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

Comparative Analysis of Lactobacillus plantarum WCFS1 Transcriptomes by Using DNA Microarray and Next-Generation Sequencing Technologies

(2012) Milkha M. Leimena et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

(2012) Erwin G Zoetendal et al.   ISME Journal

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

(2012) Xuejian Xiong et al.   PLoS One

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

Microarray Analysis and Barcoded Pyrosequencing Provide Consistent Microbial Profiles Depending on the Source of Human Intestinal Samples

(2011) Bartholomeus van den Bogert et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A pipeline for RNA-seq data processing and quality assessment

(2011) Angela Goncalves et al.   BIOINFORMATICS

Metagenomics: Key to Human Gut Microbiota

(2011) Simone Maccaferri et al.   DIGESTIVE DISEASES

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys

(2011) Jeffrey J Werner et al.   ISME Journal

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

(2011) Petr Baldrian et al.   ISME Journal

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

The Active Human Gut Microbiota Differs from the Total Microbiota

(2011) Francesc Peris-Bondia et al.   PLoS One

Composition bias and the origin of ORFan genes

(2010) Inbal Yomtovian et al.   BIOINFORMATICS

High temporal and inter-individual variation detected in the human ileal microbiota

(2010) Carien C. G. M. Booijink et al.   ENVIRONMENTAL MICROBIOLOGY

Linking bacterial identities and ecosystem processes: can ‘omic’ analyses be more than the sum of their parts?

(2010) Sergio E. Morales et al.   FEMS MICROBIOLOGY ECOLOGY

High-Throughput Identification of Bacteria and Yeast by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Conventional Medical Microbiology Laboratories

(2010) S. Q. van Veen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

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

The amazing world of bacterial structured RNAs

(2010) Eric Westhof   GENOME BIOLOGY

Structure and Complexity of a Bacterial Transcriptome

(2009) K. D. Passalacqua et al.   JOURNAL OF BACTERIOLOGY

A perspective: Metatranscriptomics as a tool for the discovery of novel biocatalysts

(2009) Falk Warnecke et al.   JOURNAL OF BIOTECHNOLOGY

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

(2009) D. R. Yoder-Himes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking phylogenetic identities of bacteria to starch fermentation in anin vitromodel of the large intestine by RNA-based stable isotope probing

(2008) Petia Kovatcheva-Datchary et al.   ENVIRONMENTAL MICROBIOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

(2008) Z. M.-P. Lee et al.   NUCLEIC ACIDS RESEARCH

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

(2008) Jack A. Gilbert et al.   PLoS One

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