www.plantcell.org/cgi/doi/10.1105/tpc.114.124388},
volume = {26},
year = {2014}
}

@article{Pearce2015,
abstract = {BACKGROUND: The gibberellin (GA) pathway plays a central role in the regulation of plant development, with the 2-oxoglutarate-dependent dioxygenases (2-ODDs: GA20ox, GA3ox, GA2ox) that catalyse the later steps in the biosynthetic pathway of particularly importance in regulating bioactive GA levels. Although GA has important impacts on crop yield and quality, our understanding of the regulation of GA biosynthesis during wheat and barley development remains limited. In this study we identified or assembled genes encoding the GA 2-ODDs of wheat, barley and Brachypodium distachyon and characterised the wheat genes by heterologous expression and transcript analysis.$\backslash$n$\backslash$nRESULTS: The wheat, barley and Brachypodium genomes each contain orthologous copies of the GA20ox, GA3ox and GA2ox genes identified in rice, with the exception of OsGA3ox1 and OsGA2ox5 which are absent in these species. Some additional paralogs of 2-ODD genes were identified: notably, a novel gene in the wheat B genome related to GA3ox2 was shown to encode a GA 1-oxidase, named as TaGA1ox-B1. This enzyme is likely to be responsible for the abundant 1$\beta$-hydroxylated GAs present in developing wheat grains. We also identified a related gene in barley, located in a syntenic position to TaGA1ox-B1, that encodes a GA 3,18-dihydroxylase which similarly accounts for the accumulation of unusual GAs in barley grains. Transcript analysis showed that some paralogs of the different classes of 2-ODD were expressed mainly in a single tissue or at specific developmental stages. In particular, TaGA20ox3, TaGA1ox1, TaGA3ox3 and TaGA2ox7 were predominantly expressed in developing grain. More detailed analysis of grain-specific gene expression showed that while the transcripts of biosynthetic genes were most abundant in the endosperm, genes encoding inactivation and signalling components were more highly expressed in the seed coat and pericarp.$\backslash$n$\backslash$nCONCLUSIONS: The comprehensive expression and functional characterisation of the multigene families encoding the 2-ODD enzymes of the GA pathway in wheat and barley will provide the basis for a better understanding of GA-regulated development in these species. This analysis revealed the existence of a novel, endosperm-specific GA 1-oxidase in wheat and a related GA 3,18-dihydroxylase enzyme in barley that may play important roles during grain expansion and development.},
author = {Pearce, Stephen and Huttly, Alison K and Prosser, Ian M and Li, Yi-dan and Vaughan, Simon P and Gallova, Barbora and Patil, Archana and Coghill, Jane A and Dubcovsky, Jorge and Hedden, Peter and Phillips, Andrew L},
doi = {10.1186/s12870-015-0520-7},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Pearce et al/BMC Plant Biology/art{\%}3A10.1186{\%}2Fs12870-015-0520-7.pdf:pdf},
isbn = {1287001505},
issn = {1471-2229},
journal = {BMC plant biology},
keywords = {Biocatalysis,Biosynthetic Pathways,Biosynthetic Pathways: genetics,Brachypodium,Brachypodium: enzymology,Brachypodium: genetics,Gene Expression Regulation, Plant,Genes, Plant,Gibberellins,Gibberellins: biosynthesis,Hordeum,Hordeum: enzymology,Hordeum: genetics,Mixed Function Oxygenases,Mixed Function Oxygenases: genetics,Multigene Family,Oryza,Oryza: enzymology,Oryza: genetics,Phylogeny,Poaceae,Poaceae: enzymology,Poaceae: genetics,RNA, Messenger,RNA, Messenger: genetics,RNA, Messenger: metabolism,Sequence Analysis, RNA,Signal Transduction,Signal Transduction: genetics,Triticum,Triticum: enzymology,Triticum: genetics},
mendeley-groups = {expVIP},
pages = {130},
pmid = {26044828},
publisher = {BMC Plant Biology},
title = {{Heterologous expression and transcript analysis of gibberellin biosynthetic genes of grasses reveals novel functionality in the GA3ox family.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4455330{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {15},
year = {2015}
}

@article{Liu2015,
abstract = {BACKGROUND: Hexaploid wheat (Triticum aestivum) is a globally important crop. Heat, drought and their combination dramatically reduce wheat yield and quality, but the molecular mechanisms underlying wheat tolerance to extreme environments, especially stress combination, are largely unknown. As an allohexaploid, wheat consists of three closely related subgenomes (A, B, and D), and was reported to show improved tolerance to stress conditions compared to tetraploid. But so far very little is known about how wheat coordinates the expression of homeologous genes to cope with various environmental constraints on the whole-genome level.$\backslash$n$\backslash$nRESULTS: To explore the transcriptional response of wheat to the individual and combined stress, we performed high-throughput transcriptome sequencing of seedlings under normal condition and subjected to drought stress (DS), heat stress (HS) and their combination (HD) for 1 h and 6 h, and presented global gene expression reprograms in response to these three stresses. Gene Ontology (GO) enrichment analysis of DS, HS and HD responsive genes revealed an overlap and complexity of functional pathways between each other. Moreover, 4,375 wheat transcription factors were identified on a whole-genome scale based on the released scaffold information by IWGSC, and 1,328 were responsive to stress treatments. Then, the regulatory network analysis of HSFs and DREBs implicated they were both involved in the regulation of DS, HS and HD response and indicated a cross-talk between heat and drought stress. Finally, approximately 68.4 {\%} of homeologous genes were found to exhibit expression partitioning in response to DS, HS or HD, which was further confirmed by using quantitative RT-PCR and Nullisomic-Tetrasomic lines.$\backslash$n$\backslash$nCONCLUSIONS: A large proportion of wheat homeologs exhibited expression partitioning under normal and abiotic stresses, which possibly contributes to the wide adaptability and distribution of hexaploid wheat in response to various environmental constraints.},
author = {Liu, Zhenshan and Xin, Mingming and Qin, Jinxia and Peng, Huiru and Ni, Zhongfu and Yao, Yingyin and Sun, Qixin},
doi = {10.1186/s12870-015-0511-8},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Liu et al/BMC Plant Biology/art{\%}3A10.1186{\%}2Fs12870-015-0511-8.pdf:pdf},
isbn = {1287001505},
issn = {1471-2229},
journal = {BMC Plant Biology},
keywords = {Acclimatization,Droughts,Gene Expression Profiling,Gene Expression Regulation,Hot Temperature,Physiological,Plant,Plant Proteins,Plant Proteins: genetics,Plant Proteins: metabolism,Seedlings,Seedlings: genetics,Seedlings: metabolism,Stress,Transcriptome,Triticum,Triticum: genetics,Triticum: metabolism},
mendeley-groups = {expVIP},
month = {dec},
number = {1},
pages = {152},
pmid = {26092253},
publisher = {BMC Plant Biology},
title = {{Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)}},
url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-015-0511-8 http://www.biomedcentral.com/1471-2229/15/152},
volume = {15},
year = {2015}
}
@article{Barrero2015,
abstract = {BACKGROUND: Next-generation sequencing technologies provide new opportunities to identify the genetic components responsible for trait variation. However, in species with large polyploid genomes, such as bread wheat, the ability to rapidly identify genes underlying quantitative trait loci (QTL) remains non-trivial. To overcome this, we introduce a novel pipeline that analyses, by RNA-sequencing, multiple near-isogenic lines segregating for a targeted QTL. RESULTS: We use this approach to characterize a major and widely utilized seed dormancy QTL located on chromosome 4AL. It exploits the power and mapping resolution afforded by large multi-parent mapping populations, whilst reducing complexity by using multi-allelic contrasts at the targeted QTL region. Our approach identifies two adjacent candidate genes within the QTL region belonging to the ABA-induced Wheat Plasma Membrane 19 family. One of them, PM19-A1, is highly expressed during grain maturation in dormant genotypes. The second, PM19-A2, shows changes in sequence causing several amino acid alterations between dormant and non-dormant genotypes. We confirm that PM19 genes are positive regulators of seed dormancy. CONCLUSIONS: The efficient identification of these strong candidates demonstrates the utility of our transcriptomic pipeline for rapid QTL to gene mapping. By using this approach we are able to provide a comprehensive genetic analysis of the major source of grain dormancy in wheat. Further analysis across a diverse panel of bread and durum wheats indicates that this important dormancy QTL predates hexaploid wheat. The use of these genes by wheat breeders could assist in the elimination of pre-harvest sprouting in wheat.},
author = {Barrero, J M and Cavanagh, C and Verbyla, K L and Tibbits, J F and Verbyla, A P and Huang, B E and Rosewarne, G M and Stephen, S and Wang, P and Whan, A and Rigault, P and Hayden, M J and Gubler, F},
doi = {10.1186/s13059-015-0665-6},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Barrero et al/Genome Biol/art{\%}3A10.1186{\%}2Fs13059-015-0665-6.pdf:pdf},
isbn = {1465-6914 (Electronic)$\backslash$r1465-6906 (Linking)},
issn = {1474-760X},
journal = {Genome Biol},
mendeley-groups = {expVIP},
pages = {93},
pmid = {25962727},
publisher = {???},
title = {{Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25962727},
volume = {16},
year = {2015}
}

