Strains, functions and dynamics in the expanded Human Microbiome Project

[1]  Suzanne M. Paley,et al.  The MetaCyc database of metabolic pathways and enzymes , 2017, Nucleic Acids Res..

[2]  Duy Tin Truong,et al.  Microbial strain-level population structure and genetic diversity from metagenomes , 2017, Genome research.

[3]  J. Sung,et al.  Prevotella as a Hub for Vaginal Microbiota under the Influence of Host Genetics and Their Association with Obesity. , 2017, Cell host & microbe.

[4]  K. Aagaard,et al.  Maturation of the Infant Microbiome Community Structure and Function Across Multiple Body Sites and in Relation to Mode of Delivery , 2017, Nature Medicine.

[5]  R. Knight,et al.  Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort , 2016, mSystems.

[6]  Emily R. Davenport,et al.  Heritable components of the human fecal microbiome are associated with visceral fat , 2016, Genome Biology.

[7]  K. Honda,et al.  The microbiota in adaptive immune homeostasis and disease , 2016, Nature.

[8]  T. R. Licht,et al.  Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut , 2016, Nature Microbiology.

[9]  J. Raes,et al.  Population-level analysis of gut microbiome variation , 2016, Science.

[10]  D. Kasper,et al.  How colonization by microbiota in early life shapes the immune system , 2016, Science.

[11]  Morris A. Swertz,et al.  Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity , 2016, Science.

[12]  C. Huttenhower,et al.  The healthy human microbiome , 2016, Genome Medicine.

[13]  Robert D. Finn,et al.  The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..

[14]  Duy Tin Truong,et al.  MetaPhlAn2 for enhanced metagenomic taxonomic profiling , 2015, Nature Methods.

[15]  Rob Knight,et al.  ConStrains identifies microbial strains in metagenomic datasets , 2015, Nature Biotechnology.

[16]  Katherine H. Huang,et al.  Identifying personal microbiomes using metagenomic codes , 2015, Proceedings of the National Academy of Sciences.

[17]  Michael Y. Galperin,et al.  Expanded microbial genome coverage and improved protein family annotation in the COG database , 2014, Nucleic Acids Res..

[18]  Peter B. McGarvey,et al.  UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches , 2014, Bioinform..

[19]  Rob Knight,et al.  Temporal variability is a personalized feature of the human microbiome , 2014, Genome Biology.

[20]  Allyson L. Byrd,et al.  Biogeography and individuality shape function in the human skin metagenome , 2014, Nature.

[21]  Jens Roat Kultima,et al.  An integrated catalog of reference genes in the human gut microbiome , 2014, Nature Biotechnology.

[22]  P. Schloss,et al.  Dynamics and associations of microbial community types across the human body , 2014, Nature.

[23]  Curtis Huttenhower,et al.  Functional and phylogenetic assembly of microbial communities in the human microbiome. , 2014, Trends in microbiology.

[24]  Arthur Brady,et al.  MetaRef: a pan-genomic database for comparative and community microbial genomics , 2013, Nucleic Acids Res..

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

[26]  Hongzhe Li,et al.  Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents , 2013, PloS one.

[27]  Shital Patel,et al.  The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters , 2013, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[28]  I. Johansson,et al.  Oral Microbial Profile Discriminates Breast-fed From Formula-fed Infants , 2013, Journal of pediatric gastroenterology and nutrition.

[29]  Erin Beck,et al.  TIGRFAMs and Genome Properties in 2013 , 2012, Nucleic Acids Res..

[30]  Alison S. Waller,et al.  Genomic variation landscape of the human gut microbiome , 2012, Nature.

[31]  Jian Wang,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[32]  F. Raymond,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Ray Meta: scalable de novo metagenome assembly and profiling , 2012 .

[33]  Timothy L. Tickle,et al.  Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment , 2012, Genome Biology.

[34]  Bernard Henrissat,et al.  Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome , 2012, PLoS Comput. Biol..

[35]  Siu-Ming Yiu,et al.  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..

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

[37]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.

[38]  H. Flint,et al.  Microbial degradation of complex carbohydrates in the gut , 2012, Gut microbes.

[39]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[40]  Zaid Abdo,et al.  Temporal Dynamics of the Human Vaginal Microbiota , 2012, Science Translational Medicine.

[41]  D. Relman,et al.  Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome , 2011, The ISME Journal.

[42]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[43]  Alison S. Waller,et al.  Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data , 2012, PloS one.

[44]  Arend Hintze,et al.  Scaling metagenome sequence assembly with probabilistic de Bruijn graphs , 2011, Proceedings of the National Academy of Sciences.

[45]  Yongan Zhao,et al.  RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data , 2011, Bioinform..

[46]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[47]  Hideaki Tanaka,et al.  MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads , 2011, BCB '11.

[48]  Samuel V. Angiuoli,et al.  The IGS Standard Operating Procedure for Automated Prokaryotic Annotation , 2011, Standards in genomic sciences.

[49]  Hideaki Sugawara,et al.  The Sequence Read Archive , 2010, Nucleic Acids Res..

[50]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[51]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[52]  Jonathan Crabtree,et al.  Ergatis: a web interface and scalable software system for bioinformatics workflows , 2010, Bioinform..

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

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

[55]  A. Schwiertz,et al.  Microbiota and SCFA in Lean and Overweight Healthy Subjects , 2010, Obesity.

[56]  W. Verstraete,et al.  Denitrification in human dental plaque , 2010, BMC Biology.

[57]  Geoffrey Burnstock,et al.  The double life of ATP. , 2009, Scientific American.

[58]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[59]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[60]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[61]  Peter B. McGarvey,et al.  UniRef: comprehensive and non-redundant UniProt reference clusters , 2007, Bioinform..

[62]  S. Poulsen,et al.  Haptocorrin in humans , 2007, Clinical chemistry and laboratory medicine.

[63]  E. Levy,et al.  Short-chain fatty acids: ready for prime time? , 2006, Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition.

[64]  H. Mori,et al.  Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.

[65]  C. Rock,et al.  Coenzyme A: back in action. , 2005, Progress in lipid research.

[66]  M. Kimura A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[67]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[68]  Erik L. L. Sonnhammer,et al.  A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences , 1998, ISMB.

[69]  D. Rubin,et al.  Inference from Iterative Simulation Using Multiple Sequences , 1992 .