SAMSA: a comprehensive metatranscriptome analysis pipeline

Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation

(2015) Michael Reck et al.   BMC GENOMICS

Intestinal Epithelial Cell Tyrosine Kinase 2 Transduces IL-22 Signals To Protect from Acute Colitis

(2015) Eva Hainzl et al.   JOURNAL OF IMMUNOLOGY

A RESTful API for Accessing Microbial Community Data for MG-RAST

(2015) Andreas Wilke et al.   PLoS Computational Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community

(2013) Mallory Embree et al.   ISME Journal

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21

(2011) Valerio Costa et al.   PLoS One

The Human Gutome: Nutrigenomics of the Host–Microbiome Interactions

(2010) Dimiter V. Dimitrov   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Isolation and analysis of mRNA from environmental microbial communities

(2008) Ken C. McGrath et al.   JOURNAL OF MICROBIOLOGICAL METHODS