This repository has been archived by the owner on Jan 7, 2020. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path2019_srp.bib
472 lines (427 loc) · 13.2 KB
/
2019_srp.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
@article{hejazi2018+supervised,
year = {2018+},
author = {Hejazi, Nima S and {Kherad-Pajouh}, Sara and {van der Laan}, Mark J
and Hubbard, Alan E},
title = {Supervised variance moderation of locally efficient
estimators in high-dimensional biology}
}
@article{hejazi2017biotmle,
author = {Hejazi, Nima S and Cai, Weixin and Hubbard, Alan E},
title = {{biotmle}: Targeted Learning for Biomarker Discovery},
journal = {The Journal of Open Source Software},
volume = {2},
number = {15},
month = {July},
year = {2017},
publisher = {The Open Journal}
}
@article{chen2012personal,
title={Personal omics profiling reveals dynamic molecular and medical
phenotypes},
author={Chen, Rui and Mias, George I and Li-Pook-Than, Jennifer and Jiang,
Lihua and Lam, Hugo YK and Chen, Rong and Miriami, Elana and Karczewski,
Konrad J and Hariharan, Manoj and Dewey, Frederick E and others},
journal={Cell},
volume={148},
number={6},
pages={1293--1307},
year={2012},
publisher={Elsevier}
}
@article{holland1986statistics,
title={Statistics and causal inference},
author={Holland, Paul W},
journal={Journal of the American statistical Association},
volume={81},
number={396},
pages={945--960},
year={1986},
publisher={Taylor \& Francis}
}
@article{ioannidis2005why,
title={Why most published research findings are false},
author={Ioannidis, John PA},
journal={PLoS Med},
volume={2},
number={8},
pages={e124},
year={2005},
publisher={Public Library of Science}
}
@article{young2009machine,
title={A Machine-Learning Algorithm for Estimating and Ranking the Impact of
Environmental Risk Factors in Exploratory Epidemiological Studies},
author={Young, Jessica G and Hubbard, Alan E and Eskenazi, Brenda and Jewell,
Nicholas P},
year={2009},
publisher={bepress}
}
@article{rappaport2010environment,
title={Environment and disease risks},
author={Rappaport, Stephen M and Smith, Martyn T},
journal={Science},
volume={330},
number={6003},
pages={460--461},
year={2010},
publisher={American Association for the Advancement of Science}
}
@article{rappaport2012biomarkers,
title={Biomarkers intersect with the exposome},
author={Rappaport, Stephen M},
journal={Biomarkers},
volume={17},
number={6},
pages={483--489},
year={2012},
publisher={Taylor \& Francis}
}
@article{patel2010environment,
title={An environment-wide association study (EWAS) on type 2 diabetes
mellitus},
author={Patel, Chirag J and Bhattacharya, Jayanta and Butte, Atul J},
journal={PloS one},
volume={5},
number={5},
pages={e10746},
year={2010},
publisher={Public Library of Science}
}
@article{manolio2010genomewide,
title={Genomewide association studies and assessment of the risk of disease},
author={Manolio, Teri A},
journal={New England Journal of Medicine},
volume={363},
number={2},
pages={166--176},
year={2010},
publisher={Mass Medical Soc}
}
@article{bembom2009biomarker,
title={Biomarker discovery using targeted maximum-likelihood estimation:
Application to the treatment of antiretroviral-resistant HIV infection},
author={Bembom, Oliver and Petersen, Maya L and Rhee, Soo-Yon and Fessel, W
Jeffrey and Sinisi, Sandra E and Shafer, Robert W and {van der Laan}, Mark
J},
journal={Statistics in medicine},
volume={28},
number={1},
pages={152--172},
year={2009},
publisher={Wiley Online Library}
}
@article{bang2005doubly,
title={Doubly robust estimation in missing data and causal inference models},
author={Bang, Heejung and Robins, James M},
journal={Biometrics},
volume={61},
number={4},
pages={962--973},
year={2005},
publisher={Wiley Online Library}
}
@article{vdl2006targeted,
title={Targeted maximum likelihood learning},
author={{van der Laan}, Mark J and Rubin, Daniel},
journal={The International Journal of Biostatistics},
volume={2},
number={1},
year={2006}
}
@book{vdl2011targeted,
title={Targeted learning: causal inference for observational and experimental
data},
author={{van der Laan}, Mark J and Rose, Sherri},
year={2011},
publisher={Springer Science \& Business Media}
}
@book{vdl2018targeted,
title={Targeted Learning in Data Science: Causal Inference for Complex
Longitudinal Studies},
author={{van der Laan}, Mark J and Rose, Sherri},
year={2018},
publisher={Springer Science \& Business Media}
}
@article{gruber2009targeted,
title={Targeted maximum likelihood estimation: A gentle introduction},
author={Gruber, Susan and {van der Laan}, Mark J},
year={2009},
publisher={bepress}
}
@article{gruber2011tmle,
title={tmle: An R package for targeted maximum likelihood estimation},
author={Gruber, Susan and {van der Laan}, Mark J},
year={2011},
publisher={bepress}
}
@incollection{smyth2005limma,
title={{Limma}: linear models for microarray data},
author={Smyth, Gordon K},
booktitle={Bioinformatics and computational biology solutions using R and
Bioconductor},
pages={397--420},
year={2005},
publisher={Springer}
}
@article{smyth2004linear,
title = {Linear Models and Empirical Bayes Methods for Assessing Differential
Expression in Microarray Experiments},
author = {Smyth, Gordon K},
journal={Statistical Applications in Genetics and Molecular Biology},
volume={3},
number={1},
pages={1--25},
year={2004}
}
@article{wang2012detecting,
title={Detecting disease-associated genes with confounding variable
adjustment and the impact on genomic meta-analysis: with application to
major depressive disorder},
author={Wang, Xingbin and Lin, Yan and Song, Chi and Sibille, Etienne and
Tseng, George C},
journal={BMC bioinformatics},
volume={13},
number={1},
pages={1},
year={2012},
publisher={BioMed Central}
}
@article{benjamini1995controlling,
title={Controlling the false discovery rate: a practical and powerful
approach to multiple testing},
author={Benjamini, Yoav and Hochberg, Yosef},
journal={Journal of the royal statistical society. Series B
(Methodological)},
pages={289--300},
year={1995},
publisher={{JSTOR}}
}
@article{vdl2007super,
title={{Super Learner}},
author={{van der Laan}, Mark J and Polley, Eric C and Hubbard, Alan E},
journal={Statistical applications in genetics and molecular biology},
volume={6},
number={1},
year={2007}
}
@book{friedman2001elements,
title={The elements of statistical learning},
author={Friedman, Jerome and Hastie, Trevor and Tibshirani, Robert},
year={2001},
publisher={Springer series in statistics Springer, Berlin}
}
@book{pearl2000causality,
title={Causality},
author={Pearl, Judea},
year={2000},
publisher={Cambridge university press}
}
@article{rosenbaum1983central,
title={The central role of the propensity score in observational studies for
causal effects},
author={Rosenbaum, Paul R and Rubin, Donald B},
journal={Biometrika},
volume={70},
number={1},
pages={41--55},
year={1983},
publisher={Biometrika Trust}
}
@manual{R,
title = {{R}: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {{R Foundation for Statistical Computing}},
address = {Vienna, Austria},
year = {2018},
url = {https://www.R-project.org/}
}
@article{gruber2010application,
title={An application of collaborative targeted maximum likelihood estimation
in causal inference and genomics},
author={Gruber, Susan and {van der Laan}, Mark J},
journal={The International Journal of Biostatistics},
volume={6},
number={1},
year={2010}
}
@book{tsiatis2007semiparametric,
author = {Tsiatis, Anastasios},
publisher = {Springer Science \& Business Media},
title = {Semiparametric theory and missing data},
year = {2007}
}
@article{mchale2011global,
author = {McHale, Cliona M and Zhang, Luoping and Lan, Qing and Vermeulen,
Roel and Li, Guilan and Hubbard, Alan E and Porter, Kristin E and Thomas,
Reuben and Portier, Christopher J and Shen, Min and others},
journal = {Environmental health perspectives},
number = {5},
pages = {628},
publisher = {National Institute of Environmental Health Sciences},
title = {Global gene expression profiling of a population exposed to a range
of benzene levels},
volume = {119},
year = {2011}
}
@incollection{tuglus2011targeted,
title={Targeted methods for biomarker discovery},
author={Tuglus, Catherine and {van der Laan}, Mark J},
booktitle={Targeted Learning},
pages={367--382},
year={2011},
publisher={Springer}
}
@article{hubbard2008population,
title={Population intervention models in causal inference},
author={Hubbard, Alan E and {van der Laan}, Mark J},
journal={Biometrika},
volume={95},
number={1},
pages={35--47},
year={2008},
publisher={Oxford University Press}
}
@article{law2014voom,
title={voom: Precision weights unlock linear model analysis tools for RNA-seq
read counts},
author={Law, Charity W and Chen, Yunshun and Shi, Wei and Smyth, Gordon K},
journal={Genome biology},
volume={15},
number={2},
pages={R29},
year={2014},
publisher={BioMed Central}
}
@article{ritchie2015limma,
title={limma powers differential expression analyses for RNA-sequencing and
microarray studies},
author={Ritchie, Matthew E and Phipson, Belinda and Wu, Di and Hu, Yifang and
Law, Charity W and Shi, Wei and Smyth, Gordon K},
journal={Nucleic acids research},
volume={43},
number={7},
pages={e47--e47},
year={2015},
publisher={Oxford University Press}
}
@article{huber2015orchestrating,
title={Orchestrating high-throughput genomic analysis with Bioconductor},
author={Huber, Wolfgang and Carey, Vincent J and Gentleman, Robert and
Anders, Simon and Carlson, Marc and Carvalho, Benilton S and Bravo, Hector
Corrada and Davis, Sean and Gatto, Laurent and Girke, Thomas and others},
journal={Nature methods},
volume={12},
number={2},
pages={115--121},
year={2015},
publisher={Nature Research}
}
@article{gentleman2004bioconductor,
year = {2004},
publisher = {Springer Nature},
volume = {5},
number = {10},
pages = {R80},
title = {Bioconductor: open software development for computational biology
and bioinformatics},
author = {Robert C Gentleman and Vincent J Carey and Douglas M Bates and Ben
Bolstad and Marcel Dettling and Sandrine Dudoit and Byron Ellis and Laurent
Gautier and Yongchao Ge and Jeff Gentry and Kurt Hornik and Torsten Hothorn
and Wolfgang Huber and Stefano Iacus and Rafael Irizarry and Friedrich
Leisch and Cheng Li and Martin Maechler and Anthony J Rossini and Gunther
Sawitzki and Colin Smith and Gordon Smyth and Luke Tierney and Jean YH Yang
and Jianhua Zhang},
journal = {Genome Biology}
}
@article{breiman1996stacked,
title={Stacked regressions},
author={Breiman, Leo},
journal={Machine learning},
volume={24},
number={1},
pages={49--64},
year={1996},
publisher={Springer}
}
@book{hastie2009elements,
title={The Elements of Statistical Learning: Data Mining, Inference, and
Prediction},
author={Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome},
series={Springer Series in Statistics},
year={2009},
publisher={Springer New York}
}
@book{vaart2000asymptotic,
title={Asymptotic Statistics},
author={{van der Vaart}, Aad W},
series={Cambridge Series in Statistical and Probabilistic Mathematics},
year={2000},
publisher={Cambridge University Press}
}
@article{vdl2004asymptotic,
title={Asymptotic optimality of likelihood-based cross-validation},
author={{van der Laan}, Mark J and Dudoit, Sandrine and Keles, Sunduz},
journal={Statistical Applications in Genetics and Molecular Biology},
volume={3},
number={1},
pages={1--23},
year={2004}
}
@misc{vdl2003unifiedcv,
title={Unified cross-validation methodology for selection among estimators
and a general cross-validated adaptive epsilon-net estimator: Finite sample
oracle inequalities and examples},
author={{van der Laan}, Mark J and Dudoit, Sandrine},
year={2003},
publisher={bepress}
}
@article{vdl2006cross,
title={The cross-validated adaptive epsilon-net estimator},
author={{van der Laan}, Mark J and Dudoit, Sandrine and {van der Vaart}, Aad
W},
journal={Statistics \& Decisions},
volume={24},
number={3},
pages={373--395},
year={2006}
}
@article{dudoit2005asymptotics,
title={Asymptotics of cross-validated risk estimation in estimator selection
and performance assessment},
author={Dudoit, Sandrine and {van der Laan}, Mark J},
journal={Statistical Methodology},
volume={2},
number={2},
pages={131--154},
year={2005},
publisher={Elsevier}
}
@article{vaart2006oracle,
title={Oracle inequalities for multi-fold cross validation},
author={{van der Vaart}, Aad W and Dudoit, Sandrine and {van der Laan}, Mark
J},
journal={Statistics \& Decisions},
volume={24},
number={3},
pages={351--371},
year={2006}
}
@article{wolpert1992stacked,
title={Stacked generalization},
author={Wolpert, David H},
journal={Neural networks},
volume={5},
number={2},
pages={241--259},
year={1992},
publisher={Elsevier}
}
@article{pollard2008supervised,
title={Supervised distance matrices},
author={Pollard, Katherine S and van der Laan, Mark J},
journal={Statistical applications in genetics and molecular biology},
volume={7},
number={1},
year={2008},
publisher={De Gruyter}
}