-
1
-
-
72949091232
-
Bacterial community variation in human body habitats across space and time
-
Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, et al. (2009) Bacterial community variation in human body habitats across space and time. Science 326: 1694–1697. doi: 10.1126/science.1177486 19892944
-
(2009)
Science
, vol.326
, pp. 1694-1697
-
-
Costello, E.K.1
Lauber, C.L.2
Hamady, M.3
Fierer, N.4
Gordon, J.I.5
-
2
-
-
84883864245
-
Meta-analyses of studies of the human microbiota
-
Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, et al. (2013) Meta-analyses of studies of the human microbiota. Genome research 23: 1704–1714. doi: 10.1101/gr.151803.112 23861384
-
(2013)
Genome research
, vol.23
, pp. 1704-1714
-
-
Lozupone, C.A.1
Stombaugh, J.2
Gonzalez, A.3
Ackermann, G.4
Wendel, D.5
-
3
-
-
79952763661
-
Succession of microbial consortia in the developing infant gut microbiome
-
Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, et al. (2011) Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences of the United States of America 108 Suppl 1: 4578–4585. doi: 10.1073/pnas.1000081107 20668239
-
(2011)
Proceedings of the National Academy of Sciences of the United States of America
, vol.108
, pp. 4578-4585
-
-
Koenig, J.E.1
Spor, A.2
Scalfone, N.3
Fricker, A.D.4
Stombaugh, J.5
-
4
-
-
84864722033
-
Gut microbiota composition correlates with diet and health in the elderly
-
Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM, et al. (2012) Gut microbiota composition correlates with diet and health in the elderly. Nature 488: 178–184. doi: 10.1038/nature11319 22797518
-
(2012)
Nature
, vol.488
, pp. 178-184
-
-
Claesson, M.J.1
Jeffery, I.B.2
Conde, S.3
Power, S.E.4
O'Connor, E.M.5
-
5
-
-
84862141704
-
Human gut microbiome viewed across age and geography
-
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, et al. (2012) Human gut microbiome viewed across age and geography. Nature 486: 222–227. doi: 10.1038/nature11053 22699611
-
(2012)
Nature
, vol.486
, pp. 222-227
-
-
Yatsunenko, T.1
Rey, F.E.2
Manary, M.J.3
Trehan, I.4
Dominguez-Bello, M.G.5
-
6
-
-
77957075815
-
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
-
De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, et al. (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences of the United States of America 107: 14691–14696. doi: 10.1073/pnas.1005963107 20679230
-
(2010)
Proceedings of the National Academy of Sciences of the United States of America
, vol.107
, pp. 14691-14696
-
-
De Filippo, C.1
Cavalieri, D.2
Di Paola, M.3
Ramazzotti, M.4
Poullet, J.B.5
-
7
-
-
84872246853
-
Metagenomic analyses of alcohol induced pathogenic alterations in the intestinal microbiome and the effect of Lactobacillus rhamnosus GG treatment
-
Bull-Otterson L, Feng W, Kirpich I, Wang Y, Qin X, et al. (2013) Metagenomic analyses of alcohol induced pathogenic alterations in the intestinal microbiome and the effect of Lactobacillus rhamnosus GG treatment. PloS one 8: e53028. doi: 10.1371/journal.pone.0053028 23326376
-
(2013)
