An integrated catalog of reference genes in the human gut microbiome

Jens Roat Kultima | P. Bork | Qiang Feng | Suisha Liang | Huijue Jia | Dongya Zhang | Junhua Li | Liang Xiao | J. Al-Aama | Huanming Yang | Jian Wang | K. Kristiansen | M. Arumugam | Jun Wang | H. Nielsen | A. S. Juncker | S. Sunagawa | E. Le Chatelier | T. Nielsen | C. Manichanh | Jean-Michel Batto | N. Borruel | F. Casellas | J. Doré | F. Guarner | T. Hansen | S. Kennedy | F. Levenez | N. Pons | O. Pedersen | E. Prifti | J. Tap | S. Tims | Takuji Yamada | P. Renault | S. Brunak | E. Zoetendal | M. Kleerebezem | S. Ehrlich | D. Mende | T. Bruls | M. Leclerc | Huanzi Zhong | Bing Chen | Wenwei Zhang | Weineng Chen | Zhaoxi Zhang | F. Artiguenave | J. Parkhill | Xun Xu | C. Bréchot | M. Rescigno | H. Blottière | E. Varela | M. Derrien | M. Antolín | Jian Wang | T. Hansen | S. Ehrlich | J. Wang | E. Maguin | W. D. de Vos | R. Oozeer | X. Cai | Juan Wang | Hailong Zhao | S. Edris | M. van de Guchte | R. Dervyn | C. Juste | Jun Wang | C. Delorme | Xun Xu | A. Torrejon | Juan Wang | A. Jamet | Sherif Edris | Séverine Layec | É. Pelletier | Q. Feng | G. Denariaz | Xianghang Cai | L. Xiao | J. Al-Aama | Francisco Guarner | Jean Weissenbach | F. Guarner | C. M'rini | D. Lepaslier | É. Guédon | Jian Wang | Jian Wang | J. V. H. van Hylckama Vlieg | Nicolas Emmanuelle Jean-Michel Sean Florence Yohanan Eric Pons Le Chatelier Batto Kennedy Haimet Wi | Florence Haimet | Yohanan Winogradski | K. Turner | P. Viega | J. Knoll | Alexandre Mérieux | Antonella Cultrone | Ghalia Khaci | Gaetana Vandemeulebrouck | Nicolas Sanchez | Jun Wang | Edi Prifti | Juan Wang | Juan Wang | Juan Wang | Juan Wang | Manimozhiyan Arumugam | Jian Wang | Juan Wang | Juan Wang | Jun Wang | Juan Wang | Juan Wang | Juan Wang | Juan Wang | Juan Wang

[1]  Jennifer L. O'Day Statistical Significance for Genome Wide Studies Under Unequal Variance , 2015 .

[2]  Jens Roat Kultima,et al.  Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes , 2014, Nature Biotechnology.

[3]  Lawrence A. David,et al.  Diet rapidly and reproducibly alters the human gut microbiome , 2013, Nature.

[4]  I-Min A. Chen,et al.  IMG 4 version of the integrated microbial genomes comparative analysis system , 2013, Nucleic Acids Res..

[5]  Alexandros Stamatakis,et al.  Metagenomic species profiling using universal phylogenetic marker genes , 2013, Nature Methods.

[6]  P. Bork,et al.  Accurate and universal delineation of prokaryotic species , 2013, Nature Methods.

[7]  P. Bork,et al.  Richness of human gut microbiome correlates with metabolic markers , 2013, Nature.

[8]  Jian Wang,et al.  Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota , 2013, Nature Communications.

[9]  J. Clemente,et al.  The Long-Term Stability of the Human Gut Microbiota , 2013 .

[10]  Peer Bork,et al.  Country-specific antibiotic use practices impact the human gut resistome , 2013, Genome research.

[11]  Fredrik H. Karlsson,et al.  Gut metagenome in European women with normal, impaired and diabetic glucose control , 2013, Nature.

[12]  J. Collins,et al.  Antibiotic Treatment Expands the Resistance Reservoir and Ecological Network of the Phage Metagenome , 2013, Nature.

[13]  Shizhong Li,et al.  A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor , 2013, Biotechnology for Biofuels.

[14]  Brandi L. Cantarel,et al.  Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease , 2012, PloS one.

[15]  Peer Bork,et al.  MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit , 2012, PloS one.

[16]  Qiang Feng,et al.  A metagenome-wide association study of gut microbiota in type 2 diabetes , 2012, Nature.

[17]  Forest Rohwer,et al.  Going viral: next-generation sequencing applied to phage populations in the human gut , 2012, Nature Reviews Microbiology.

[18]  B. Birren,et al.  The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing , 2012, PloS one.

[19]  Katherine H. Huang,et al.  A framework for human microbiome research , 2012, Nature.

[20]  John Parkinson,et al.  Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing , 2012, PloS one.

[21]  J. Clemente,et al.  The Impact of the Gut Microbiota on Human Health: An Integrative View , 2012, Cell.

[22]  Damian Szklarczyk,et al.  eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges , 2011, Nucleic Acids Res..

[23]  F. Bushman,et al.  The human gut virome: inter-individual variation and dynamic response to diet. , 2011, Genome research.

[24]  R. Knight,et al.  Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions , 2011, Front. Microbio..

[25]  P. Bork,et al.  Enterotypes of the human gut microbiome , 2011, Nature.

[26]  Qun Ma,et al.  Cryptic prophages help bacteria cope with adverse environments , 2010, Nature communications.

[27]  Peer Bork,et al.  SmashCommunity: a metagenomic annotation and analysis tool , 2010, Bioinform..

[28]  B. Haas,et al.  A Catalog of Reference Genomes from the Human Microbiome , 2010, Science.

[29]  M. Borodovsky,et al.  Ab initio gene identification in metagenomic sequences , 2010, Nucleic acids research.

[30]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[31]  Huanming Yang,et al.  De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.

[32]  J. Marchesi Prokaryotic and eukaryotic diversity of the human gut. , 2010, Advances in applied microbiology.

[33]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[34]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[35]  J. Doré,et al.  Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. , 2009, FEMS microbiology ecology.

[36]  B. Roe,et al.  A core gut microbiome in obese and lean twins , 2008, Nature.

[37]  J. Marchesi,et al.  Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces , 2008, The ISME Journal.

[38]  Peer Bork,et al.  Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer , 2007, Science.

[39]  Hiroshi Mori,et al.  Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes , 2007, DNA research : an international journal for rapid publication of reports on genes and genomes.

[40]  Taraneh Hemami Most wanted , 2007, SIGGRAPH '07.

[41]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[42]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[43]  B. Snel,et al.  Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.

[44]  Kuninori Shiwaku,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 , 2003, Journal of occupational health.

[45]  John D. Storey,et al.  Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[46]  John D. Storey A direct approach to false discovery rates , 2002 .

[47]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[48]  J. Mullikin,et al.  SSAHA: a fast search method for large DNA databases. , 2001, Genome research.

[49]  J. Woo,et al.  Prediction of hypertension, diabetes, dyslipidaemia or albuminuria using simple anthropometric indexes in Hong Kong Chinese , 1999, International Journal of Obesity.

[50]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[51]  A Chao,et al.  Estimating population size via sample coverage for closed capture-recapture models. , 1994, Biometrics.

[52]  A. Chao Estimating the population size for capture-recapture data with unequal catchability. , 1987, Biometrics.