@article{Choulet2014,
author = {Choulet, F. and Alberti, A. and Theil, S. and Glover, N. and Barbe, V. and Daron, J. and Pingault, L. and Sourdille, P. and Couloux, A. and Paux, E. and Leroy, P. and Mangenot, S. and Guilhot, N. and {Le Gouis}, J. and Balfourier, F. and Alaux, M. and Jamilloux, V. and Poulain, J. and Durand, C. and Bellec, A. and Gaspin, C. and Safar, J. and Dolezel, J. and Rogers, J. and Vandepoele, K. and Aury, J.-M. and Mayer, K. and Berges, H. and Quesneville, H. and Wincker, P. and Feuillet, C.},
doi = {10.1126/science.1249721},
issn = {0036-8075},
journal = {Science},
mendeley-groups = {expVIP},
month = {jul},
number = {6194},
pages = {1249721--1249721},
title = {{Structural and functional partitioning of bread wheat chromosome 3B}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1249721},
volume = {345},
year = {2014}
}

@article{Pearce2015b,
abstract = {BACKGROUND: For functional genomics studies, it is important to understand the dynamic expression profiles of transcribed genes in different tissues, stages of development and in response to environmental stimuli. The proliferation in the use of next-generation sequencing technologies by the plant research community has led to the accumulation of large volumes of expression data. However, analysis of these datasets is complicated by the frequent occurrence of polyploidy among economically-important crop species. In addition, processing and analyzing such large volumes of sequence data is a technical and time-consuming task, limiting their application in functional genomics studies, particularly for smaller laboratories which lack access to high-powered computing infrastructure. Wheat is a good example of a young polyploid species with three similar genomes (97 {\%} identical among homoeologous genes), rapidly accumulating RNA-seq datasets and a large research community.$\backslash$n$\backslash$nDESCRIPTION: We present WheatExp, an expression database and visualization tool to analyze and compare homoeologue-specific transcript profiles across a broad range of tissues from different developmental stages in polyploid wheat. Beginning with publicly-available RNA-seq datasets, we developed a pipeline to distinguish between homoeologous transcripts from annotated genes in tetraploid and hexaploid wheat. Data from multiple studies is processed and compiled into a database which can be queried either by BLAST or by searching for a known gene of interest by name or functional domain. Expression data of multiple genes can be displayed side-by-side across all expression datasets providing immediate access to a comprehensive panel of expression data for specific subsets of wheat genes.$\backslash$n$\backslash$nCONCLUSIONS: The development of a publicly accessible expression database hosted on the GrainGenes website - http://wheat.pw.usda.gov/WheatExp/ - coupled with a simple and readily-comparable visualization tool will empower the wheat research community to use RNA-seq data and to perform functional analyses of target genes. The presented expression data is homoeologue-specific allowing for the analysis of relative contributions from each genome to the overall expression of a gene, a critical consideration for breeding applications. Our approach can be expanded to other polyploid species by adjusting sequence mapping parameters according to the specific divergence of their genomes.},
author = {Pearce, Stephen and Vazquez-Gross, Hans and Herin, Sayer Y and Hane, David and Wang, Yi and Gu, Yong Q and Dubcovsky, Jorge},
doi = {10.1186/s12870-015-0692-1},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Pearce et al/BMC plant biology/art{\%}3A10.1186{\%}2Fs12870-015-0692-1.pdf:pdf},
isbn = {1471-2229},
issn = {1471-2229},
journal = {BMC plant biology},
keywords = {Expression,Wheat,RNA-seq,Polyploidy,Homoeologue-sp,correspondence,edu,expression,homoeologue-specific,jdubcovsky,polyploidy,rna-seq,ucdavis,wheat,wheatexp},
mendeley-groups = {expVIP},
number = {1},
pages = {299},
pmid = {26705106},
publisher = {BMC Plant Biology},
title = {{WheatExp: an RNA-seq expression database for polyploid wheat.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4690421{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {15},
year = {2015}
}

@article{Petryszak2016,
author = {Petryszak, Robert and Keays, Maria and Tang, Y. Amy and Fonseca, Nuno A. and Barrera, Elisabet and Burdett, Tony and F{\"{u}}llgrabe, Anja and Fuentes, Alfonso Mu{\~{n}}oz-Pomer and Jupp, Simon and Koskinen, Satu and Mannion, Oliver and Huerta, Laura and Megy, Karine and Snow, Catherine and Williams, Eleanor and Barzine, Mitra and Hastings, Emma and Weisser, Hendrik and Wright, James and Jaiswal, Pankaj and Huber, Wolfgang and Choudhary, Jyoti and Parkinson, Helen E. and Brazma, Alvis},
doi = {10.1093/nar/gkv1045},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Petryszak et al/Nucleic Acids Research/Nucl. Acids Res.-2016-Petryszak-D746-52.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Research},
mendeley-groups = {expVIP},
month = {jan},
number = {D1},
pages = {D746--D752},
title = {{Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1045},
volume = {44},
year = {2016}
}

@article{Fox2014,
author = {Fox, Samuel E and Geniza, Matthew and Hanumappa, Mamatha and Naithani, Sushma and Sullivan, Chris and Preece, Justin and Tiwari, Vijay K and Elser, Justin and Leonard, Jeffrey M and Sage, Abigail and Gresham, Cathy and Kerhornou, Arnaud and Bolser, Dan and Mccarthy, Fiona and Kersey, Paul and Lazo, Gerard R and Jaiswal, Pankaj},
doi = {10.1371/journal.pone.0096855},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Fox et al/Unknown/journal.pone.0096855.PDF:PDF},
mendeley-groups = {expVIP},
number = {5},
title = {{De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum}},
volume = {9},
year = {2014}
}


