-
1
-
-
0242384034
-
Review and re-analysis of domain-specific 16S primers
-
Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55: 541-555.
-
(2003)
J Microbiol Methods
, vol.55
, pp. 541-555
-
-
Baker, G.C.1
Smith, J.J.2
Cowan, D.A.3
-
2
-
-
38349026259
-
Differential clustering of bowel biopsy-associated bacterial profiles of specimens collected in Mexico and Canada: what do these profiles represent?
-
Bibiloni R, Tandon P, Vargas-Voracka F, Barreto-Zuniga R, Lupian-Sanchez A, Rico-Hinojosa MA, Guban J, Fedorak R, Tannock GW (2008) Differential clustering of bowel biopsy-associated bacterial profiles of specimens collected in Mexico and Canada: what do these profiles represent? J Med Microbiol 57: 111-117.
-
(2008)
J Med Microbiol
, vol.57
, pp. 111-117
-
-
Bibiloni, R.1
Tandon, P.2
Vargas-Voracka, F.3
Barreto-Zuniga, R.4
Lupian-Sanchez, A.5
Rico-Hinojosa, M.A.6
Guban, J.7
Fedorak, R.8
Tannock, G.W.9
-
3
-
-
0023526239
-
Estimating the population size for capture-recapture data with unequal catchability
-
Chao A (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43: 783-791.
-
(1987)
Biometrics
, vol.43
, pp. 783-791
-
-
Chao, A.1
-
4
-
-
76849116160
-
A molecular analysis of fecal and mucosal bacterial communities in irritable bowel syndrome
-
Codling C, O'Mahony L, Shanahan F, Quigley EM, Marchesi JR (2010) A molecular analysis of fecal and mucosal bacterial communities in irritable bowel syndrome. Dig Dis Sci 55: 392-397.
-
(2010)
Dig Dis Sci
, vol.55
, pp. 392-397
-
-
Codling, C.1
O'Mahony, L.2
Shanahan, F.3
Quigley, E.M.4
Marchesi, J.R.5
-
5
-
-
33846072878
-
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
-
Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35: D169-D172.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Cole, J.R.1
Chai, B.2
Farris, R.J.3
Wang, Q.4
Kulam-Syed-Mohideen, A.S.5
McGarrell, D.M.6
Bandela, A.M.7
Cardenas, E.8
Garrity, G.M.9
Tiedje, J.M.10
-
6
-
-
58149200948
-
The ribosomal database project: improved alignments and new tools for rRNA analysis
-
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
Fish, J.4
Chai, B.5
Farris, R.J.6
Kulam-Syed-Mohideen, A.S.7
McGarrell, D.M.8
Marsh, T.9
Garrity, G.M.10
Tiedje, J.M.11
-
7
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 5069-5072
-
-
Desantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Andersen, G.L.10
-
8
-
-
20544444045
-
Diversity of the human intestinal microbial flora
-
Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638.
-
(2005)
Science
, vol.308
, pp. 1635-1638
-
-
Eckburg, P.B.1
Bik, E.M.2
Bernstein, C.N.3
Purdom, E.4
Dethlefsen, L.5
Sargent, M.6
Gill, S.R.7
Nelson, K.E.8
Relman, D.A.9
-
9
-
-
0000122573
-
PHYLIP-Phylogeny Inference Package (Version 3.2)
-
Felsenstein J (1989) PHYLIP-Phylogeny Inference Package (Version 3. 2). Cladistics 5: 164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
10
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359.
-
(2006)
Science
, vol.312
, pp. 1355-1359
-
-
Gill, S.R.1
Pop, M.2
Deboy, R.T.3
Eckburg, P.B.4
Turnbaugh, P.J.5
Samuel, B.S.6
Gordon, J.I.7
Relman, D.A.8
Fraser-Liggett, C.M.9
Nelson, K.E.10
-
11
-
-
0037425743
-
Gut flora in health and disease
-
Guarner F, Malagelada JR (2003) Gut flora in health and disease. Lancet 361: 512-519.
-
(2003)
Lancet
, vol.361
, pp. 512-519
-
-
Guarner, F.1
Malagelada, J.R.2
-
12
-
-
34748886657
-
PAST: Paleontological statistics software package for education and data analysis
-
Hammer Ø, Harper DAT, Ryan PD (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeontol Electronica 4: 9.
-
(2001)
Palaeontol Electronica
, vol.4
, pp. 9
-
-
Hammer, O.1
Harper, D.A.T.2
Ryan, P.D.3
-
13
-
-
34547685588
-
Importance of microbial colonization of the gut in early life to the development of immunity
-
Kelly D, King T, Aminov R (2007) Importance of microbial colonization of the gut in early life to the development of immunity. Mutat Res 622: 58-69.
-
(2007)
Mutat Res
, vol.622
, pp. 58-69
-
-
Kelly, D.1
King, T.2
Aminov, R.3
-
14
-
-
18944401261
-
Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD
-
Lepage P, Seksik P, Sutren M, de la Cochetière MF, Jian R, Marteau P, Doré J (2005) Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD. Inflamm Bowel Dis 11: 473-480.
-
(2005)
Inflamm Bowel Dis
, vol.11
, pp. 473-480
-
-
Lepage, P.1
Seksik, P.2
Sutren, M.3
de la Cochetière, M.F.4
Jian, R.5
Marteau, P.6
Doré, J.7
-
15
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
16
-
-
33748713890
-
UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context
-
Lozupone C, Hamady M, Knight R (2006) UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinform 7: 371.
-
(2006)
BMC Bioinform
, vol.7
, pp. 371
-
-
Lozupone, C.1
Hamady, M.2
Knight, R.3
-
17
-
-
59849113547
-
Microbes in gastrointestinal health and disease
-
Neish AS (2009) Microbes in gastrointestinal health and disease. Gastroenterology 136: 65-80.
-
(2009)
Gastroenterology
, vol.136
, pp. 65-80
-
-
Neish, A.S.1
-
18
-
-
68649113028
-
Vegan: community ecology package
-
http://vegan.r-forge.r-project.org
-
Oksanen J, Kindt R, Legendre P, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H (2008) Vegan: community ecology package. R package version 1. 15-1. http://cran. r-project. org/, http://vegan. r-forge. r-project. org/.
-
(2008)
R package version 1. 15-1
-
-
Oksanen, J.1
Kindt, R.2
Legendre, P.3
O'Hara, R.B.4
Simpson, G.L.5
Solymos P.Stevens, M.H.H.6
Wagner, H.7
-
19
-
-
9944245052
-
In vitro alterations of intestinal bacterial microbiota in fecal samples during storage
-
Ott SJ, Musfeldt M, Timmis KN, Hampe J, Wenderoth DF, Schreiber S (2004) In vitro alterations of intestinal bacterial microbiota in fecal samples during storage. Diagn Microbiol Infect Dis 50: 237-245.
-
(2004)
Diagn Microbiol Infect Dis
, vol.50
, pp. 237-245
-
-
Ott, S.J.1
Musfeldt, M.2
Timmis, K.N.3
Hampe, J.4
Wenderoth, D.F.5
Schreiber, S.6
-
20
-
-
3242809884
-
Microbiota composition of the intestinal mucosa: association with fecal microbiota?
-
Ouwehand AC, Salminen S, Arvola T, Ruuska T, Isolauri E (2004) Microbiota composition of the intestinal mucosa: association with fecal microbiota? Microbiol Immunol 48: 497-500.
-
(2004)
Microbiol Immunol
, vol.48
, pp. 497-500
-
-
Ouwehand, A.C.1
Salminen, S.2
Arvola, T.3
Ruuska, T.4
Isolauri, E.5
-
21
-
-
77950668578
-
EnvDB, a database for describing the environmental distribution of prokaryotic taxa
-
Pignatelli M, Moya A, Tamames J (2009) EnvDB, a database for describing the environmental distribution of prokaryotic taxa. Environ Microbiol Rep 1: 191-197.
-
(2009)
Environ Microbiol Rep
, vol.1
, pp. 191-197
-
-
Pignatelli, M.1
Moya, A.2
Tamames, J.3
-
22
-
-
65449125343
-
Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era
-
Preidis GA, Versalovic J (2009) Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Gastroenterology 136: 2015-2031.
-
(2009)
Gastroenterology
, vol.136
, pp. 2015-2031
-
-
Preidis, G.A.1
Versalovic, J.2
-
23
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich SD, Wang J (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.S.5
Manichanh, C.6
Nielsen, T.7
Pons, N.8
Levenez, F.9
Yamada, T.10
Mende, D.R.11
Li, J.12
Xu, J.13
Li, S.14
Li, D.15
Cao, J.16
Wang, B.17
Liang, H.18
Zheng, H.19
Xie, Y.20
Tap, J.21
Lepage, P.22
Bertalan, M.23
Batto, J.M.24
Hansen, T.25
Le Paslier, D.26
Linneberg, A.27
Nielsen, H.B.28
Pelletier, E.29
Renault, P.30
Sicheritz-Ponten, T.31
Turner, K.32
Zhu, H.33
Yu, C.34
Li, S.35
Jian, M.36
Zhou, Y.37
Li, Y.38
Zhang, X.39
Li, S.40
Qin, N.41
Yang, H.42
Wang, J.43
Brunak, S.44
Doré, J.45
Guarner, F.46
Kristiansen, K.47
Pedersen, O.48
Parkhill, J.49
Weissenbach, J.50
Metahit, C.51
Bork, P.52
Ehrlich, S.D.53
Wang, J.54
more..
-
24
-
-
84907095419
-
R: A language and environment for statistical computing
-
R Development Core Team,ISBN 3-900051-07-0, URL
-
R Development Core Team (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www. R-project. org/.
-
(2009)
R Foundation for Statistical Computing, Vienna, Austria
-
-
-
25
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
Hollister, E.B.6
Lesniewski, R.A.7
Oakley, B.B.8
Parks, D.H.9
Robinson, C.J.10
Sahl, J.W.11
Stres, B.12
Thallinger, G.G.13
van Horn, D.J.14
Weber, C.F.15
-
26
-
-
84856043672
-
A mathematical theory of communication
-
Shannon CE (1948) A mathematical theory of communication. Bell Syst Tech J 27: 379-423.
-
(1948)
Bell Syst Tech J
, vol.27
, pp. 379-423
-
-
Shannon, C.E.1
-
27
-
-
46049086230
-
Analysis of bacterial bowel communities of IBD patients: what has it revealed?
-
Sokol H, Lay C, Seksik P, Tannock GW (2008) Analysis of bacterial bowel communities of IBD patients: what has it revealed? Inflamm Bowel Dis 14: 858-867.
-
(2008)
Inflamm Bowel Dis
, vol.14
, pp. 858-867
-
-
Sokol, H.1
Lay, C.2
Seksik, P.3
Tannock, G.W.4
-
29
-
-
70349233883
-
Towards the human intestinal microbiota phylogenetic core
-
Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Muñoz-Tamayo R, Paslier DL, Nalin R, Dore J, Leclerc M (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11: 2574-2584.
-
(2009)
Environ Microbiol
, vol.11
, pp. 2574-2584
-
-
Tap, J.1
Mondot, S.2
Levenez, F.3
Pelletier, E.4
Caron, C.5
Furet, J.P.6
Ugarte, E.7
Muñoz-Tamayo, R.8
Paslier, D.L.9
Nalin, R.10
Dore, J.11
Leclerc, M.12
-
30
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
-
(2006)
Nature
, vol.444
, pp. 1027-1031
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Mahowald, M.A.3
Magrini, V.4
Mardis, E.R.5
Gordon, J.I.6
-
31
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
Hamady, M.2
Yatsunenko, T.3
Cantarel, B.L.4
Duncan, A.5
Ley, R.E.6
Sogin, M.L.7
Jones, W.J.8
Roe, B.A.9
Affourtit, J.P.10
Egholm, M.11
Henrissat, B.12
Heath, A.C.13
Knight, R.14
Gordon, J.I.15
-
32
-
-
0036300743
-
Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces
-
Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans AD, de Vos WM (2002) Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 68: 3401-3407.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 3401-3407
-
-
Zoetendal, E.G.1
von Wright, A.2
Vilpponen-Salmela, T.3
Ben-Amor, K.4
Akkermans, A.D.5
de Vos, W.M.6
-
33
-
-
54349126970
-
High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota
-
Zoetendal EG, Rajilić-Stojanović M, de Vos WM (2008) High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57: 1605-1615.
-
(2008)
Gut
, vol.57
, pp. 1605-1615
-
-
Zoetendal, E.G.1
Rajilić-Stojanović, M.2
de Vos, W.M.3
|