PloS one
, vol.8
, pp. e53028
-
-
Bull-Otterson, L.1
Feng, W.2
Kirpich, I.3
Wang, Y.4
Qin, X.5
-
8
-
-
79952756960
-
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
-
Dethlefsen L, Relman DA, (2011) Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academy of Sciences of the United States of America 108 Suppl 1: 4554–4561. doi: 10.1073/pnas.1000087107 20847294
-
(2011)
Proceedings of the National Academy of Sciences of the United States of America
, vol.108
, pp. 4554-4561
-
-
Dethlefsen, L.1
Relman, D.A.2
-
9
-
-
84864300619
-
Inflammatory bowel disease in Asia: a systematic review
-
Prideaux L, Kamm MA, De Cruz PP, Chan FK, Ng SC, (2012) Inflammatory bowel disease in Asia: a systematic review. Journal of gastroenterology and hepatology 27: 1266–1280. doi: 10.1111/j.1440-1746.2012.07150.x 22497584
-
(2012)
Journal of gastroenterology and hepatology
, vol.27
, pp. 1266-1280
-
-
Prideaux, L.1
Kamm, M.A.2
De Cruz, P.P.3
Chan, F.K.4
Ng, S.C.5
-
10
-
-
82955233474
-
Treating Clostridium difficile infection with fecal microbiota transplantation
-
Bakken JS, Borody T, Brandt LJ, Brill JV, Demarco DC, et al. (2011) Treating Clostridium difficile infection with fecal microbiota transplantation. Clinical gastroenterology and hepatology: the official clinical practice journal of the American Gastroenterological Association 9: 1044–1049. doi: 10.1016/j.cgh.2011.08.014 21871249
-
(2011)
Clinical gastroenterology and hepatology: the official clinical practice journal of the American Gastroenterological Association
, vol.9
, pp. 1044-1049
-
-
Bakken, J.S.1
Borody, T.2
Brandt, L.J.3
Brill, J.V.4
Demarco, D.C.5
-
11
-
-
84857067037
-
Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis
-
Buffie CG, Jarchum I, Equinda M, Lipuma L, Gobourne A, et al. (2012) Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infection and immunity 80: 62–73. doi: 10.1128/IAI.05496-11 22006564
-
(2012)
Infection and immunity
, vol.80
, pp. 62-73
-
-
Buffie, C.G.1
Jarchum, I.2
Equinda, M.3
Lipuma, L.4
Gobourne, A.5
-
12
-
-
85027927719
-
Enterotypes of the human gut microbiome
-
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, et al. (2011) Enterotypes of the human gut microbiome. Nature 473: 174–180. doi: 10.1038/nature09944 21508958
-
(2011)
Nature
, vol.473
, pp. 174-180
-
-
Arumugam, M.1
Raes, J.2
Pelletier, E.3
Le Paslier, D.4
Yamada, T.5
-
13
-
-
84873510063
-
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets
-
Koren O, Knights D, Gonzalez A, Waldron L, Segata N, et al. (2013) A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS computational biology 9: e1002863. doi: 10.1371/journal.pcbi.1002863 23326225
-
(2013)
PLoS computational biology
, vol.9
, pp. e1002863
-
-
Koren, O.1
Knights, D.2
Gonzalez, A.3
Waldron, L.4
Segata, N.5
-
14
-
-
84904019414
-
Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate
-
Bokulich NA, Thorngate JH, Richardson PM, Mills DA, (2013) Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. Proceedings of the National Academy of Sciences of the United States of America.