@article{Pearce2014,
author = {Pearce, Stephen and Tabbita, Facundo and Cantu, Dario and Buffalo, Vince and Avni, Raz and Vazquez-gross, Hans and Zhao, Rongrong and Conley, Christopher J and Distelfeld, Assaf and Dubcovksy, Jorge},
doi = {10.1186/s12870-014-0368-2},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Pearce et al/Unknown/art{\%}3A10.1186{\%}2Fs12870-014-0368-2.pdf:pdf},
isbn = {1287001403682},
keywords = {gpc,iron transport,senescence,wheat,zinc transport,zip},
mendeley-groups = {expVIP},
pages = {1--23},
title = {{Regulation of Zn and Fe transporters by the GPC1 gene during early wheat monocarpic senescence}},
year = {2014}
}


@article{Kolesnikov2015,
author = {Kolesnikov, Nikolay and Hastings, Emma and Keays, Maria and Melnichuk, Olga and Tang, Y Amy and Williams, Eleanor and Dylag, Miroslaw and Kurbatova, Natalja and Brandizi, Marco and Burdett, Tony and Megy, Karyn and Pilicheva, Ekaterina and Rustici, Gabriella and Tikhonov, Andrew and Parkinson, Helen and Petryszak, Robert and Sarkans, Ugis and Brazma, Alvis},
doi = {10.1093/nar/gku1057},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Kolesnikov et al/Unknown/Nucl. Acids Res.-2015-Kolesnikov-D1113-6.pdf:pdf},
mendeley-groups = {expVIP},
number = {October 2014},
pages = {1113--1116},
title = {{ArrayExpress update –– simplifying data submissions}},
volume = {43},
year = {2015}
}

@article{Anders2015,
author = {Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang},
doi = {10.1093/bioinformatics/btu638},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Anders, Pyl, Huber/Unknown/Bioinformatics-2015-Anders-166-9.pdf:pdf},
mendeley-groups = {expVIP},
number = {2},
pages = {166--169},
title = {{Genome analysis HTSeq — a Python framework to work with high-throughput sequencing data}},
volume = {31},
year = {2015}
}

@article{Li2010,
  doi = {10.1093/bioinformatics/btp698},
  url = {http://dx.doi.org/10.1093/bioinformatics/btp698},
  year  = {2010},
  month = {jan},
  publisher = {Oxford University Press ({OUP})},
  volume = {26},
  number = {5},
  pages = {589--595},
  author = {Heng Li and Richard Durbin},
  title = {Fast and accurate long-read alignment with Burrows-Wheeler transform},
  journal = {Bioinformatics}
}

@article{Langmead2012,
  doi = {10.1038/nmeth.1923},
  url = {http://dx.doi.org/10.1038/nmeth.1923},
  year  = {2012},
  month = {mar},
  publisher = {Nature Publishing Group},
  volume = {9},
  number = {4},
  pages = {357--359},
  author = {Ben Langmead and Steven L Salzberg},
  title = {Fast gapped-read alignment with Bowtie 2},
  journal = {Nature Methods}
}

@misc{Davey2015,
  doi = {10.7490/f1000research.1110111.1},
  url = {https://doi.org/10.7490/f1000research.1110111.1},
  author = {Robert Davey and Anthony Etuk and Felix Shaw and Alejandra Gonzalez-Beltran and Philippe Rocca-Serra and Susanna Sansone},
  publisher = {F1000Research},
  title = {COPO: Aiding the journey from data to publication in the plant sciences},
  year = {2015}
}

@article{Stam1981,
abstract = {------------Beginning of NIL terminology ; Donor:parent ratio = (1/2){\^{}}x, x=number of crosses total ; Implication of linkage block measurements. -----------The length was estimated of a chromosome segment with a desired marker gene introgressed from a donor by backcrossing into a recurrent parent. It was found that, for instance, for a chromosome with a length of 100 cM the length of the segment is 32 cM in the BC6. Differences between two near-isogenic lines often ascribed to the difference in genotype at the marker locus may be caused by genes linked to the marker gene.},
author = {Stam, P. and Zeven, A. C.},
doi = {10.1007/BF00033982},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Stam, Zeven/Euphytica/10.1007@BF00033982.pdf:pdf},
isbn = {ISSN 0014-2336},
issn = {00142336},
journal = {Euphytica},
keywords = {Backcross,length of donor chromosome segment,near-isogenic line},
mendeley-groups = {Wheat},
number = {2},
pages = {227--238},
pmid = {15802512},
title = {{The theoretical proportion of the donor genome in near-isogenic lines of self-fertilizers bred by backcrossing}},
volume = {30},
year = {1981}
}

@article{alberts2014molecular,
  title={Molecular Biology of the Cell (6th edn)},
  author={Bruce Alberts and Alexander Johnson and Julian Lewis and David Morgan and Martin Raff and Keith Roberts and Peter Walter},
  year={2014},
  publisher={Garland Science}
}
@article{li2008mapping,
  title={Mapping short DNA sequencing reads and calling variants using mapping quality scores},
  author={Li, Heng and Ruan, Jue and Durbin, Richard},
  journal={Genome research},
  volume={18},
  number={11},
  pages={1851--1858},
  year={2008},
  publisher={Cold Spring Harbor Lab}
}
@article{sims2014sequencing,
  title={Sequencing depth and coverage: key considerations in genomic analyses},
  author={Sims, David and Sudbery, Ian and Ilott, Nicholas E and Heger, Andreas and Ponting, Chris P},
  journal={Nature Reviews Genetics},
  volume={15},
  number={2},
  pages={121--132},
  year={2014},
  publisher={Nature Publishing Group}
}
@manual{truseq,
author = {{Illumina Inc}},
title = {{TruSeq RNA Sample Preparation v2 Guide}},
date = {March 2014},
language = {English},
version = {Version 2.15026495},
organization = {Illumina Inc},
pagetotal = {132},
pubstate = {March 2014},
}
@online{RNAseqlopedia,
  author = {{Cresko Lab}},
  title = {{RNA-}seqlopedia},
  year = 2015,
  url = {http://rnaseq.uoregon.edu/},
  urldate = {2016-09-20}
}
@online{statquest,
  author = {Stat Quest},
  title = {{StatQuest: RPKM, FPKM and TPM}},
  year = 2015,
  url = {https://statquest.org/},
  urldate = {2016-09-20}
}

@article{wang2009rna,
  title={RNA-Seq: a revolutionary tool for transcriptomics},
  author={Wang, Zhong and Gerstein, Mark and Snyder, Michael},
  journal={Nature reviews genetics},
  volume={10},
  number={1},
  pages={57--63},
  year={2009},
  publisher={Nature Publishing Group}
}
@article{Wagner2012,
abstract = {Measures of RNA abundance are important for many areas of biology and often obtained from high-throughput RNA sequencing methods such as Illumina sequence data. These measures need to be normalized to remove technical biases inherent in the sequencing approach, most notably the length of the RNA species and the sequencing depth of a sample. These biases are corrected in the widely used reads per kilobase per million reads (RPKM) measure. Here, we argue that the intended meaning of RPKM is a measure of relative molar RNA concentration (rmc) and show that for each set of transcripts the average rmc is a constant, namely the inverse of the number of transcripts mapped. Further, we show that RPKM does not respect this invariance property and thus cannot be an accurate measure of rmc. We propose a slight modification of RPKM that eliminates this inconsistency and call it TPM for transcripts per million. TPM respects the average invariance and eliminates statistical biases inherent in the RPKM measure.},
author = {Wagner, G{\"{u}}nter P. and Kin, Koryu and Lynch, Vincent J.},
doi = {10.1007/s12064-012-0162-3},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Wagner, Kin, Lynch/Theory in Biosciences/Wagner, Kin, and Lynch (2012).pdf:pdf},
isbn = {1611-7530 (Electronic)$\backslash$r1431-7613 (Linking)},
issn = {14317613},
journal = {Theory in Biosciences},
keywords = {NextGen sequencing,RNA quantification,RPKM},
mendeley-groups = {expVIP},
number = {4},
pages = {281--285},
pmid = {22872506},
title = {{Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples}},
volume = {131},
year = {2012}
}

@article{Patro2014,
abstract = {We introduce Sailfish, a computational method for quantifying the abundance of previously annotated RNA isoforms from RNA-seq data. Because Sailfish entirely avoids mapping reads, a time-consuming step in all current methods, it provides quantification estimates much faster than do existing approaches (typically 20 times faster) without loss of accuracy. By facilitating frequent reanalysis of data and reducing the need to optimize parameters, Sailfish exemplifies the potential of lightweight algorithms for efficiently processing sequencing reads.},
archivePrefix = {arXiv},
arxivId = {1308.3700},
author = {Patro, Rob and Mount, Stephen M and Kingsford, Carl},
doi = {10.1038/nbt.2862},
eprint = {1308.3700},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Patro, Mount, Kingsford/Nature Biotechnology/patro2014.pdf:pdf},
isbn = {1308.3700},
issn = {1546-1696},
journal = {Nature biotechnology},
mendeley-groups = {expVIP},
number = {5},
pages = {462--464},
pmid = {24752080},
publisher = {Nature Publishing Group},
title = {{Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24752080},
volume = {32},
year = {2014}
}

@article{Sears1985,
author = {Sears, E R and Miller, T E},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Sears, Miller/Cereal Research Communications/10.2307@23783009.pdf:pdf},
journal = {Cereal Research Communications},
mendeley-groups = {Wheat},
number = {2/3},
pages = {261--263},
title = {{The History of Chinese Spreing}},
volume = {13},
year = {1985}
}

@article{Allen2016,
author = {Allen, Alexandra M. and Winfield, Mark O. and Burridge, Amanda J. and Downie, Rowena C. and Benbow, Harriet R. and Barker, Gary L.A. and Wilkinson, Paul A. and Coghill, Jane and Waterfall, Christy and Davassi, Alessandro and Scopes, Geoff and Pirani, Ali and Webster, Teresa and Brew, Fiona and Bloor, Claire and Griffiths, Simon and Bentley, Alison R. and Alda, Mark and Jack, Peter and Phillips, Andrew L. and Edwards, Keith J},
doi = {10.1111/pbi.12635},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Allen et al/Plant Biotechnology Journal/Allen{\_}et{\_}al-2016-Plant{\_}Biotechnology{\_}Journal.pdf:pdf},
issn = {14677644},
journal = {Plant Biotechnology Journal},
mendeley-groups = {Wheat},
month = {sep},
title = {{Characterisation of a Wheat Breeders' Array suitable for high throughput SNP genotyping of global accessions of hexaploid bread wheat ( Triticum aestivium )}},
url = {http://doi.wiley.com/10.1111/pbi.12635},
year = {2016}
}

@article{Cheng2014,
author = {Cheng, Feng and Wu, Jian and Wang, Xiaowu},
doi = {10.1038/hortres.2014.24},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Cheng, Wu, Wang/Horticulture Research/hortres201424.pdf:pdf},
issn = {2052-7276},
journal = {Horticulture Research},
mendeley-groups = {Brassicas},
month = {may},
number = {February},
pages = {14024},
title = {{Genome triplication drove the diversification of Brassica plants}},
url = {http://www.nature.com/articles/hortres201424},
volume = {1},
year = {2014}
}

@article{Simmonds2014,
author = {Simmonds, James and Scott, Peter and Leverington-Waite, Michelle and Turner, Adrian S and Brinton, Jemima and Korzun, Viktor and Snape, John and Uauy, Cristobal},
doi = {10.1186/s12870-014-0191-9},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Simmonds et al/BMC Plant Biology/art{\%}3A10.1186{\%}2Fs12870-014-0191-9.pdf:pdf},
issn = {1471-2229},
journal = {BMC Plant Biology},
keywords = {grain shape,grain size,green canopy duration,nils,qtl,wheat,yield},
mendeley-groups = {QTLs},
month = {dec},
number = {1},
pages = {191},
title = {{Identification and independent validation of a stable yield and thousand grain weight QTL on chromosome 6A of hexaploid wheat (Triticum aestivum L.)}},
url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0191-9},
volume = {14},
year = {2014}
}

@article{Shatalina2013,
abstract = {Agronomically important traits are frequently controlled by rare, genotype-specific alleles. Such genes can only be mapped in a population derived from the donor genotype. This requires the development of a specific genetic map, which is difficult in wheat because of the low level of polymorphism among elite cultivars. The absence of sufficient polymorphism, the complexity of the hexaploid wheat genome as well as the lack of complete sequence information make the construction of genetic maps with a high density of reproducible and polymorphic markers challenging. We developed a genotype-specific genetic map of chromosome 3B from winter wheat cultivars Arina and Forno. Chromosome 3B was isolated from the two cultivars and then sequenced to 10-fold coverage. This resulted in a single-nucleotide polymorphisms (SNP) database of the complete chromosome. Based on proposed synteny with the Brachypodium model genome and gene annotation, sequences close to coding regions were used for the development of 70 SNP-based markers. They were mapped on a Arina × Forno Recombinant Inbred Lines population and found to be spread over the complete chromosome 3B. While overall synteny was well maintained, numerous exceptions and inversions of syntenic gene order were identified. Additionally, we found that the majority of recombination events occurred in distal parts of chromosome 3B, particularly in hot-spot regions. Compared with the earlier map based on SSR and RFLP markers, the number of markers increased fourfold. The approach presented here allows fast development of genotype-specific polymorphic markers that can be used for mapping and marker-assisted selection.},
author = {Shatalina, Margarita and Wicker, Thomas and Buchmann, Jan P. and Oberhaensli, Simone and {\v{S}}imkov{\'{a}}, Hana and Dole{\v{z}}el, Jaroslav and Keller, Beat},
doi = {10.1111/pbi.12003},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Shatalina et al/Plant Biotechnology Journal/Shatalina{\_}et{\_}al-2013-Plant{\_}Biotechnology{\_}Journal.pdf:pdf},
isbn = {1467-7644},
issn = {14677644},
journal = {Plant Biotechnology Journal},
keywords = {Brachypodium,Genetic mapping,Single-nucleotide polymorphism,Synteny,Wheat},
mendeley-groups = {QTLs},
month = {jan},
number = {1},
pages = {23--32},
pmid = {23046423},
title = {{Genotype-specific SNP map based on whole chromosome 3B sequence information from wheat cultivars Arina and Forno}},
url = {http://doi.wiley.com/10.1111/pbi.12003},
volume = {11},
year = {2013}
}

@article{Lopez-Maestre2016,
abstract = {SNPs (Single Nucleotide Polymorphisms) are ge-netic markers whose precise identification is a pre-requisite for association studies. Methods to iden-tify them are currently well developed for model species, but rely on the availability of a (good) reference genome, and therefore cannot be ap-plied to non-model species. They are also mostly tailored for whole genome (re-)sequencing experi-ments, whereas in many cases, transcriptome se-quencing can be used as a cheaper alternative which already enables to identify SNPs located in tran-scribed regions. In this paper, we propose a method that identifies, quantifies and annotates SNPs with-out any reference genome, using RNA-seq data only. Individuals can be pooled prior to sequencing, if not enough material is available from one individual. Us-ing pooled human RNA-seq data, we clarify the pre-cision and recall of our method and discuss them with respect to other methods which use a reference genome or an assembled transcriptome. We then val-idate experimentally the predictions of our method using RNA-seq data from two non-model species. The method can be used for any species to anno-tate SNPs and predict their impact on the protein se-quence. We further enable to test for the association of the identified SNPs with a phenotype of interest.},
author = {Lopez-Maestre, H{\'{e}}{\`{e}}ne and Brinza, Lilia and Marchet, Camille and Kielbassa, Janice and Bastien, Sylv{\`{e}}re and Boutigny, Mathilde and Monnin, David and Filali, Adil El and Carareto, Claudia Marcia and Vieira, Cristina and Picard, Franck and Kremer, Natacha and Vavre, Fabrice and Sagot, Marie-France and Lacroix, Vincent},
doi = {10.1093/nar/gkw655},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Lopez-Maestre et al/Nucleic Acids Research/Nucl. Acids Res.-2016-Lopez-Maestre-nar{\_}gkw655.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Research},
mendeley-groups = {Algorithms},
month = {jul},
pages = {gkw655},
pmid = {27458203},
title = {{SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkw655},
year = {2016}
}

@article{Cingolani2012,
abstract = {Copy number variation (CNV) in the genome is a complex phenomenon, and not completely understood. We have developed a method, CNVnator, for CNV discovery and genotyping from read-depth (RD) analysis of personal genome sequencing. Our method is based on combining the established mean-shift approach with additional refinements (multiple-bandwidth partitioning and GC correction) to broaden the range of discovered CNVs. We calibrated CNVnator using the extensive validation performed by the 1000 Genomes Project. Because of this, we could use CNVnator for CNV discovery and genotyping in a population and characterization of atypical CNVs, such as de novo and multi-allelic events. Overall, for CNVs accessible by RD, CNVnator has high sensitivity (86{\%}-96{\%}), low false-discovery rate (3{\%}-20{\%}), high genotyping accuracy (93{\%}-95{\%}), and high resolution in breakpoint discovery ({\textless}200 bp in 90{\%} of cases with high sequencing coverage). Furthermore, CNVnator is complementary in a straightforward way to split-read and read-pair approaches: It misses CNVs created by retrotransposable elements, but more than half of the validated CNVs that it identifies are not detected by split-read or read-pair. By genotyping CNVs in the CEPH, Yoruba, and Chinese-Japanese populations, we estimated that at least 11{\%} of all CNV loci involve complex, multi-allelic events, a considerably higher estimate than reported earlier. Moreover, among these events, we observed cases with allele distribution strongly deviating from Hardy-Weinberg equilibrium, possibly implying selection on certain complex loci. Finally, by combining discovery and genotyping, we identified six potential de novo CNVs in two family trios.},
author = {Cingolani, Pablo and Platts, Adrian and Wang, Le Lily and Coon, Melissa and Nguyen, Tung and Wang, Luan and Land, Susan J. and Lu, Xiangyi and Ruden, Douglas M.},
doi = {10.4161/fly.19695},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Cingolani et al/Unknown/SnpEff{\_}paper.pdf:pdf},
isbn = {1549-5469 (Electronic) 1088-9051 (Linking)},
issn = {1933-6934},
journal = {Fly},
keywords = {2012 landes bioscience,drosophila melanogaster,next generation dna sequencing,personal genomes,whole-genome snp analysis},
mendeley-groups = {Algorithms},
number = {2},
pages = {80--92},
pmid = {21324876},
title = {{A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff}},
url = {http://www.tandfonline.com/doi/abs/10.4161/fly.19695},
volume = {6},
year = {2012}
}

@techreport{McLaren2016,
abstract = {The Ensembl Variant Effect Predictor (VEP) is a powerful toolset for the analysis, annotation and prioritization of genomic variants, including in non-coding regions. The VEP accurately predicts the effects of sequence variants on transcripts, protein products, regulatory regions and binding motifs by leveraging the high quality, broad scope, and integrated nature of the Ensembl databases. In addition, it enables comparison with a large collection of existing publicly available variation data within Ensembl to provide insights into population and ancestral genetics, phenotypes and disease. The VEP is open source and free to use. It is available via a simple web interface (http://www.Ensembl.org/vep), a powerful downloadable package, and both Ensembl's Perl and REST application program interface (API) services.},
author = {McLaren, William and Gil, Laurent and Hunt, Sarah E and Riat, Harpreet Singh and Ritchie, Graham R. S. and Thormann, Anja and Flicek, Paul and Cunningham, Fiona},
booktitle = {bioRxiv},
doi = {10.1101/042374},
file = {:Users/ramirezr/Documents/Mendeley Desktop/McLaren et al/bioRxiv/art{\%}3A10.1186{\%}2Fs13059-016-0974-4.pdf:pdf},
isbn = {1474760X (Electronic)},
issn = {1474-760X},
keywords = {genome,ngs,snp,variant annotation},
mendeley-groups = {Algorithms},
month = {mar},
pages = {042374},
pmid = {27268795},
publisher = {Genome Biology},
title = {{The Ensembl Variant Effect Predictor}},
url = {http://biorxiv.org/content/early/2016/03/04/042374.abstract http://biorxiv.org/lookup/doi/10.1101/042374},
year = {2016}
}

@article{Rustenholz2010,
abstract = {Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B). However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B.},
author = {Rustenholz, Camille and Hedley, Pete E and Morris, Jenny and Choulet, Fr{\'{e}}d{\'{e}}ric and Feuillet, Catherine and Waugh, Robbie and Paux, Etienne},
doi = {10.1186/1471-2164-11-714},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Rustenholz et al/BMC Genomics/art{\%}3A10.1186{\%}2F1471-2164-11-714.pdf:pdf},
isbn = {1471216411},
issn = {1471-2164},
journal = {BMC Genomics},
mendeley-groups = {Wheat},
number = {1},
pages = {714},
pmid = {21167071},
title = {{Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources}},
url = {http://www.biomedcentral.com/1471-2164/11/714 http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-714},
volume = {11},
year = {2010}
}

@article{Jehan2006,
author = {Jehan, Tabassum and Lakhanpaul, Suman},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Jehan, Lakhanpaul/Unknown/Single{\_}nucleotide{\_}polymorphism{\_}SNP-Methods{\_}and{\_}app.pdf:pdf},
isbn = {0972-5849},
issn = {09725849},
journal = {Indian Journal of Biotechnology},
keywords = {00,8 c12n15,application in plants,cl,disequilibrium,diversity analysis,genotyping assay,int,ipc code,ld,linkage,microarrays,s ingle nucleotide polymorphism,snp},
mendeley-groups = {QTLs},
number = {4},
pages = {435},
title = {{Single nucleotide polymorphism (SNP)-methods and applications in plant genetics: a review}},
volume = {5},
year = {2006}
}

