-
1
-
-
84858376593
-
The impact of the gut microbiota on human health: An integrative view
-
Clemente, J.C., Ursell, L.K., Parfrey, L.W. & Knight, R. The impact of the gut microbiota on human health: an integrative view. Cell 148, 1258-1270 (2012).
-
(2012)
Cell
, vol.148
, pp. 1258-1270
-
-
Clemente, J.C.1
Ursell, L.K.2
Parfrey, L.W.3
Knight, R.4
-
2
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
-
3
-
-
84862286169
-
A framework for human microbiome research
-
The Human Microbiome Project Consortium
-
The Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486, 215-221 (2012).
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
-
4
-
-
84867074831
-
A metagenome-wide association study of gut microbiota in type 2 diabetes
-
Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55-60 (2012).
-
(2012)
Nature
, vol.490
, pp. 55-60
-
-
Qin, J.1
-
5
-
-
84878709716
-
Gut metagenome in European women with normal, impaired and diabetic glucose control
-
Karlsson, F.H. et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498, 99-103 (2013).
-
(2013)
Nature
, vol.498
, pp. 99-103
-
-
Karlsson, F.H.1
-
6
-
-
84883110880
-
Richness of human gut microbiome correlates with metabolic markers
-
Le Chatelier, E. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541-546 (2013).
-
(2013)
Nature
, vol.500
, pp. 541-546
-
-
Le Chatelier, E.1
-
7
-
-
84905730761
-
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
-
doi:10.1038/nbt.2939 6 July
-
Nielsen, H.B. et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Biotechnol. doi:10.1038/nbt.2939 (6 July 2014).
-
(2014)
Biotechnol
-
-
Nielsen, H.B.1
-
8
-
-
84860477454
-
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing
-
Xiong, X. et al. Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLOS ONE 7, e36009 (2012).
-
(2012)
PLOS ONE
, vol.7
-
-
Xiong, X.1
-
9
-
-
84892828465
-
Diet rapidly and reproducibly alters the human gut microbiome
-
David, L.A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559-563 (2014).
-
(2014)
Nature
, vol.505
, pp. 559-563
-
-
David, L.A.1
-
10
-
-
84870322666
-
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease
-
Erickson, A.R. et al. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLOS ONE 7, e49138 (2012).
-
(2012)
PLOS ONE
, vol.7
-
-
Erickson, A.R.1
-
11
-
-
84905742451
-
Supporting data for the paper: An integrated catalog of reference genes in the human gut microbiome
-
doi:10.5524/100064
-
Li, J. et al. Supporting data for the paper: "An integrated catalog of reference genes in the human gut microbiome." GigaScience Database doi:10.5524/100064 (2014).
-
(2014)
GigaScience Database
-
-
Li, J.1
-
12
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
DOI 10.1093/bioinformatics/btl158
-
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659 (2006). (Pubitemid 43985301)
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
13
-
-
84867634981
-
MOCAT: A metagenomics assembly and gene prediction toolkit
-
Kultima, J.R. et al. MOCAT: a metagenomics assembly and gene prediction toolkit. PLOS ONE 7, e47656 (2012).
-
(2012)
PLOS ONE
, vol.7
-
-
Kultima, J.R.1
-
14
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
DOI 10.1128/AEM.00062-07
-
Wang, Q., Garrity, G.M., Tiedje, J.M. & Cole, J.R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267 (2007). (Pubitemid 47326658)
-
(2007)
Applied and Environmental Microbiology
, vol.73
, Issue.16
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
15
-
-
84891820094
-
IMG 4 version of the integrated microbial genomes comparative analysis system
-
Markowitz, V.M. et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 42, D560-D567 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
-
-
Markowitz, V.M.1
-
16
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh, P.J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480-484 (2009).
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
-
17
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
Kurokawa, K. et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14, 169-181 (2007).
-
(2007)
DNA Res.
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
-
18
-
-
0023526239
-
Estimating the population size for capture-recapture data with unequal catchability
-
Chao, A. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43, 783-791 (1987).
-
(1987)
Biometrics
, vol.43
, pp. 783-791
-
-
Chao, A.1
-
19
-
-
0028562529
-
Estimating population size via sample coverage for closed capture- recapture models
-
Lee, S.M. & Chao, A. Estimating population size via sample coverage for closed capture-recapture models. Biometrics 50, 88-97 (1994). (Pubitemid 24138576)
-
(1994)
Biometrics
, vol.50
, Issue.1
, pp. 88-97
-
-
Lee, S.-M.1
Chao, A.2
-
20
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 265-272
-
-
Li, R.1
-
21
-
-
77955902981
-
Ab initio gene identification in metagenomic sequences
-
Zhu, W., Lomsadze, A. & Borodovsky, M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 38, e132 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Zhu, W.1
Lomsadze, A.2
Borodovsky, M.3
-
22
-
-
84883464181
-
Accurate and universal delineation of prokaryotic species
-
Mende, D.R., Sunagawa, S., Zeller, G. & Bork, P. Accurate and universal delineation of prokaryotic species. Nat. Methods 10, 881-884 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 881-884
-
-
Mende, D.R.1
Sunagawa, S.2
Zeller, G.3
Bork, P.4
-
23
-
-
85027927719
-
Enterotypes of the human gut microbiome
-
Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174-180 (2011).
-
(2011)
Nature
, vol.473
, pp. 174-180
-
-
Arumugam, M.1
-
24
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000). (Pubitemid 30047706)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
25
-
-
84861203603
-
EggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges
-
Powell, S. et al. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 40, D284-D289 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Powell, S.1
-
26
-
-
57349131283
-
Micro-eukaryotic diversity of the human distal gut microbiota: Qualitative assessment using culture-dependent and-independent analysis of faeces
-
Scanlan, P.D. & Marchesi, J.R. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and-independent analysis of faeces. ISME J. 2, 1183-1193 (2008).
-
(2008)
ISME J.
, vol.2
, pp. 1183-1193
-
-
Scanlan, P.D.1
Marchesi, J.R.2
-
27
-
-
77954304079
-
Prokaryotic and eukaryotic diversity of the human gut
-
Marchesi, J.R. Prokaryotic and eukaryotic diversity of the human gut. Adv. Appl. Microbiol. 72, 43-62 (2010).
-
(2010)
Adv. Appl. Microbiol.
, vol.72
, pp. 43-62
-
-
Marchesi, J.R.1
-
28
-
-
83755222630
-
Microbial eukaryotes in the human microbiome: Ecology, evolution, and future directions
-
Parfrey, L.W., Walters, W.A. & Knight, R. Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Front. Microbiol. 2, 153 (2011).
-
(2011)
Front. Microbiol.
, vol.2
, pp. 153
-
-
Parfrey, L.W.1
Walters, W.A.2
Knight, R.3
-
29
-
-
84879744885
-
The long-term stability of the human gut microbiota
-
Faith, J.J. et al. The long-term stability of the human gut microbiota. Science 341, 1237439 (2013).
-
(2013)
Science
, vol.341
, pp. 1237439
-
-
Faith, J.J.1
-
30
-
-
84880050412
-
Country-specific antibiotic use practices impact the human gut resistome
-
Forslund, K. et al. Country-specific antibiotic use practices impact the human gut resistome. Genome Res. 23, 1163-1169 (2013).
-
(2013)
Genome Res
, vol.23
, pp. 1163-1169
-
-
Forslund, K.1
-
31
-
-
84880831180
-
Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota
-
Hu, Y. et al. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat. Commun. 4, 2151 (2013).
-
(2013)
Nat. Commun.
, vol.4
, Issue.2151
-
-
Hu, Y.1
-
32
-
-
77954627922
-
Viruses in the faecal microbiota of monozygotic twins and their mothers
-
Reyes, A. et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334-338 (2010).
-
(2010)
Nature
, vol.466
, pp. 334-338
-
-
Reyes, A.1
-
33
-
-
80053528043
-
The human gut virome: Inter-individual variation and dynamic response to diet
-
Minot, S. et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21, 1616-1625 (2011).
-
(2011)
Genome Res
, vol.21
, pp. 1616-1625
-
-
Minot, S.1
-
34
-
-
79251573217
-
Cryptic prophages help bacteria cope with adverse environments
-
Wang, X. et al. Cryptic prophages help bacteria cope with adverse environments. Nat. Commun. 1, 147 (2010).
-
Nat. Commun.
, vol.1
, Issue.147
, pp. 2010
-
-
Wang, X.1
-
35
-
-
84865169911
-
Going viral: Next-generation sequencing applied to phage populations in the human gut
-
Reyes, A., Semenkovich, N.P., Whiteson, K., Rohwer, F. & Gordon, J.I. Going viral: next-generation sequencing applied to phage populations in the human gut. Nat. Rev. Microbiol. 10, 607-617 (2012).
-
(2012)
Nat. Rev. Microbiol.
, vol.10
, pp. 607-617
-
-
Reyes, A.1
Semenkovich, N.P.2
Whiteson, K.3
Rohwer, F.4
Gordon, J.I.5
-
36
-
-
84880509968
-
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
-
Modi, S.R., Lee, H.H., Spina, C.S. & Collins, J.J. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499, 219-222 (2013).
-
(2013)
Nature
, vol.499
, pp. 219-222
-
-
Modi, S.R.1
Lee, H.H.2
Spina, C.S.3
Collins, J.J.4
-
37
-
-
65549150087
-
Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR
-
Furet, J.-P. et al. Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. FEMS Microbiol. Ecol. 68, 351-362 (2009).
-
(2009)
FEMS Microbiol. Ecol.
, vol.68
, pp. 351-362
-
-
Furet, J.-P.1
-
38
-
-
84872151297
-
A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor
-
Li, A. et al. A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. Biotechnol. Biofuels 6, 3 (2013).
-
(2013)
Biotechnol. Biofuels
, vol.6
, pp. 3
-
-
Li, A.1
-
39
-
-
84888884475
-
Metagenomic species profiling using universal phylogenetic marker genes
-
Sunagawa, S. et al. Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods 10, 1196-1199 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 1196-1199
-
-
Sunagawa, S.1
-
40
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
DOI 10.1126/science.1123061
-
Ciccarelli, F.D. et al. Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287 (2006). (Pubitemid 43334717)
-
(2006)
Science
, vol.311
, Issue.5765
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
Von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
41
-
-
36249021315
-
Genome-wide experimental determination of barriers to horizontal gene transfer
-
DOI 10.1126/science.1147112
-
Sorek, R. et al. Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318, 1449-1452 (2007). (Pubitemid 350208955)
-
(2007)
Science
, vol.318
, Issue.5855
, pp. 1449-1452
-
-
Sorek, R.1
Zhu, Y.2
Creevey, C.J.3
Francino, M.P.4
Bork, P.5
Rubin, E.M.6
-
42
-
-
67650711615
-
SOAP2: An improved ultrafast tool for short read alignment
-
Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-1967 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1966-1967
-
-
Li, R.1
-
43
-
-
84864384245
-
The most wanted" taxa from the human microbiome for whole genome sequencing
-
Fodor, A.A. et al. The "most wanted" taxa from the human microbiome for whole genome sequencing. PLOS ONE 7, e41294 (2012).
-
(2012)
PLOS ONE
, vol.7
-
-
Fodor, A.A.1
-
44
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P.D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541 (2009).
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
-
45
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent, W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
46
-
-
78449297680
-
Smash Community: A metagenomic annotation and analysis tool
-
Arumugam, M., Harrington, E.D., Foerstner, K.U., Raes, J. & Bork, P. SmashCommunity: a metagenomic annotation and analysis tool. Bioinformatics 26, 2977-2978 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2977-2978
-
-
Arumugam, M.1
Harrington, E.D.2
Foerstner, K.U.3
Raes, J.4
Bork, P.5
-
47
-
-
77953050946
-
A catalog of reference genomes from the human microbiome
-
Nelson, K.E. et al. A catalog of reference genomes from the human microbiome. Science 328, 994-999 (2010).
-
(2010)
Science
, vol.328
, pp. 994-999
-
-
Nelson, K.E.1
-
48
-
-
0034764307
-
SSAHA: A fast search method for large DNA databases
-
DOI 10.1101/gr.194201
-
Ning, Z., Cox, A.J. & Mullikin, J.C. SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725-1729 (2001). (Pubitemid 33040499)
-
(2001)
Genome Research
, vol.11
, Issue.10
, pp. 1725-1729
-
-
Ning, Z.1
Cox, A.J.2
Mullikin, J.C.3
-
49
-
-
0003200806
-
The Asia Pacific perspective: Redefining obesity and its treatment
-
World Health Organization Western Pacific Region & WHO/IASO/IOTF Ltd.
-
World Health Organization Western Pacific Region & WHO/IASO/IOTF. The Asia Pacific perspective: redefining obesity and its treatment. Heal. Commun. Aust. Pty. Ltd. (2000) at http://www.wpro.who.int/nutrition/documents/ Redefining-obesity/en/index.html.
-
(2000)
Heal. Commun. Aust. Pty
-
-
-
50
-
-
0347992980
-
The New BMI Criteria for Asians by the Regional Office for the Western Pacific Region of WHO are Suitable for Screening of Overweight to Prevent Metabolic Syndrome in Elder Japanese Workers
-
DOI 10.1539/joh.45.335
-
Anuurad, E. et al. The new BMI criteria for Asians by the regional office for the western pacific region of WHO are suitable for screening of overweight to prevent metabolic syndrome in elder Japanese workers. J. Occup. Health 45, 335-343 (2003). (Pubitemid 38036188)
-
(2003)
Journal of Occupational Health
, vol.45
, Issue.6
, pp. 335-343
-
-
Anuurad, E.1
Shiwaku, K.2
Nogi, A.3
Kitajima, K.4
Enkhmaa, B.5
Shimono, K.6
Yamane, Y.7
-
51
-
-
0032702909
-
Prediction of hypertension, diabetes, dyslipidaemia or albuminuria using simple anthropometric indexes in Hong Kong Chinese
-
Ko, G.T., Chan, J.C., Cockram, C.S. & Woo, J. Prediction of hypertension, diabetes, dyslipidaemia or albuminuria using simple anthropometric indexes in Hong Kong Chinese. Int. J. Obes. Relat. Metab. Disord. 23, 1136-1142 (1999).
-
(1999)
Int. J. Obes. Relat. Metab. Disord.
, vol.23
, pp. 1136-1142
-
-
Ko, G.T.1
Chan, J.C.2
Cockram, C.S.3
Woo, J.4
-
53
-
-
0042424602
-
Statistical significance for genome-wide studies
-
Storey, J.D. & Tibshirani, R. Statistical significance for genome-wide studies. Proc. Natl. Acad. Sci. USA 100, 9440-9445 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
|