-
(2013)
Proceedings of the National Academy of Sciences of the United States of America
-
-
Bokulich, N.A.1
Thorngate, J.H.2
Richardson, P.M.3
Mills, D.A.4
-
15
-
-
84888865593
-
Differential abundance analysis for microbial marker-gene surveys
-
Paulson JN, Stine OC, Bravo HC, Pop M, (2013) Differential abundance analysis for microbial marker-gene surveys. Nature methods 10: 1200–1202. doi: 10.1038/nmeth.2658 24076764
-
(2013)
Nature methods
, vol.10
, pp. 1200-1202
-
-
Paulson, J.N.1
Stine, O.C.2
Bravo, H.C.3
Pop, M.4
-
16
-
-
67650021209
-
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
-
Hamady M, Knight R, (2009) Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome research 19: 1141–1152. doi: 10.1101/gr.085464.108 19383763
-
(2009)
Genome research
, vol.19
, pp. 1141-1152
-
-
Hamady, M.1
Knight, R.2
-
17
-
-
84859972408
-
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
-
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, et al. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 109: 6241–6246. doi: 10.1073/pnas.1117018109 22454494
-
(2012)
Proceedings of the National Academy of Sciences of the United States of America
, vol.109
, pp. 6241-6246
-
-
Schoch, C.L.1
Seifert, K.A.2
Huhndorf, S.3
Robert, V.4
Spouge, J.L.5
-
18
-
-
84866174523
-
Genomic approaches to studying the human microbiota
-
Weinstock GM, (2012) Genomic approaches to studying the human microbiota. Nature 489: 250–256. doi: 10.1038/nature11553 22972298
-
(2012)
Nature
, vol.489
, pp. 250-256
-
-
Weinstock, G.M.1
-
19
-
-
29144464937
-
UniFrac: a new phylogenetic method for comparing microbial communities
-
Lozupone C, Knight R, (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Applied and environmental microbiology 71: 8228–8235. 16332807
-
(2005)
Applied and environmental microbiology
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
20
-
-
33947269742
-
Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities
-
Lozupone CA, Hamady M, Kelley ST, Knight R, (2007) Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Applied and environmental microbiology 73: 1576–1585. 17220268
-
(2007)
Applied and environmental microbiology
, vol.73
, pp. 1576-1585
-
-
Lozupone, C.A.1
Hamady, M.2
Kelley, S.T.3
Knight, R.4
-
22
-
-
0141990695
-
Theoretical and Empirical Analysis of ReliefF and RReliefF
-
Robnik-Sikonja M, Kononenko I, (2003) Theoretical and Empirical Analysis of ReliefF and RReliefF. Machine Learning 53: 23–69.
-
(2003)
Machine Learning
, vol.53
, pp. 23-69
-
-
Robnik-Sikonja, M.1
Kononenko, I.2
-
23
-
-
0002154022
-
A new method for non-parametric multivariate analysis of variance
-
Anderson MJ, (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecology 26: 32–46.
-
(2001)
Austral Ecology
, vol.26
, pp. 32-46
-
-
Anderson, M.J.1
-
24
-
-
0027804103
-
Non-parametric multivariate analysis of changes in community structure
-
Clarke KR, (1993) Non-parametric multivariate analysis of changes in community structure. Australian Journal of Ecology 18: 117–143.
-
(1993)
Australian Journal of Ecology
, vol.18
, pp. 117-143
-
-
Clarke, K.R.1
-
25
-
-
84923080032
-
Gut microbiome of the Hadza hunter-gatherers
-
Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, et al. (2014) Gut microbiome of the Hadza hunter-gatherers. Nature communications 5: 3654. doi: 10.1038/ncomms4654 24736369
-
(2014)
Nature communications
, vol.5
, pp. 3654
-
-
Schnorr, S.L.1
Candela, M.2
Rampelli, S.3
Centanni, M.4
Consolandi, C.5
-
26
-
-
79251625980
-
Supervised classification of human microbiota
-
Knights D, Costello EK, Knight R, (2011) Supervised classification of human microbiota. FEMS microbiology reviews 35: 343–359. doi: 10.1111/j.1574-6976.2010.00251.x 21039646
-
(2011)
FEMS microbiology reviews
, vol.35
, pp. 343-359
-
-
Knights, D.1
Costello, E.K.2
Knight, R.3
-
27
-
-
84923857557
-
A comprehensive evaluation of multicategory classification methods for microbiomic data
-
Statnikov A, Henaff M, Narendra V, Konganti K, Li Z, et al. (2013) A comprehensive evaluation of multicategory classification methods for microbiomic data. Microbiome 1: 11. doi: 10.1186/2049-2618-1-11 24456583
-
(2013)
Microbiome
, vol.1
, pp. 11
-
-
Statnikov, A.1
Henaff, M.2
Narendra, V.3
Konganti, K.4
Li, Z.5
-
28
-
-
84863105536
-
Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease
-
Papa E, Docktor M, Smillie C, Weber S, Preheim SP, et al. (2012) Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PloS one 7: e39242. doi: 10.1371/journal.pone.0039242 22768065
-
(2012)
PloS one
, vol.7
, pp. e39242
-
-
Papa, E.1
Docktor, M.2
Smillie, C.3
Weber, S.4
Preheim, S.P.5
-
29
-
-
77950904616
-
Forensic identification using skin bacterial communities
-
Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, et al. (2010) Forensic identification using skin bacterial communities. Proceedings of the National Academy of Sciences of the United States of America 107: 6477–6481. doi: 10.1073/pnas.1000162107 20231444
-
(2010)
Proceedings of the National Academy of Sciences of the United States of America
, vol.107
, pp. 6477-6481
-
-
Fierer, N.1
Lauber, C.L.2
Zhou, N.3
McDonald, D.4
Costello, E.K.5
-
30
-
-
79959383523
-
Metagenomic biomarker discovery and explanation
-
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, et al. (2011) Metagenomic biomarker discovery and explanation. Genome biology 12: R60. doi: 10.1186/gb-2011-12-6-r60 21702898
-
(2011)
Genome biology
, vol.12
, pp. R60
-
-
Segata, N.1
Izard, J.2
Waldron, L.3
Gevers, D.4
Miropolsky, L.5
-
31
-
-
84894519300
-
Phylogeny-based classification of microbial communities
-
Tanaseichuk O, Borneman J, Jiang T, (2014) Phylogeny-based classification of microbial communities. Bioinformatics 30: 449–456. doi: 10.1093/bioinformatics/btt700 24369151
-
(2014)
Bioinformatics
, vol.30
, pp. 449-456
-
-
Tanaseichuk, O.1
Borneman, J.2
Jiang, T.3
-
32
-
-
9544250384
-
Comparing two K-category assignments by a K-category correlation coefficient
-
Gorodkin J, (2004) Comparing two K-category assignments by a K-category correlation coefficient. Computational biology and chemistry 28: 367–374. 15556477
-
(2004)
Computational biology and chemistry
, vol.28
, pp. 367-374
-
-
Gorodkin, J.1
-
33
-
-
84926328970
-
-
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads.
-
-
-
-
34
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R, (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194–2200. doi: 10.1093/bioinformatics/btr381 21700674
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
35
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and environmental microbiology 72: 5069–5072. 16820507
-
(2006)
Applied and environmental microbiology
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
-
36
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and environmental microbiology 73: 5261–5267. 17586664
-
(2007)
Applied and environmental microbiology
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
37
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460–2461. doi: 10.1093/bioinformatics/btq461 20709691
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
38
-
-
75249107844
-
PyNAST: a flexible tool for aligning sequences to a template alignment
-
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, et al. (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266–267. doi: 10.1093/bioinformatics/btp636 19914921
-
(2010)
Bioinformatics
, vol.26
, pp. 266-267
-
-
Caporaso, J.G.1
Bittinger, K.2
Bushman, F.D.3
DeSantis, T.Z.4
Andersen, G.L.5
-
39
-
-
77949718257
-
FastTree 2—approximately maximum-likelihood trees for large alignments
-
Price MN, Dehal PS, Arkin AP, (2010) FastTree 2—approximately maximum-likelihood trees for large alignments. PloS one 5: e9490. doi: 10.1371/journal.pone.0009490 20224823
-
(2010)
PloS one
, vol.5
, pp. e9490
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
42
-
-
84926391394
-
-
Breiman L, Friedman JH, Olshen RA, Stone CJ, trees R (1984) Classification and Regression Trees: Wads-worth & Brooks/Cole Advanced Books & Software.
-
-
-
-
43
-
-
77954202497
-
DendroPy: a Python library for phylogenetic computing
-
Sukumaran J, Holder MT, (2010) DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569–1571. doi: 10.1093/bioinformatics/btq228 20421198
-
(2010)
Bioinformatics
, vol.26
, pp. 1569-1571
-
-
Sukumaran, J.1
Holder, M.T.2
|