@article{Ali2014,
abstract = {Analyses of large-scale population structure of pathogens enable the identification of migration patterns, diversity reservoirs or longevity of populations, the understanding of current evolutionary trajectories and the anticipation of future ones. This is particularly important for long-distance migrating fungal pathogens such as Puccinia striiformis f.sp. tritici (PST), capable of rapid spread to new regions and crop varieties. Although a range of recent PST invasions at continental scales are well documented, the worldwide population structure and the center of origin of the pathogen were still unknown. In this study, we used multilocus microsatellite genotyping to infer worldwide population structure of PST and the origin of new invasions based on 409 isolates representative of distribution of the fungus on six continents. Bayesian and multivariate clustering methods partitioned the set of multilocus genotypes into six distinct genetic groups associated with their geographical origin. Analyses of linkage disequilibrium and genotypic diversity indicated a strong regional heterogeneity in levels of recombination, with clear signatures of recombination in the Himalayan (Nepal and Pakistan) and near-Himalayan regions (China) and a predominant clonal population structure in other regions. The higher genotypic diversity, recombinant population structure and high sexual reproduction ability in the Himalayan and neighboring regions suggests this area as the putative center of origin of PST. We used clustering methods and approximate Bayesian computation (ABC) to compare different competing scenarios describing ancestral relationship among ancestral populations and more recently founded populations. Our analyses confirmed the Middle East-East Africa as the most likely source of newly spreading, high-temperature-adapted strains; Europe as the source of South American, North American and Australian populations; and Mediterranean-Central Asian populations as the origin of South African populations. Although most geographic populations are not markedly affected by recent dispersal events, this study emphasizes the influence of human activities on recent long-distance spread of the pathogen.},
author = {Ali, Sajid and Gladieux, Pierre and Leconte, Marc and Gautier, Ang{\'{e}}lique and Justesen, Annemarie F. and Hovm{\o}ller, Mogens S. and Enjalbert, J{\'{e}}r{\^{o}}me and de Vallavieille-Pope, Claude},
doi = {10.1371/journal.ppat.1003903},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Ali et al/PLoS Pathogens/journal.ppat.1003903.PDF:PDF},
isbn = {1553-7374 (Electronic)$\backslash$r1553-7366 (Linking)},
issn = {15537366},
journal = {PLoS Pathogens},
mendeley-groups = {Yr15},
number = {1},
pmid = {24465211},
title = {{Origin, Migration Routes and Worldwide Population Genetic Structure of the Wheat Yellow Rust Pathogen Puccinia striiformis f.sp. tritici}},
volume = {10},
year = {2014}
}

@article{Akhunov2010,
abstract = {BACKGROUND: A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. RESULTS: Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. CONCLUSIONS: In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.},
author = {Akhunov, Eduard D and Akhunova, Alina R and Anderson, Olin D and Anderson, James A and Blake, Nancy and Clegg, Michael T and Coleman-Derr, Devin and Conley, Emily J and Crossman, Curt C and Deal, Karin R and Dubcovsky, Jorge and Gill, Bikram S and Gu, Yong Q and Hadam, Jakub and Heo, Hwayoung and Huo, Naxin and Lazo, Gerard R and Luo, Ming-Cheng and Ma, Yaqin Q and Matthews, David E and McGuire, Patrick E and Morrell, Peter L and Qualset, Calvin O and Renfro, James and Tabanao, Dindo and Talbert, Luther E and Tian, Chao and Toleno, Donna M and Warburton, Marilyn L and You, Frank M and Zhang, Wenjun and Dvorak, Jan},
doi = {10.1186/1471-2164-11-702},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Akhunov et al/Unknown/art{\%}3A10.1186{\%}2F1471-2164-11-702.pdf:pdf},
isbn = {1471-2164 (Electronic)$\backslash$r1471-2164 (Linking)},
issn = {1471-2164},
journal = {BMC genomics},
keywords = {Chromosome Mapping,Chromosomes, Plant,Chromosomes, Plant: genetics,Codon,Codon: genetics,Databases, Genetic,Expressed Sequence Tags,Gene Deletion,Genes, Plant,Genes, Plant: genetics,Genetic,Genetic Linkage,Genetic Loci,Genetic Loci: genetics,Genetic Variation,Genome, Plant,Genome, Plant: genetics,Haplotypes,Haplotypes: genetics,Molecular Sequence Data,Nucleotides,Nucleotides: genetics,Plant,Plant: genetics,Polymorphism, Single Nucleotide,Polymorphism, Single Nucleotide: genetics,Polyploidy,Single Nucleotide,Single Nucleotide: genetics,Triticum,Triticum: genetics},
mendeley-groups = {QTLs},
number = {1},
pages = {702},
pmid = {21156062},
title = {{Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes.}},
url = {http://www.biomedcentral.com/1471-2164/11/702},
volume = {11},
year = {2010}
}


@article{Sollars2016,
author = {Sollars, Elizabeth S. A. and Harper, Andrea L and Kelly, Laura J and Sambles, Christine M. and Ramirez-Gonzalez, Ricardo H. and Swarbreck, David and Kaithakottil, Gemy and Cooper, Endymion D and Uauy, Cristobal and Havlickova, Lenka and Worswick, Gemma and Studholme, David J. and Zohren, Jasmin and Salmon, Deborah L. and Clavijo, Bernardo J and Li, Yi and He, Zhesi and Fellgett, Alison and McKinney, Lea Vig and Nielsen, Lene Rostgaard and Douglas, Gerry C. and Kj{\ae}r, Erik Dahl and Downie, J Allan and Boshier, David and Lee, Steve and Clark, Jo and Grant, Murray and Bancroft, Ian and Caccamo, Mario and Buggs, Richard J. A.},
doi = {10.1038/nature20786},
file = {:Users/ramirezr/Library/Application Support/Mendeley Desktop/Downloaded/Sollars et al. - 2016 - Genome sequence and genetic diversity of European ash trees.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
month = {dec},
number = {7636},
pages = {212--216},
pmid = {28024298},
title = {{Genome sequence and genetic diversity of European ash trees}},
url = {http://www.nature.com/doifinder/10.1038/nature20786},
volume = {541},
year = {2016}
}

@article{Dubcovsky2007,
abstract = {Wheat was domesticated about 10,000 years ago and has since spread worldwide to become one of the major crops. Its adaptability to diverse environments and end uses is surprising given the diversity bottlenecks expected from recent domestication and polyploid speciation events. Wheat compensates for these bottlenecks by capturing part of the genetic diversity of its progenitors and by generating new diversity at a relatively fast pace. Frequent gene deletions and disruptions generated by a fast replacement rate of repetitive sequences are buffered by the polyploid nature of wheat, resulting in subtle dosage effects on which selection can operate.},
author = {Dubcovsky, Jorge and Dvorak, Jan},
doi = {10.1126/science.1143986},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Dubcovsky, Dvorak/Science (New York, N.Y.)/nihms754477.pdf:pdf},
isbn = {1095-9203 (Electronic)},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
mendeley-groups = {Wheat},
number = {5833},
pages = {1862--6},
pmid = {17600208},
title = {{Genome plasticity a key factor in the success of polyploid wheat under domestication.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17600208$\backslash$nhttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4737438},
volume = {316},
year = {2007}
}
@article{ElBaidouri2016,
abstract = {The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events.},
author = {{El Baidouri}, Moaine and Murat, Florent and Veyssiere, Maeva and Molinier, M{\'{e}}lanie and Flores, Raphael and Burlot, Laura and Alaux, Michael and Quesneville, Hadi and Pont, Caroline and Salse, J{\'{e}}r{\^{o}}me},
doi = {10.1111/nph.14113},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Baidouri et al/Unknown/10.1111@nph.14113.pdf:pdf},
issn = {1469-8137},
journal = {The New phytologist},
keywords = {ancestor,and of intense debate,articles published in new,decades,evolution,in 2015,in the scientific community,of hexaploid bread wheat,origin,over the last few,phytologist discussed the origin,polyploidization,three,wheat},
mendeley-groups = {Wheat},
number = {2014},
pmid = {27551821},
title = {{Reconciling the evolutionary origin of bread wheat (Triticum aestivum).}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27551821},
year = {2016}
}

