The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

From genomics to metagenomics

(2012) Narayan Desai et al.   CURRENT OPINION IN BIOTECHNOLOGY

Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing

(2012) Martha Zakrzewski et al.   JOURNAL OF BIOTECHNOLOGY

Toward interoperable bioscience data

(2012) Susanna-Assunta Sansone et al.   NATURE GENETICS

Badomics words and the power and peril of the ome-meme

(2012) Jonathan A Eisen   GigaScience

The activity level of a microbial community function can be predicted from its metatranscriptome

(2011) Damian E Helbling et al.   ISME Journal

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing

(2011) Samuel V. Angiuoli et al.   PLoS One

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

The rational exploration of microbial diversity

(2008) Christopher Quince et al.   ISME Journal