Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Metagenomic exploration reveals high levels of microbial arsenic metabolism genes in activated sludge and coastal sediments

(2013) Lin Cai et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

(2013) Milkha M Leimena et al.   BMC GENOMICS

Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation

(2013) Ji Young Jung et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

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

(2013) Mallory Embree et al.   ISME Journal

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Expression patterns reveal niche diversification in a marine microbial assemblage

(2012) Scott M Gifford et al.   ISME Journal

Application of metatranscriptomics to soil environments

(2012) Lilia C. Carvalhais et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge

(2012) Ke Yu et al.   PLoS One

Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing

(2012) Xuejian Xiong et al.   PLoS One

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Progress in prokaryotic transcriptomics

(2011) Melanie J Filiatrault   CURRENT OPINION IN MICROBIOLOGY

Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach

(2011) Meng Qi et al.   PLoS One

Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods

(2010) Ulrike Mäder et al.   CURRENT OPINION IN BIOTECHNOLOGY

Studying bacterial transcriptomes using RNA-seq

(2010) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean

(2010) Ian Hewson et al.   ENVIRONMENTAL MICROBIOLOGY

Quantitative analysis of a deeply sequenced marine microbial metatranscriptome

(2010) Scott M Gifford et al.   ISME Journal

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

(2010) Shaomei He et al.   NATURE METHODS

The case for cloud computing in genome informatics

(2010) Lincoln D Stein   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean

(2009) Ian Hewson et al.   ISME Journal

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA