This repository has been archived by the owner on Nov 20, 2018. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathmain.bib
254 lines (253 loc) · 10.6 KB
/
main.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
@preamble{ "\newcommand{\noopsort}[1]{} " }
@article{sanger_two_1965,
title = {A two-dimensional fractionation procedure for radioactive nucleotides},
journal = {J Mol Biol},
volume = {13},
number = {2},
pages = {373--IN4},
year = {1965},
doi = {10.1016/S0022-2836(65)80104-8},
url = {http://www.sciencedirect.com/science/article/pii/S0022283665801048},
author = {Sanger, F. and Brownlee, G. G. and Barrell, B. G.}
}
@article{pace_phylogeny_2012,
author = {Pace, N. R. and Sapp, J. and Goldenfeld, N.},
title = {Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life},
volume = {109},
number = {4},
pages = {1011--1018},
year = {2012},
doi = {10.1073/pnas.1109716109},
url = {http://www.pnas.org/content/109/4/1011.abstract},
journal = {Proc Natl Acad Sci USA}
}
@article{woese_phylogenetic_1977,
author = {Woese, C. R. and Fox, G. E.},
title = {Phylogenetic structure of the prokaryotic domain: The primary kingdoms},
volume = {74},
number = {11},
pages = {5088--5090},
year = {1977},
doi = {10.1073/pnas.74.11.5088},
url = {http://www.pnas.org/content/74/11/5088.abstract},
journal = {Proc Natl Acad Sci USA}
}
@article{case_use_2007,
author = {Case, R. J. and Boucher, Y. and Dahll\"{o}f, I. and Holmstr\"{o}m, C. and Doolittle, W. F. and Kjelleberg, S.},
title = {Use of 16{S} r{RNA} and rpo{B} Genes as Molecular Markers for Microbial Ecology Studies},
volume = {73},
number = {1},
pages = {278--288},
year = {2007},
doi = {10.1128/AEM.01177-06},
url = {http://aem.asm.org/content/73/1/278.abstract},
journal = {Appl Environ Microbiol}
}
@article{giovannoni_genetic_1990,
author = {Giovannoni, S. J. and Britschgi, T. B. and Moyer, C. L. and Field, K. G.},
title = {Genetic diversity in {Sargasso} {Sea} bacterioplankton},
journal = {Nature},
year = {1990},
volume = {345},
pages = {60--63},
doi = {10.1038/345060a0}
}
@article{hamady_error_2008,
author = {Hamady, M. and Walker, J. J. and Harris, J. K. and Gold, N. J. and Knight, R.},
title = {Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex},
journal = {Nat Meth},
year = {2008},
volume = {5},
number = {3},
pages = {235--237},
doi = {10.1038/nmeth.1184},
url = {http://dx.doi.org/10.1038/nmeth.1184}
}
@article{kassam_fecal_2013,
author = {Kassam, Z. and Lee, C. H. and Yuan, Y. and Hunt, R. H.},
title = {Fecal Microbiota Transplantation for \textit{{Clostridium} difficile} Infection: Systematic Review and Meta-Analysis},
journal = {Am J Gastroenterol},
year = {2013},
volume = {108},
number = {4},
pages = {500--508},
doi = {10.1038/ajg.2013.59}
}
@article{smits_therapeutic_2013,
title = {Therapeutic Potential of Fecal Microbiota Transplantation},
journal = {Gastroenterology},
volume = {145},
number = {5},
pages = {946--953},
year = {2013},
doi = {10.1053/j.gastro.2013.08.058},
url = {http://www.sciencedirect.com/science/article/pii/S0016508513012791},
author = {Smits, L. P. and Bouter, K. E. C. and de {V}os, W. M. and Borody, T. J. and Nieuwdorp, M.}
}
@article{moayyedi_fecal_2015,
author = {Moayyedi, P. and Surette, M. G. and Kim, P. T. and Libertucci, J. and Wolfe, M. and Onischi, C. and Armstrong, D. and Marshall, J. K. and Kassam, Z. and Reinisch, W. and Lee, C. H.},
title = {Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial},
journal = {Gastroenterology},
year = {2015},
volume = {149},
number = {1},
pages = {102--109.e6},
doi = {10.1053/j.gastro.2015.04.001},
url = {http://dx.doi.org/10.1053/j.gastro.2015.04.001}
}
@article{rossen_findings_2015,
title = {Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis},
journal = {Gastroenterology},
volume = {149},
number = {1},
pages = {110--118},
year = {2015},
doi = {10.1053/j.gastro.2015.03.045},
author = {Rossen, N. G. and Fuentes, S. and van der Spek, M. J. and Tijssen, J. G. and Hartman, J. H. A. and Duflou, A. and L\"{o}wenberg, M. and van den Brink, G. R. and Mathus-Vliegen, E. M. H. and de Vos, W. M. and Zoetendal, E. G. and D'Haens, G. R. and Ponsioen, C. Y.}
}
@article{anders_high_2010,
author = {Anders, S. and Huber, W.},
title = {Differential expression analysis for sequence count data},
journal = {Genome Biol},
year = {2010},
volume = {11},
number = {10},
pages = {1--12},
doi = {10.1186/gb-2010-11-10-r106},
url = {http://dx.doi.org/10.1186/gb-2010-11-10-r106}
}
@article{segata_metagenomic_2011,
author = {Segata, N. and Izard, J. and Waldron, L. and Gevers, D. and Miropolsky, L. and Garrett, W. S. and Huttenhower, C.},
title = {Metagenomic biomarker discovery and explanation},
journal = {Genome Biol},
year = {2011},
volume = {12},
number = {6},
pages = {1--18},
doi = {10.1186/gb-2011-12-6-r60},
url = {http://dx.doi.org/10.1186/gb-2011-12-6-r60}
}
@article{langille_predictive_2013,
author = {Langille, M. G. I. and Zaneveld, J. and Caporaso, J. G. and McDonald, D. and Knights, D. and Reyes, J. A. and Clemente, J. C. and Burkepile, D. E. and Vega Thurber, R. L. and Knight, R. and Beiko, R. G. and Huttenhower, C.},
title = {Predictive functional profiling of microbial communities using {16S} {rRNA} marker gene sequences},
journal = {Nat Biotech},
year = {2013},
volume = {31},
number = {9},
pages = {814--821},
url = {http://dx.doi.org/10.1038/nbt.2676},
doi = {10.1038/nbt.2676}
}
@article{kembel_incorporating_2012,
title = {Incorporating {16S} Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance},
author = {Kembel, S. W. and Wu, M. and Eisen, J. A. and Green, J. L. and von Mering, C.},
journal = {{PLoS} Comp Biol},
volume = {8},
number = {10},
year = {2012},
doi = {10.1371/journal.pcbi.1002743}
}
@article{hughes_counting_2001,
author = {Hughes, J. B. and Hellmann, J. J. and Ricketts, T. H. and Bohannan, B. J. M.},
title = {Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity},
journal = {Appl Environ Microbiol},
year = {2001},
volume = {67},
number = {10},
pages = {4399--4406},
doi = {10.1128/AEM.67.10.4399-4406.2001}
}
@article{dombrowski_reconstructing_2016,
author = {Dombrowski, N. and Donaho, J. A. and Gutierrez, T. and Seitz, K. W. and Teske, A. P. and Baker, B. J.},
title = {Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the {D}eepwater {H}orizon oil spill},
journal = {Nat Microbiol},
year = {2016},
volume = {1},
pages = {16057},
url = {http://dx.doi.org/10.1038/nmicrobiol.2016.57}
}
@article{jemielita_spatial_2014,
author = {Jemielita, M. and Taormina, M. J. and Burns, A. R. and Hampton, J. S. and Rolig, A. S. and Guillemin, K. and Parthasarathy, R.},
title = {Spatial and Temporal Features of the Growth of a Bacterial Species Colonizing the Zebrafish Gut},
volume = {5},
number = {6},
year = {2014},
doi = {10.1128/mBio.01751-14},
journal = {m{B}io}
}
@article{myrhvold_distributed_2015,
author = {Myhrvold, C. and Kotula, J. W. and Hicks, W. M. and Conway, N. J. and Silver, P. A.},
title = {A distributed cell division counter reveals growth dynamics in the gut microbiota},
journal = {Nat Commun},
year = {2015},
volume = {6},
doi = {10.1038/ncomms10039}
}
@article{goodman_toward_1999,
author = {Goodman, S. N.},
title = {Toward Evidence-Based Medical Statistics. 1: The $P$ Value Fallacy},
journal = {Ann Intern Med},
volume = {130},
number = {12},
pages = {995--1004},
year = {1999},
doi = {10.7326/0003-4819-130-12-199906150-00008}
}
@book{fisher_statistical_1973,
author = {Fisher, R.},
title = {Statistical Methods in Scientific Inference},
year = {1973},
edition = {3rd},
publisher = {Macmillan},
address = {New York}
}
@article{neyman_problem_1933,
author = {Neyman, J. and Pearson, E. S.},
title = {On the Problem of the Most Efficient Tests of Statistical Hypotheses},
volume = {231},
number = {694-706},
pages = {289--337},
year = {1933},
doi = {10.1098/rsta.1933.0009},
journal = {Philos Trans R Soc Lond A}
}
@article{koeth-intestinal-2013,
author = {Koeth, R. A. and Wang, Z. and Levison, B. S. and Buffa, J. A. and Org, E. and Sheehy, B. T. and Britt, E. B. and Fu, X. and Wu, Y. and Li, L. and Smith, J. D. and DiDonato, J. A. and Chen, J. and Li, H. and Wu, G. D. and Lewis, J. D. and Warrier, M. and Brown, J. M. and Krauss, R. M. and Tang, W. H. W. and Bushman, F. D. and Lusis, A. J. and Hazen, S. L.},
title = {Intestinal microbiota metabolism of \textsc{L}-carnitine, a nutrient in red meat, promotes atherosclerosis},
journal = {Nat Med},
year = {2013},
volume = {19},
number = {5},
pages = {576--585},
doi = {10.1038/nm.3145}
}
@article{papa-noninvasive-2012,
title = {Non-Invasive Mapping of the Gastrointestinal Microbiota Identifies Children with Inflammatory Bowel Disease},
author = {Papa, E. and Docktor, M. and Smillie, C. and Weber, S. and Preheim, S. P. and Gever, D. and Giannoukos, G. and Ciulla, D. and Tabbaa, D. and Ingram, J. and Schauer, D. B. and Ward, D. V. and Korzenik, J. R. and Xavier, R. J. and Bousvaros, A. and Alm, E. J.},
journal = {{PLoS ONE}},
volume = {7},
number = {6},
year = {2012},
pages = {e39242},
doi = {10.1371/journal.pone.0039242}
}
@article{sivan-commensal-2015,
author = {Sivan, A. and Corrales, L. and Hubert, N. and Williams, J. B. and Aquino-Michaels, K. and Earley, Z. M. and Benyamin, F. W. and Man Lei, Y. and Jabri, B. and Alegre, M.-L. and Chang, E. B. and Gajewski, T. F.},
title = {Commensal \textit{Bifidobacterium} promotes antitumor immunity and facilitates anti--{PD-L1} efficacy},
volume = {350},
number = {6264},
pages = {1084--1089},
year = {2015},
doi = {10.1126/science.aac4255},
journal = {Science}
}
@article{vetizou-anticancer-2015,
author = {V{\'e}tizou, M. and Pitt, J. M. and Daill{\`e}re, R. and Lepage, P. and Waldschmitt, N. and Flament, C. and Rusakiewicz, S. and Routy, B. and Roberti, M. P. and Duong, C. P. M. and Poirier-Colame, V. and Roux, A. and Becharef, S. and Formenti, S. and Golden, E. and Cording, S. and Eberl, G. and Schlitzer, A. and Ginhoux, F. and Mani, S. and Yamazaki, T. and Jacquelot, N. and Enot, D. P. and B{\'e}rard, M. and Nigou, J. and Opolon, P. and Eggermont, A. and Woerther, P.-L. and Chachaty, E. and Chaput, N. and Robert, C. and Mateus, C. and Kroemer, G. and Raoult, D. and Boneca, I. G. and Carbonnel, F. and Chamaillard, M. and Zitvogel, L.},
title = {Anticancer immunotherapy by {CTLA}-4 blockade relies on the gut microbiota},
volume = {350},
number = {6264},
pages = {1079--1084},
year = {2015},
doi = {10.1126/science.aad1329},
journal = {Science}
}