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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis

(2014) Christoph A. Thaiss et al.   CELL

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Assessing the Human Gut Microbiota in Metabolic Diseases

(2013) F. Karlsson et al.   DIABETES

Pathoscope: Species identification and strain attribution with unassembled sequencing data

(2013) O. E. Francis et al.   GENOME RESEARCH

Human Gut Microbiome and Risk for Colorectal Cancer

(2013) Jiyoung Ahn et al.   JNCI-Journal of the National Cancer Institute

Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome

(2013) Shin Yoshimoto et al.   NATURE

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

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

(2013) Fredrik H. Karlsson et al.   NATURE

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes

(2012) Feng Gao et al.   NUCLEIC ACIDS RESEARCH

IMG/M-HMP: A Metagenome Comparative Analysis System for the Human Microbiome Project

(2012) Victor M. Markowitz et al.   PLoS One

Genome-wide identification and characterization of replication origins by deep sequencing

(2012) Jia Xu et al.   GENOME BIOLOGY

Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing

(2011) Ole Skovgaard et al.   GENOME RESEARCH

JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets

(2010) Michael E. Hughes et al.   JOURNAL OF BIOLOGICAL RHYTHMS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Metabolism, cell growth and the bacterial cell cycle

(2009) Jue D. Wang et al.   NATURE REVIEWS MICROBIOLOGY

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE