Related references
Note: Only part of the references are listed.Biodiversity and functional genomics in the human microbiome
Xochitl C. Morgan et al.
TRENDS IN GENETICS (2013)
A framework for human microbiome research
Barbara A. Methe et al.
NATURE (2012)
Structure, function and diversity of the healthy human microbiome
Curtis Huttenhower et al.
NATURE (2012)
Microbial Co-occurrence Relationships in the Human Microbiome
Karoline Faust et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
Sahar Abubucker et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
Georgia Giannoukos et al.
GENOME BIOLOGY (2012)
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples
Nicola Segata et al.
GENOME BIOLOGY (2012)
Association Between Composition of the Human Gastrointestinal Microbiome and Development of Fatty Liver With Choline Deficiency
Melanie D. Spencer et al.
GASTROENTEROLOGY (2011)
A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface
Xiaoxiao Li et al.
PLOS ONE (2011)
Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
Brian D. Muegge et al.
SCIENCE (2011)
Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes
Gary D. Wu et al.
SCIENCE (2011)
Metatranscriptome Analysis of the Human Fecal Microbiota Reveals Subject-Specific Expression Profiles, with Genes Encoding Proteins Involved in Carbohydrate Metabolism Being Dominantly Expressed
Carien C. G. M. Booijink et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)
Integrated Microbial Survey Analysis of Prokaryotic Communities for the PhyloChip Microarray
Michael C. Schatz et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)
Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
Naama Tepper et al.
BIOINFORMATICS (2010)
Fast and accurate long-read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2010)
Finishing genomes with limited resources: lessons from an ensemble of microbial genomes
Niranjan Nagarajan et al.
BMC GENOMICS (2010)
Homeostasis and Inflammation in the Intestine
Wendy S. Garrett et al.
CELL (2010)
Obesity and the human microbiome
Ruth E. Ley
CURRENT OPINION IN GASTROENTEROLOGY (2010)
Comparative Metagenomics and Population Dynamics of the Gut Microbiota in Mother and Infant
Parag A. Vaishampayan et al.
GENOME BIOLOGY AND EVOLUTION (2010)
Convergent temporal dynamics of the human infant gut microbiota
Pal Trosvik et al.
ISME JOURNAL (2010)
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
Micah Hamady et al.
ISME JOURNAL (2010)
Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice
Chenhong Zhang et al.
ISME JOURNAL (2010)
A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion
Morten O. A. Sommer et al.
MOLECULAR SYSTEMS BIOLOGY (2010)
Segmented filamentous bacteria take the stage
I. I. Ivanov et al.
MUCOSAL IMMUNOLOGY (2010)
Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota
Jan-Hendrik Hehemann et al.
NATURE (2010)
A human gut microbial gene catalogue established by metagenomic sequencing
Junjie Qin et al.
NATURE (2010)
QIIME allows analysis of high-throughput community sequencing data
J. Gregory Caporaso et al.
NATURE METHODS (2010)
A protocol for generating a high-quality genome-scale metabolic reconstruction
Ines Thiele et al.
NATURE PROTOCOLS (2010)
Database resources of the National Center for Biotechnology Information
Eric W. Sayers et al.
NUCLEIC ACIDS RESEARCH (2010)
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
J. Muller et al.
NUCLEIC ACIDS RESEARCH (2010)
KEGG for representation and analysis of molecular networks involving diseases and drugs
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2010)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Ron Caspi et al.
NUCLEIC ACIDS RESEARCH (2010)
Oral Biofilm Architecture on Natural Teeth
Vincent Zijnge et al.
PLOS ONE (2010)
Airway Microbiota and Pathogen Abundance in Age-Stratified Cystic Fibrosis Patients
Michael J. Cox et al.
PLOS ONE (2010)
The Human Nasal Microbiota and Staphylococcus aureus Carriage
Daniel N. Frank et al.
PLOS ONE (2010)
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
Maria G. Dominguez-Bello et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
A Catalog of Reference Genomes from the Human Microbiome
Karen E. Nelson et al.
SCIENCE (2010)
The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies
Patrick D. Schloss
PLOS COMPUTATIONAL BIOLOGY (2010)
A Primer on Metagenomics
John C. Wooley et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)
Visual and statistical comparison of metagenomes
Suparna Mitra et al.
BIOINFORMATICS (2009)
BLAST plus : architecture and applications
Christiam Camacho et al.
BMC BIOINFORMATICS (2009)
Genome assembly reborn: recent computational challenges
Mihai Pop
BRIEFINGS IN BIOINFORMATICS (2009)
Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria
Ivaylo I. Ivanov et al.
CELL (2009)
Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre
Rachel S. Poretsky et al.
ENVIRONMENTAL MICROBIOLOGY (2009)
Global diversity in the human salivary microbiome
Ivan Nasidze et al.
GENOME RESEARCH (2009)
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
Micah Hamady et al.
GENOME RESEARCH (2009)
Omics data and levels of evidence for biomarker discovery
Debashis Ghosh et al.
GENOMICS (2009)
Shotgun metaproteomics of the human distal gut microbiota
Nathan C. Verberkmoes et al.
ISME JOURNAL (2009)
The role of the intestinal microbiota in enteric infection
Inna Sekirov et al.
JOURNAL OF PHYSIOLOGY-LONDON (2009)
A core gut microbiome in obese and lean twins
Peter J. Turnbaugh et al.
NATURE (2009)
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column
Yanmei Shi et al.
NATURE (2009)
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
Arthur Brady et al.
NATURE METHODS (2009)
ESSAY What are the consequences of the disappearing human microbiota?
Martin J. Blaser et al.
NATURE REVIEWS MICROBIOLOGY (2009)
Orphelia: predicting genes in metagenomic sequencing reads
Katharina J. Hoff et al.
NUCLEIC ACIDS RESEARCH (2009)
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
J. R. Cole et al.
NUCLEIC ACIDS RESEARCH (2009)
Quantifying environmental adaptation of metabolic pathways in metagenomics
Tara A. Gianoulis et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites
William R. Wikoff et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Topographical and Temporal Diversity of the Human Skin Microbiome
Elizabeth A. Grice et al.
SCIENCE (2009)
The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
Peter J. Turnbaugh et al.
SCIENCE TRANSLATIONAL MEDICINE (2009)
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes
Yuzhen Ye et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Pneumococcal Capsular Polysaccharide Structure Predicts Serotype Prevalence
Daniel M. Weinberger et al.
PLOS PATHOGENS (2009)
Metabolic-network-driven analysis of bacterial ecological strategies
Shiri Freilich et al.
GENOME BIOLOGY (2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead et al.
GENOME BIOLOGY (2009)
Genome-scale models of bacterial metabolism: reconstruction and applications
Maxime Durot et al.
FEMS MICROBIOLOGY REVIEWS (2009)
The gut microbiota shapes intestinal immune responses during health and disease
June L. Round et al.
NATURE REVIEWS IMMUNOLOGY (2009)
Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities
Ainslie E. F. Little et al.
ANNUAL REVIEW OF MICROBIOLOGY (2008)
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
F. Meyer et al.
BMC BIOINFORMATICS (2008)
An invitation to the marriage of metagenomics and metabolomics
Peter J. Turnbaugh et al.
CELL (2008)
Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome
Peter J. Turnbaugh et al.
CELL HOST & MICROBE (2008)
A renaissance for the pioneering 16S rRNA gene
Susannah G. Tringe et al.
CURRENT OPINION IN MICROBIOLOGY (2008)
Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model
Francois-Pierre J. Martin et al.
MOLECULAR SYSTEMS BIOLOGY (2008)
Microbiology - Metagenomics
Philip Hugenholtz et al.
NATURE (2008)
Gut microbiota: a potential new territory for drug targeting
Wei Jia et al.
NATURE REVIEWS DRUG DISCOVERY (2008)
Systems microbiology - Timeline - Molecular eco-systems biology: towards an understanding of community function
Jeroen Raes et al.
NATURE REVIEWS MICROBIOLOGY (2008)
A Bioinformatician's Guide to Metagenomics
Victor Kunin et al.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2008)
Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities
Jack A. Gilbert et al.
PLOS ONE (2008)
Evolution of mammals and their gut microbes
Ruth E. Ley et al.
SCIENCE (2008)
The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing
Les Dethlefsen et al.
PLOS BIOLOGY (2008)
IMG/M: a data management and analysis system for metagenomes
Victor M. Markowitz et al.
NUCLEIC ACIDS RESEARCH (2008)
KEGG for linking genomes to life and the environment
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2008)
The Pfam protein families database
Robert D. Finn et al.
NUCLEIC ACIDS RESEARCH (2008)
SILVA:: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
Elmar Pruesse et al.
NUCLEIC ACIDS RESEARCH (2007)
An ecological and evolutionary perspective on human-microbe mutualism and disease
Les Dethlefsen et al.
NATURE (2007)
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
Ken Kurokawa et al.
DNA RESEARCH (2007)
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
Qiong Wang et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
KAAS: an automatic genome annotation and pathway reconstruction server
Yuki Moriya et al.
NUCLEIC ACIDS RESEARCH (2007)
Optimization based automated curation of metabolic reconstructions
Vinay Satish Kumar et al.
BMC BIOINFORMATICS (2007)
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Ewan Birney et al.
NATURE (2007)
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
Konstantinos Mavromatis et al.
NATURE METHODS (2007)
Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes
Jonathan A. Eisen
PLOS BIOLOGY (2007)
Metabolic modeling of a mutualistic microbial community
Sergey Stolyar et al.
MOLECULAR SYSTEMS BIOLOGY (2007)
Accurate phylogenetic classification of variable-length DNA fragments
Alice Carolyn McHardy et al.
NATURE METHODS (2007)
The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific
Douglas B. Rusch et al.
PLOS BIOLOGY (2007)
Locating proteins in the cell using TargetP, SignalP and related tools
Olof Emanuelsson et al.
NATURE PROTOCOLS (2007)
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels
Qinghu Ren et al.
NUCLEIC ACIDS RESEARCH (2007)
Microbial ecology - Human gut microbes associated with obesity
Ruth E. Ley et al.
NATURE (2006)
An obesity-associated gut microbiome with increased capacity for energy harvest
Peter J. Turnbaugh et al.
NATURE (2006)
Systems approach to refining genome annotation
Jennifer L. Reed et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection
John F. Rawls et al.
CELL (2006)
Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation
Eoin L. Brodie et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)
Microbial diversity in the deep sea and the underexplored rare biosphere
Mitchell L. Sogin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
The gut flora as a forgotten organ
Ann M. O'Hara et al.
EMBO REPORTS (2006)
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
T. Z. DeSantis et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)
A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism
Buck S. Samuel et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution
M. van de Guchte et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
An application of statistics to comparative metagenomics
Beltran Rodriguez-Brito et al.
BMC BIOINFORMATICS (2006)
Metaproteomics: studying functional gene expression in microbial ecosystems
P Wilmes et al.
TRENDS IN MICROBIOLOGY (2006)
UniFrac: a new phylogenetic method for comparing microbial communities
C Lozupone et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)
Oral microbial communities in sickness and in health
HF Jenkinson et al.
TRENDS IN MICROBIOLOGY (2005)
Obesity alters gut microbial ecology
RE Ley et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Bioinformatics for whole-genome shotgun sequencing of microbial communities
K Chen et al.
PLOS COMPUTATIONAL BIOLOGY (2005)
Metagenomics and industrial applications
P Lorenz et al.
NATURE REVIEWS MICROBIOLOGY (2005)
Gut microorganisms, mammalian metabolism and personalized health care
JK Nicholson et al.
NATURE REVIEWS MICROBIOLOGY (2005)
Genome-wide association studies for common diseases and complex traits
JN Hirschhorn et al.
NATURE REVIEWS GENETICS (2005)
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
R Overbeek et al.
NUCLEIC ACIDS RESEARCH (2005)
Environmental genome shotgun sequencing of the Sargasso Sea
JC Venter et al.
SCIENCE (2004)
Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota
JF Rawls et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Community structure and metabolism through reconstruction of microbial genomes from the environment
GW Tyson et al.
NATURE (2004)
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
T Huber et al.
BIOINFORMATICS (2004)
Application of tetranucleotide frequencies for the assignment of genomic fragments
H Teeling et al.
ENVIRONMENTAL MICROBIOLOGY (2004)
Metagenomics: Application of genomics to uncultured microorganisms
J Handelsman
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2004)
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
ML Green et al.
BMC BIOINFORMATICS (2004)
Metagenomics: Genomic analysis of microbial communities
CS Riesenfeld et al.
ANNUAL REVIEW OF GENETICS (2004)
The COG database: an updated version includes eukaryotes
RL Tatusov et al.
BMC BIOINFORMATICS (2003)
Harmful algal blooms: causes, impacts and detection
KG Sellner et al.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY (2003)
The TIGRFAMs database of protein families
DH Haft et al.
NUCLEIC ACIDS RESEARCH (2003)
Spatial arrangements and associative behavior of species in an in vitro oral biofilm model
M Guggenheim et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2001)
Initial sequencing and analysis of the human genome
ES Lander et al.
NATURE (2001)
Share Paper