@article{Gross2012,
abstract = {An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News {\&} Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.},
author = {Gross, B L},
doi = {10.1038/hdy.2011.80},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Gross/Heredity/hdy201180a.pdf:pdf},
isbn = {0018-067X},
issn = {0018-067X},
journal = {Heredity},
mendeley-groups = {Wheat},
number = {3},
pages = {157--158},
pmid = {21915149},
publisher = {Nature Publishing Group},
title = {{Genetic and phenotypic divergence of homoploid hybrid species from parental species}},
url = {http://dx.doi.org/10.1038/hdy.2011.80},
volume = {108},
year = {2012}
}
@article{Niu2014,
abstract = {Production of doubled haploids (DHs) is an important methodology to speed the process of breeding and development of mapping populations in crops. The procedure for DH production includes two major steps: haploid induction and chromosome doubling. In recent years, wide hybridization between wheat and maize has become a main approach for haploid production in wheat. In this method, the maize chromosomes are completely eliminated during the early development of the hybrid seeds after wheat spikes were pollinated with maize pollen. Numerous wheat cultivars and mapping populations have been developed using wheat– maize hybridization. In this study, we review the procedures of DH pro-duction of durum and common wheat via wide hybridization with maize, the factors which affect the efficiency of DH production, and the mecha-nism of selective elimination of the maize genome during the early development of the hybrid embryos. We also report a highly efficient protocol for DH production in durum and common wheat, which was established based on the optimal conditions for each of the factors that affect the efficiency of DH production.},
author = {Niu, Zhixia and Jiang, Aixiang and {Abu Hammad}, Wesam and Oladzadabbasabadi, Atena and Xu, Steven S. and Mergoum, Mohamed and Elias, Elias M.},
doi = {10.1111/pbr.12162},
editor = {Hartl, L.},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Niu et al/Plant Breeding/Niu{\_}et{\_}al-2014-Plant{\_}Breeding.pdf:pdf},
issn = {01799541},
journal = {Plant Breeding},
keywords = {Chromosome doubling,Chromosome elimination,Common wheat,Doubled haploid production,Durum wheat,Wide hybridization},
mendeley-groups = {Wheat},
month = {jun},
number = {3},
pages = {313--320},
title = {{Review of doubled haploid production in durum and common wheat through wheat × maize hybridization}},
url = {http://doi.wiley.com/10.1111/pbr.12162},
volume = {133},
year = {2014}
}

@article{Goodwin2016,
abstract = {Since the completion of the human genome project in 2003, extraordinary progress has been made in genome sequencing technologies, which has led to a decreased cost per megabase and an increase in the number and diversity of sequenced genomes. An astonishing complexity of genome architecture has been revealed, bringing these sequencing technologies to even greater advancements. Some approaches maximize the number of bases sequenced in the least amount of time, generating a wealth of data that can be used to understand increasingly complex phenotypes. Alternatively, other approaches now aim to sequence longer contiguous pieces of DNA, which are essential for resolving structurally complex regions. These and other strategies are providing researchers and clinicians a variety of tools to probe genomes in greater depth, leading to an enhanced understanding of how genome sequence variants underlie phenotype and disease.},
author = {Goodwin, Sara and McPherson, John D and McCombie, W Richard},
doi = {10.1038/nrg.2016.49},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Goodwin, Mcpherson, Mccombie/Nature Publishing Group/goodwin2016.pdf:pdf},
isbn = {1471-0064 (Electronic) 1471-0056 (Linking)},
issn = {1471-0056},
journal = {Nat Rev Genet},
mendeley-groups = {Sequencing},
number = {6},
pages = {333--351},
pmid = {27184599},
publisher = {Nature Publishing Group},
title = {{Coming of age: ten years of next-generation sequencing technologies}},
url = {http://dx.doi.org/10.1038/nrg.2016.49$\backslash$nhttp://10.1038/nrg.2016.49},
volume = {17},
year = {2016}
}
@article{Cooper2013,
author = {Cooper, Laurel and Walls, Ramona L and Elser, Justin and Gandolfo, Maria A and Stevenson, Dennis W and Smith, Barry and Preece, Justin and Athreya, Balaji and Mungall, Christopher J and Rensing, Stefan and Hiss, Manuel and Lang, Daniel and Reski, Ralf and Berardini, Tanya Z and Li, Donghui and Huala, Eva},
doi = {10.1093/pcp/pcs163},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Cooper et al/Unknown/Plant Cell Physiol-2013-Cooper-e1.pdf:pdf},
keywords = {anatomy,bioinformatics comparative genomics,genome annotation ontology plant},
mendeley-groups = {Random},
number = {2},
pages = {1--23},
title = {{The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses Special Focus Issue – Databases}},
volume = {54},
year = {2013}
}

@article{Jordan2015,
author = {Jordan, Katherine W and Wang, Shichen and Lun, Yanni and Gardiner, Laura-Jayne and MacLachlan, Ron and Hucl, Pierre and Wiebe, Krysta and Wong, Debbie and Forrest, Kerrie L and Sharpe, Andrew G and Sidebottom, Christine Hd and Hall, Neil and Toomajian, Christopher and Close, Timothy and Dubcovsky, Jorge and Akhunova, Alina and Talbert, Luther and Bansal, Urmil K and Bariana, Harbans S and Hayden, Matthew J and Pozniak, Curtis and Jeddeloh, Jeffrey a and Hall, Anthony and Akhunov, Eduard},
doi = {10.1186/s13059-015-0606-4},
file = {:Users/ramirezr/Documents/Mendeley Desktop/Jordan et al/Genome Biology/art{\%}3A10.1186{\%}2Fs13059-015-0606-4.pdf:pdf},
isbn = {1305901506064},
issn = {1465-6906},
journal = {Genome Biology},
mendeley-groups = {JournalClub,QTLs},
number = {1},
pages = {1--18},
title = {{A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes}},
url = {http://genomebiology.com/2015/16/1/48},
volume = {16},
year = {2015}
}

@article{Untergasser2012,
abstract = {Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3's functionality. In this article, we describe Primer3's current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement-a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.},
author = {Untergasser, Andreas and Cutcutache, Ioana and Koressaar, Triinu and Ye, Jian and Faircloth, Brant C and Remm, Maido and Rozen, Steven G},
doi = {10.1093/nar/gks596},
file = {:Users/ramirezr/Dropbox/Mendeley Desktop/gks596.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Research},
mendeley-groups = {Bioinformatics},
number = {15},
pages = {1--12},
pmid = {22730293},
title = {{Primer3-new capabilities and interfaces}},
volume = {40},
year = {2012}
}


@article{Chou1992,
abstract = {A Hot Start Polymerase Chain Reaction (PCR) entails the withholding of at least one reagent from the reaction mixture until the reaction tube temperature has reached 60-80 degrees C. Hot Start amplification with an AmpliWax vapor barrier uses a layer of solid wax to separate the retained reagent(s) and the test sample from the bulk of the reagents until the first heating step of automated thermal cycling melts the wax and convectively mixes the two aqueous layers. Wax-mediated Hot Start PCR greatly increases the specificity, yield, and precision of amplifying low copy numbers of three HIV targets. In the presence of 1 microgram of human placental DNA (1.6 x 10(5) diploid genomes) the specificity improvement entails considerable to complete reduction in the amplification of mis-primed sequences and putative primer oligomers. When mis-priming is negligible, the procedural improvement still suppresses putative primer oligomerization. Hot Start PCR with an AmpliWax vapor barrier permits routine amplification of a single target molecule with detection by ethidium stained gel electrophoresis; nonisotopically visualized probing suffices for confirmation. The improved amplification performance is evident for target copy numbers below approximately 10(3).},
author = {Chou, Quin and Russell, Marion and Birch, David E. and Raymond, Jonathan and Bloch, Will},
doi = {10.1093/nar/20.7.1717},
file = {:Users/ramirezr/Dropbox/Mendeley Desktop/nar00081-0266.pdf:pdf},
isbn = {0305-1048 (Print)$\backslash$r0305-1048 (Linking)},
issn = {0305-1048},
journal = {Nucleic Acids Research},
mendeley-groups = {Bioinformatics},
number = {7},
pages = {1717--1723},
pmid = {1579465},
title = {{Prevention of pre-PCR mis-priming and primer dimerization improves low-copy-number amplifications}},
url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/20.7.1717},
volume = {20},
year = {1992}
}

@article{Breslauer1986,
abstract = {We report the complete thermodynamic library of all 10 Watson-Crick DNA nearest-neighbor interactions. We obtained the relevant thermodynamic data from calorimetric studies on 19 DNA oligomers and 9 DNA polymers. We show how these thermodynamic data can be used to calculate the stability and predict the temperature-dependent behavior of any DNA duplex structure from knowledge of its base sequence. We illustrate our method of calculation by using the nearest-neighbor data to predict transition enthalpies and free energies for a series of DNA oligomers. These predicted values are in excellent agreement with the corresponding values determined experimentally. This agreement demonstrates that a DNA duplex structure thermodynamically can be considered to be the sum of its nearest-neighbor interactions. Armed with this knowledge and the nearest-neighbor thermodynamic data reported here, scientists now will be able to predict the stability (delta G degree) and the melting behavior (delta H degree) of any DNA duplex structure from inspection of its primary sequence. This capability should prove valuable in numerous applications, such as predicting the stability of a probe-gene complex; selecting optimal conditions for a hybridization experiment; deciding on the minimum length of a probe; predicting the influence of a specific transversion or transition on the stability of an affected DNA region; and predicting the relative stabilities of local domains within a DNA duplex.},
author = {Breslauer, K J and Frank, R and Blocker, H. and Marky, L A},
doi = {10.1073/pnas.83.11.3746},
file = {:Users/ramirezr/Dropbox/Mendeley Desktop/pnas00315-0187.pdf:pdf},
isbn = {0027-8424 (Print)$\backslash$n0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
keywords = {Base Composition,Base Sequence,DNA,Nucleic Acid Conformation,Nucleic Acid Denaturation,Oligodeoxyribonucleotides,Thermodynamics},
mendeley-groups = {Bioinformatics},
month = {jun},
number = {11},
pages = {3746--3750},
pmid = {3459152},
title = {{Predicting DNA duplex stability from the base sequence.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=323600{\&}tool=pmcentrez{\&}rendertype=abstract http://www.pnas.org/cgi/doi/10.1073/pnas.83.11.3746},
volume = {83},
year = {1986}
}

@article{Rychlik1995,
abstract = {Taq and Pfu DNA polymerases were tested for their propensity to prime from mismatched primers. Two series of bacteriophage lambda primers were designed with progressively longer mismatched 5' termini. Effects of the primer concentration, annealing temperature, salt and solvent concentrations on PCR yield were tested. At the standard PCR conditions, priming was detectable when the 3'-terminal portion of the partially mismatched primer formed a continuous duplex more stable than -11 kcal/mol with the target DNA. In the presence of low magnesium ion concentrations, priming was significantly reduced, but glycerol (5{\%}) and formamide (2.5{\%}) had only a slight effect (Taq DNA polymerase). Although priming specificities of Taq and Pfu DNA polymerases were similar, the solvents had no effect on Pfu DNA polymerase-directed PCR. Oligonucleotides that are GC rich at their 3' ends exhibit high priming efficiency but are also prone to false priming, since the shorter fragments of their 3' ends are stable enough to serve as primers.},
author = {Rychlik, W},
issn = {0736-6205},
journal = {BioTechniques},
mendeley-groups = {Bioinformatics},
month = {jan},
number = {1},
pages = {84--6, 88--90},
pmid = {7702859},
title = {{Priming efficiency in PCR.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/7702859},
volume = {18},
year = {1995}
}

@misc{mullis1987process,
  title={Process for amplifying, detecting, and/or-cloning nucleic acid sequences},
  author={Mullis, K.B. and Erlich, H.A. and Arnheim, N. and Horn, G.T. and Saiki, R.K. and Scharf, S.J.},
  url={http://www.google.co.jp/patents/US4683195},
  year={1987},
  month={jul},
  publisher={Google Patents},
  note={US Patent 4,683,195}
}

@article{Borrill2015,
author = {Borrill, Philippa and Adamski, Nikolai and Uauy, Cristobal},
doi = {10.1111/nph.13533},
file = {:Users/ramirezr/Downloads/Borrill{\_}et{\_}al-2015-New{\_}Phytologist.pdf:pdf},
issn = {0028646X},
journal = {New Phytologist},
keywords = {functional genomics,genomes,genomics,homoeologues,in,next-generation sequencing,polyploid,targeting induced local lesions,tilling,triticum aestivum},
mendeley-groups = {Wheat},
month = {dec},
number = {4},
pages = {1008--1022},
title = {{Genomics as the key to unlocking the polyploid potential of wheat}},
url = {http://doi.wiley.com/10.1111/nph.13533},
volume = {208},
year = {2015}
}

@article{Clavijo2016,
abstract = {Advances in genome sequencing and assembly technologies are generating many high quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimised data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents more than 78{\%} of the genome with a scaffold N50 of 88.8kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNAseq and PacBio full-length cDNAs to identify 104,091 high confidence protein-coding genes and 10,156 non-coding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.},
author = {Clavijo, Bernardo J and Venturini, Luca and Schudoma, Christian and {Garcia Accinelli}, Gonzalo and Kaithakottil, Gemy and Wright, Jonathan and Borrill, Philippa and Kettleborough, George and Heavens, Darren and Chapman, Helen and Lipcombe, James and Barker, Tom and Lu, Fu-hao and McKenzie, Neil and Raats, Dina and {Ramirez Gonzalez}, Ricardo H. and Coince, Aurore and Peel, Ned and Percival-Alwyn, Lawrence and Duncan, Owen and Tr{\"{o}}sch, Josua and Yu, Goutai and Bolser, Dan and Naamati, Guy and Kerhornou, Arnaud and Spannagl, Manuel and Gundlach, Heidrun and Haberer, Georg and Davey, Robert P and Fosker, Christine and {Di Palma}, Federica and Phillips, Andrew and Millar, A Harvey and Kersey, Paul J and Uauy, Cristobal and Krasileva, Ksenia V and Swarbreck, David and Bevan, Michael W and Clark, Matthew D},
doi = {http://dx.doi.org/10.1101/080796},
file = {:private/var/folders/nm/r68pwf8s32v8rl9gzv{\_}wpf10pl0s2v/T/WebKitPDFs-NVDPBo/080796.full.pdf:pdf},
journal = {bioRxiv},
keywords = {2011,agronomic genes,annotation,com-,complex genomes,cost-effective assembly of many,enabled the rapid and,gnerre et al,improvements in sequencing read,lam et al,large and,lengths and throughput have,transcriptome,wheat,whole genome shotgun assembly},
pages = {080796},
title = {{An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.}},
volume = {Jan 1},
year = {2016}
}