Structural variation in the gut microbiome associates with host health

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

A microbial signature for Crohn's disease

(2017) Victoria Pascal et al.   GUT

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Involvement of a gut–retina axis in protection against dietary glycemia-induced age-related macular degeneration

(2017) Sheldon Rowan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Flagellar Hooks and Hook Protein FlgE Participate in Host Microbe Interactions at Immunological Level

(2017) Ying Shen et al.   Scientific Reports

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

(2016) Daniel R. Mende et al.   NUCLEIC ACIDS RESEARCH

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling

(2015) Maayan Levy et al.   CELL

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

Artificial sweeteners induce glucose intolerance by altering the gut microbiota

(2014) Jotham Suez et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis

(2013) Robert A Koeth et al.   NATURE MEDICINE

Bacteria as vitamin suppliers to their host: a gut microbiota perspective

(2012) Jean Guy LeBlanc et al.   CURRENT OPINION IN BIOTECHNOLOGY

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome

(2012) Margaret L. Zupancic et al.   PLoS One

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Systemic gut microbial modulation of bile acid metabolism in host tissue compartments

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

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Butyrate Improves Insulin Sensitivity and Increases Energy Expenditure in Mice

(2009) Z. Gao et al.   DIABETES

myo-Inositol Catabolism inBacillus subtilis

(2008) Ken-ichi Yoshida et al.   JOURNAL OF BIOLOGICAL CHEMISTRY