-
2
-
-
85027927719
-
Enterotypes of the human gut microbiome
-
Arumugam M, Raes J, Pelletier E et al. (2011) Enterotypes of the human gut microbiome. Nature 473: 174-180.
-
(2011)
Nature
, vol.473
, pp. 174-180
-
-
Arumugam, M.1
Raes, J.2
Pelletier, E.3
-
4
-
-
78449296237
-
Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors
-
Benson AK, Kelly SA, Legge R et al. (2010) Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. P Natl Acad Sci USA 107: 18933-18938.
-
(2010)
P Natl Acad Sci USA
, vol.107
, pp. 18933-18938
-
-
Benson, A.K.1
Kelly, S.A.2
Legge, R.3
-
5
-
-
77956648022
-
High temporal and inter-individual variation detected in the human ileal microbiota
-
Booijink CCGM, El-Aidy S, Rajilic-Stojanovic M, Heilig HGHJ, Troost FJ, Smidt H, Kleerebezem M, De Vos WM & Zoetendal EG (2010) High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 12: 3213-3227.
-
(2010)
Environ Microbiol
, vol.12
, pp. 3213-3227
-
-
Booijink, C.C.G.M.1
El-Aidy, S.2
Rajilic-Stojanovic, M.3
Heilig, H.G.H.J.4
Troost, F.J.5
Smidt, H.6
Kleerebezem, M.7
De Vos, W.M.8
Zoetendal, E.G.9
-
6
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso JG, Kuczynski J, Stombaugh J et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
-
(2010)
Nat Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
-
8
-
-
79952757721
-
Composition, variability, and temporal stability of the intestinal microbiota of the elderly
-
Claesson MJ, Cusack S, O'Sullivan O et al. (2010) Composition, variability, and temporal stability of the intestinal microbiota of the elderly. P Natl Acad Sci USA 108: 4586-4591.
-
(2010)
P Natl Acad Sci USA
, vol.108
, pp. 4586-4591
-
-
Claesson, M.J.1
Cusack, S.2
O'Sullivan, O.3
-
9
-
-
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(Database issue): D169-D172.
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.DATABASE ISSUE
-
-
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
-
10
-
-
58149200948
-
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
-
Cole JR, Wang Q, Cardenas E et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37(Database issue): D141-D145.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.DATABASE ISSUE
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
-
11
-
-
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, Massart S, Collini S, Pieraccini G & Lionetti P (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. P Natl Acad Sci USA 107: 14691-14696.
-
(2010)
P Natl Acad Sci USA
, vol.107
, pp. 14691-14696
-
-
De Filippo, C.1
Cavalieri, D.2
Di Paola, M.3
Ramazzotti, M.4
Poullet, J.B.5
Massart, S.6
Collini, S.7
Pieraccini, G.8
Lionetti, P.9
-
12
-
-
27744580095
-
Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge
-
De La Cochetiere MF, Durand T, Lepage P, Bourreille A, Galmiche JP & Dore J (2005) Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. J Clin Microbiol 43: 5588-5592.
-
(2005)
J Clin Microbiol
, vol.43
, pp. 5588-5592
-
-
De La Cochetiere, M.F.1
Durand, T.2
Lepage, P.3
Bourreille, A.4
Galmiche, J.P.5
Dore, J.6
-
13
-
-
79952756960
-
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
-
Dethlefsen L & Relman DA (2010) Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. P Natl Acad Sci USA 108: 4554-4561.
-
(2010)
P Natl Acad Sci USA
, vol.108
, pp. 4554-4561
-
-
Dethlefsen, L.1
Relman, D.A.2
-
15
-
-
56849106496
-
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
-
Dethlefsen L, Huse S, Sogin ML & Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6: e280.
-
(2008)
PLoS Biol
, vol.6
-
-
Dethlefsen, L.1
Huse, S.2
Sogin, M.L.3
Relman, D.A.4
-
16
-
-
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.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
17
-
-
0036135946
-
Molecular Monitoring of Succession of Bacterial Communities in Human Neonates
-
Favier CF, Vaughan EE, Vos WMD & Akkermans ADL (2002) Molecular Monitoring of Succession of Bacterial Communities in Human Neonates. Society 68: 219-226.
-
(2002)
Society
, vol.68
, pp. 219-226
-
-
Favier, C.F.1
Vaughan, E.E.2
Vos, W.M.D.3
Akkermans, A.D.L.4
-
18
-
-
0031692488
-
Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes
-
Franks AH, Harmsen HJ, Raangs GC, Jansen GJ, Schut F & Welling GW (1998) Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 64: 3336-3345.
-
(1998)
Appl Environ Microbiol
, vol.64
, pp. 3336-3345
-
-
Franks, A.H.1
Harmsen, H.J.2
Raangs, G.C.3
Jansen, G.J.4
Schut, F.5
Welling, G.W.6
-
19
-
-
0141767040
-
Proper multivariate conditional autoregressive models for spatial data analysis
-
Gelfand A & Vounatsou P (2003) Proper multivariate conditional autoregressive models for spatial data analysis. Biostatistics 4: 11-25.
-
(2003)
Biostatistics
, vol.4
, pp. 11-25
-
-
Gelfand, A.1
Vounatsou, P.2
-
20
-
-
67650992376
-
-
R package version 1.26.0
-
Gentry J, Long L, Gentleman R, Falcon S, Hahne F, Sarkar D & Hansen K (2008) Rgraphviz: Provides Plotting Capabilities for R graph Objects. R package version 1.26.0.
-
(2008)
Rgraphviz: Provides Plotting Capabilities for R graph Objects
-
-
Gentry, J.1
Long, L.2
Gentleman, R.3
Falcon, S.4
Hahne, F.5
Sarkar, D.6
Hansen, K.7
-
21
-
-
0037425743
-
Gut flora in health and disease
-
Guarner F & Malagelada J-R (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
-
22
-
-
0034076597
-
Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods
-
Harmsen HJ, Wildeboer-Veloo AC, Raangs GC, Wagendorp AA, Klijn N, Bindels JG & Welling GW (2000) Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J Pediatr Gastroenterol Nutr 30: 61-67.
-
(2000)
J Pediatr Gastroenterol Nutr
, vol.30
, pp. 61-67
-
-
Harmsen, H.J.1
Wildeboer-Veloo, A.C.2
Raangs, G.C.3
Wagendorp, A.A.4
Klijn, N.5
Bindels, J.G.6
Welling, G.W.7
-
23
-
-
41949094718
-
Is meconium from healthy newborns actually sterile?
-
Jiménez E, Marín ML, Martín R, Odriozola JM, Olivares M, Xaus J, Fernández L & Rodríguez JM (2008) Is meconium from healthy newborns actually sterile? Res Microbiol 159: 187-193.
-
(2008)
Res Microbiol
, vol.159
, pp. 187-193
-
-
Jiménez, E.1
Marín, M.L.2
Martín, R.3
Odriozola, J.M.4
Olivares, M.5
Xaus, J.6
Fernández, L.7
Rodríguez, J.M.8
-
24
-
-
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
-
25
-
-
51849086745
-
Predominant role of host genetics in controlling the composition of gut microbiota
-
Khachatryan ZA, Ktsoyan ZA, Manukyan GP, Kelly D, Ghazaryan KA & Aminov RI (2008) Predominant role of host genetics in controlling the composition of gut microbiota. PLoS One 3: e3064.
-
(2008)
PLoS One
, vol.3
-
-
Khachatryan, Z.A.1
Ktsoyan, Z.A.2
Manukyan, G.P.3
Kelly, D.4
Ghazaryan, K.A.5
Aminov, R.I.6
-
26
-
-
1542469537
-
A bivariate Bayes method for improving the estimates of mortality rates with 2-fold CAR model
-
Kim H, Sun D & Tsutakawa RK (2001) A bivariate Bayes method for improving the estimates of mortality rates with 2-fold CAR model. J Am Stat Assoc 96: 1506-1521.
-
(2001)
J Am Stat Assoc
, vol.96
, pp. 1506-1521
-
-
Kim, H.1
Sun, D.2
Tsutakawa, R.K.3
-
27
-
-
23344442120
-
Obesity alters gut microbial ecology
-
Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD & Gordon JI (2005) Obesity alters gut microbial ecology. P Natl Acad Sci USA 102: 11070-11075.
-
(2005)
P Natl Acad Sci USA
, vol.102
, pp. 11070-11075
-
-
Ley, R.E.1
Backhed, F.2
Turnbaugh, P.3
Lozupone, C.A.4
Knight, R.D.5
Gordon, J.I.6
-
28
-
-
0006407254
-
Winbugs - a Bayesian modelling framework: concepts, structure, and extensibility
-
Lunn DJ, Thomas A, Best N & Spiegelhalter D (2000) Winbugs - a Bayesian modelling framework: concepts, structure, and extensibility. Stat Comput 10: 325-337.
-
(2000)
Stat Comput
, vol.10
, pp. 325-337
-
-
Lunn, D.J.1
Thomas, A.2
Best, N.3
Spiegelhalter, D.4
-
29
-
-
71549146864
-
Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces
-
Mulder IE, Schmidt B, Stokes CR et al. (2009) Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces. BMC Biol 7: 79.
-
(2009)
BMC Biol
, vol.7
, pp. 79
-
-
Mulder, I.E.1
Schmidt, B.2
Stokes, C.R.3
-
30
-
-
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
-
31
-
-
70349255569
-
-
R package version 1.17-2
-
Oksanen J, Blanchet FG, Kindt R, Legendre P, O'Hara RB, Simpson GL, Solymos P, Stevens MHH & Wagner H (2010) vegan: Community Ecology Package. R package version 1.17-2.
-
(2010)
vegan: Community Ecology Package
-
-
Oksanen, J.1
Blanchet, F.G.2
Kindt, R.3
Legendre, P.4
O'Hara, R.B.5
Simpson, G.L.6
Solymos, P.7
Stevens, M.H.H.8
Wagner, H.9
-
32
-
-
34848903220
-
From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data
-
Opgen-Rhein R & Strimmer K (2007) From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data. BMC Syst Biol 1: 37.
-
(2007)
BMC Syst Biol
, vol.1
, pp. 37
-
-
Opgen-Rhein, R.1
Strimmer, K.2
-
34
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin J, Li R, Raes J et al. (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
-
36
-
-
79951480123
-
-
R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria.
-
R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
-
(2010)
R: A Language and Environment for Statistical Computing
-
-
-
38
-
-
15944364151
-
An empirical bayes approach to inferring large-scale gene association networks
-
Schäfer J & Strimmer K (2005a) An empirical bayes approach to inferring large-scale gene association networks. Bioinformatics 21: 754-764.
-
(2005)
Bioinformatics
, vol.21
, pp. 754-764
-
-
Schäfer, J.1
Strimmer, K.2
-
39
-
-
27844521293
-
A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics
-
Schäfer J & Strimmer K (2005b) A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Stat Appl Genet Mol Biol 4:Article32.
-
(2005)
Stat Appl Genet Mol Biol
, vol.4
-
-
Schäfer, J.1
Strimmer, K.2
-
41
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss PD, Westcott SL, Ryabin T et al. (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
-
42
-
-
13444302396
-
R2winbugs: a package for running winbugs from r
-
Sturtz S, Ligges U & Gelman A (2005) R2winbugs: a package for running winbugs from r. J Stat Softw 12: 1-16.
-
(2005)
J Stat Softw
, vol.12
, pp. 1-16
-
-
Sturtz, S.1
Ligges, U.2
Gelman, A.3
-
43
-
-
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
-
44
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh PJ, Hamady M, Yatsunenko T et al. (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
-
46
-
-
2442616728
-
Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers
-
Vanhoutte T, Huys G, Brandt E & Swings J (2004) Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol Ecol 48: 437-446.
-
(2004)
FEMS Microbiol Ecol
, vol.48
, pp. 437-446
-
-
Vanhoutte, T.1
Huys, G.2
Brandt, E.3
Swings, J.4
-
47
-
-
67651121491
-
Chemotherapy treatment in pediatric patients with acute myeloid leukemia receiving antimicrobial prophylaxis leads to a relative increase of colonization with potentially pathogenic bacteria in the gut
-
van Vliet MJ, Tissing WJE, Dun CAJ, Meessen NEL, Kamps WA, de Bont ESJM & Harmsen HJM (2009) Chemotherapy treatment in pediatric patients with acute myeloid leukemia receiving antimicrobial prophylaxis leads to a relative increase of colonization with potentially pathogenic bacteria in the gut. Clin Infect Dis 49: 262-270.
-
(2009)
Clin Infect Dis
, vol.49
, pp. 262-270
-
-
van Vliet, M.J.1
Tissing, W.J.E.2
Dun, C.A.J.3
Meessen, N.E.L.4
Kamps, W.A.5
de Bont, E.S.J.M.6
Harmsen, H.J.M.7
-
48
-
-
34247384151
-
Intestinal bacteria and ageing
-
Woodmansey EJ (2007) Intestinal bacteria and ageing. J Appl Microbiol 102: 1178-1186.
-
(2007)
J Appl Microbiol
, vol.102
, pp. 1178-1186
-
-
Woodmansey, E.J.1
-
49
-
-
0031684010
-
Temperature Gradient Gel Electrophoresis Analysis of 16S rRNA from Human Fecal Samples Reveals Stable and Host-Specific Communities of Active Bacteria
-
Zoetendal EG, Akkermans ADL & Vos WMD (1998) Temperature Gradient Gel Electrophoresis Analysis of 16S rRNA from Human Fecal Samples Reveals Stable and Host-Specific Communities of Active Bacteria. Appl Environ Microbiol 64: 3854-3859.
-
(1998)
Appl Environ Microbiol
, vol.64
, pp. 3854-3859
-
-
Zoetendal, E.G.1
Akkermans, A.D.L.2
Vos, W.M.D.3
|