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bibliography.bib
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Imported from Another project/bibliography.bib, at 8:50 pm Wed, 26th Jan 22
@article{anfinsen1972formation,
title={The formation and stabilization of protein structure.},
author={Anfinsen, Christian B},
journal={Biochemical Journal},
volume={128},
number={4},
pages={737},
year={1972},
publisher={Portland Press Ltd}
}
@article{masson2019recommendations,
title={Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments},
author={Masson, Glenn R and Burke, John E and Ahn, Natalie G and Anand, Ganesh S and Borchers, Christoph and Brier, S{\'e}bastien and Bou-Assaf, George M and Engen, John R and Englander, S Walter and Faber, Johan and others},
journal={Nature Methods},
volume={16},
number={7},
pages={595--602},
year={2019},
publisher={Nature Publishing Group}
}
@article{10.1093/bioinformatics/btaa587,
author = {Puchała, Weronika and Burdukiewicz, Michał and Kistowski, Michał and Dąbrowska, Katarzyna A and Badaczewska-Dawid, Aleksandra E and Cysewski, Dominik and Dadlez, Michał},
title = "{HaDeX: an R package and web-server for analysis of data from hydrogen–deuterium exchange mass spectrometry experiments}",
journal = {Bioinformatics},
volume = {36},
number = {16},
pages = {4516-4518},
year = {2020},
month = {06},
abstract = "{Hydrogen–deuterium mass spectrometry (HDX-MS) is a rapidly developing technique for monitoring dynamics and interactions of proteins. The development of new devices has to be followed with new software suites addressing emerging standards in data analysis.We propose HaDeX, a novel tool for processing, analysis and visualization of HDX-MS experiments. HaDeX supports a reproducible analytical process, including data exploration, quality control and generation of publication-quality figures.HaDeX is available primarily as a web-server (http://mslab-ibb.pl/shiny/HaDeX/), but its all functionalities are also accessible as the R package (https://CRAN.R-project.org/package=HaDeX) and standalone software (https://sourceforge.net/projects/HaDeX/).Supplementary data are available at Bioinformatics online.}",
issn = {1367-4803}
}
@Manual{powerHaDeX,
title = {powerHaDeX: Efficient Simulation of HDX-MS Data and Tools for the Statistical Analysis},
author = {Krystyna Grzesiak and Mateusz Staniak},
year = {2021},
note = {R package version 1.0},
}
@article{liu2011hdx,
title={HDX-analyzer: a novel package for statistical analysis of protein structure dynamics},
author={Liu, Sanmin and Liu, Lantao and Uzuner, Ugur and Zhou, Xin and Gu, Manxi and Shi, Weibing and Zhang, Yixiang and Dai, Susie Y and Yuan, Joshua S},
journal={BMC bioinformatics},
volume={12},
number={1},
pages={1--10},
year={2011},
publisher={BioMed Central}
}
@article{10.1093/bioinformatics/btw420,
author = {Hourdel, Véronique and Volant, Stevenn and O’Brien, Darragh P. and Chenal, Alexandre and Chamot-Rooke, Julia and Dillies, Marie-Agnès and Brier, Sébastien},
title = "{MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets}",
journal = {Bioinformatics},
volume = {32},
number = {22},
pages = {3413-3419},
year = {2016},
month = {07},
abstract = "{Motivation: With the continued improvement of requisite mass spectrometers and UHPLC systems, Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) workflows are rapidly evolving towards the investigation of more challenging biological systems, including large protein complexes and membrane proteins. The analysis of such extensive systems results in very large HDX-MS datasets for which specific analysis tools are required to speed up data validation and interpretation.Results: We introduce a web application and a new R-package named ‘MEMHDX’ to help users analyze, validate and visualize large HDX-MS datasets. MEMHDX is composed of two elements. A statistical tool aids in the validation of the results by applying a mixed-effects model for each peptide, in each experimental condition, and at each time point, taking into account the time dependency of the HDX reaction and number of independent replicates. Two adjusted P-values are generated per peptide, one for the ‘Change in dynamics’ and one for the ‘Magnitude of ΔD’, and are used to classify the data by means of a ‘Logit’ representation. A user-friendly interface developed with Shiny by RStudio facilitates the use of the package. This interactive tool allows the user to easily and rapidly validate, visualize and compare the relative deuterium incorporation on the amino acid sequence and 3D structure, providing both spatial and temporal information.Availability and Implementation: MEMHDX is freely available as a web tool at the project home page http://memhdx.c3bi.pasteur.frContact:[email protected] or [email protected] information:Supplementary data is available at Bioinformatics online.}",
issn = {1367-4803},
}
@article{houde2011utility,
title={The utility of hydrogen/deuterium exchange mass spectrometry in biopharmaceutical comparability studies},
author={Houde, Damian and Berkowitz, Steven A and Engen, John R},
journal={Journal of pharmaceutical sciences},
volume={100},
number={6},
pages={2071--2086},
year={2011},
publisher={Elsevier}
}
@misc{huang2014introduction,
title={An Introduction to Statistical Learning: With Applications in R By Gareth James, Trevor Hastie, Robert Tibshirani, Daniela Witten},
author={Huang, Jianhua Z},
year={2014},
publisher={Springer}
}
@article{https://doi.org/10.1002/sim.1991,
author = {Durbán, M. and Harezlak, J. and Wand, M. P. and Carroll, R. J.},
title = {Simple fitting of subject-specific curves for longitudinal data},
journal = {Statistics in Medicine},
volume = {24},
number = {8},
pages = {1153-1167},
keywords = {linear mixed models, restricted likelihood ratio tests, penalized splines, acute lymphoblastic leukaemia},
abstract = {Abstract We present a simple semiparametric model for fitting subject-specific curves for longitudinal data. Individual curves are modelled as penalized splines with random coefficients. This model has a mixed model representation, and it is easily implemented in standard statistical software. We conduct an analysis of the long-term effect of radiation therapy on the height of children suffering from acute lymphoblastic leukaemia using penalized splines in the framework of semiparametric mixed effects models. The analysis revealed significant differences between therapies and showed that the growth rate of girls in the study cannot be fully explained by the group-average curve and that individual curves are necessary to reflect the individual response to treatment. We also show how to implement these models in S-PLUS and R in the appendix. Copyright © 2004 John Wiley \& Sons, Ltd.},
year = {2005}
}
@book{hastie01statisticallearning,
added-at = {2008-05-16T16:17:42.000+0200},
address = {New York, NY, USA},
author = {Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome},
biburl = {https://www.bibsonomy.org/bibtex/2f58afc5c9793fcc8ad8389824e57984c/sb3000},
interhash = {d585aea274f2b9b228fc1629bc273644},
intrahash = {f58afc5c9793fcc8ad8389824e57984c},
keywords = {ml statistics},
publisher = {Springer New York Inc.},
series = {Springer Series in Statistics},
timestamp = {2008-05-16T16:17:43.000+0200},
title = {The Elements of Statistical Learning},
year = 2001
}
@article{10.1093/ansci/1973.Symposium.10,
author = {Henderson, C. R.},
title = "{SIRE EVALUATION AND GENETIC TRENDS}",
journal = {Journal of Animal Science},
volume = {1973},
number = {Symposium},
pages = {10-41},
year = {1973},
month = {01},
abstract = "{Sire evaluation can logically be formulated as a process of prediction of future progeny of a sire produced by matings with specified females and making their records in some specified environment. Sewall Wright (1931) over 40 years ago suggested three types of prediction that might be of interest: (1) progeny of a particular mating, (2) future daughters in the same herd but out of a new sample of dams, (3) daughters out of a random sample of dams of the breed. Dr. Lush as early as 1931 had elucidated the principles of sire evaluation, Lush (1931 Lush (1933).As was pointed out by Lehman (1961), two types of selection problems have been studied by statisticians. These are Model I and Model II selection, analagous to the corresponding models of analysis of variance. In Model I the candidates for selection are fixed, for example, choices are to be made among treatments, a random sample of observations having been taken on each fixed treatment. No really unified theory has been developed for this type of selection. In contrast, Model II selection involves candidates that are regarded as a random sample from some specified population. Model II represents the classical selection problem in animal breeding and had essentially been solved by Wright and Lush early in the 1930's. Smith's (1936) application to plant breeding and, in particular, Hazel's (1943) application to animal breeding formalized the techniques.A third type of selection that has apparently been overlooked by both statisticians and animal breeders might}",
issn = {0021-8812},
}
@article{kuznetsova2017lmertest,
title={lmerTest package: tests in linear mixed effects models},
author={Kuznetsova, Alexandra and Brockhoff, Per B and Christensen, Rune HB and others},
journal={Journal of statistical software},
volume={82},
number={13},
pages={1--26},
year={2017}
}
@article{BERGER1957106,
title = {Deuterium exchange of poly-dl-alanine in aqueous solution},
journal = {Archives of Biochemistry and Biophysics},
volume = {69},
pages = {106-118},
year = {1957},
issn = {0003-9861},
doi = {https://doi.org/10.1016/0003-9861(57)90478-2},
url = {https://www.sciencedirect.com/science/article/pii/0003986157904782},
author = {Arieh Berger and K. Linderstrøm-Lang},
abstract = {The slow deuterium exchange of poly-dl-alanine (PDLA) in aqueous solution has been studied at different temperatures and different pH. The results indicate that the exchange reaction is catalyzed by both hydrogen and hydroxyl ions, and that the slow exchange may be explained by a stabilization of the helix due to internal nonpolar bonds between the methyl groups of the side chains.}
}
}