Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

(2011) Suparna Mitra et al.   BMC BIOINFORMATICS

Ecosystems biology of microbial metabolism

(2011) Niels Klitgord et al.   CURRENT OPINION IN BIOTECHNOLOGY

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

(2011) J. Raes et al.   Molecular Systems Biology

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The PTS transporters of Lactobacillus gasseri ATCC 33323

(2010) Alyssa L Francl et al.   BMC MICROBIOLOGY

Homeostasis and Inflammation in the Intestine

(2010) Wendy S. Garrett et al.   CELL

Natural Products Version 2.0: Connecting Genes to Molecules

(2010) Christopher T. Walsh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response

(2010) E. A. Grice et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A metagenomic  -glucuronidase uncovers a core adaptive function of the human intestinal microbiome

(2010) K. Gloux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human oral, gut, and plaque microbiota in patients with atherosclerosis

(2010) O. Koren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Vaginal microbiome of reproductive-age women

(2010) J. Ravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic fate and function of dietary glutamate in the gut

(2009) Douglas G Burrin et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Complex Glycan Catabolism by the Human Gut Microbiota: The Bacteroidetes Sus-like Paradigm

(2009) Eric C. Martens et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nitric Oxide Production by the Human Intestinal Microbiota by Dissimilatory Nitrate Reduction to Ammonium

(2009) Joan Vermeiren et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Common Genetic Variation and Human Traits

(2009) David B. Goldstein   NEW ENGLAND JOURNAL OF MEDICINE

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Interactions of gut microbiota with functional food components and nutraceuticals

(2009) J.M. Laparra et al.   PHARMACOLOGICAL RESEARCH

Quantifying environmental adaptation of metabolic pathways in metagenomics

(2009) T. A. Gianoulis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

(2009) Yuzhen Ye et al.   PLoS Computational Biology

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

Metabolic-network-driven analysis of bacterial ecological strategies

(2009) Shiri Freilich et al.   GENOME BIOLOGY

Annotation of metagenome short reads using proxygenes

(2008) D. Dalevi et al.   BIOINFORMATICS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

(2008) Patrick D Schloss et al.   BMC BIOINFORMATICS

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

NEW MULTIDIMENSIONAL FUNCTIONAL DIVERSITY INDICES FOR A MULTIFACETED FRAMEWORK IN FUNCTIONAL ECOLOGY

(2008) Sébastien Villéger et al.   ECOLOGY

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH

The role of microbiota in infectious disease

(2008) Bärbel Stecher et al.   TRENDS IN MICROBIOLOGY