Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline

Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation

(2014) Andrew Toseland et al.   BMC GENOMICS

Saccharide breakdown and fermentation by the honey bee gut microbiome

(2014) Fredrick J. Lee et al.   ENVIRONMENTAL MICROBIOLOGY

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation

(2014) Albi Celaj et al.   Microbiome

Gene expression of lactobacilli in murine forestomach biofilms

(2014) Clarissa Schwab et al.   Microbial Biotechnology

Effects of supplementary butyrate on butanol production and the metabolic switch in Clostridium beijerinckii NCIMB 8052: genome-wide transcriptional analysis with RNA-Seq

(2013) Yi Wang et al.   Biotechnology for Biofuels

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

(2013) Milkha M Leimena et al.   BMC GENOMICS

Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment

(2013) Vincent P Richards et al.   BMC GENOMICS

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

A multi-omic analysis of an Enterococcus faecium mutant reveals specific genetic mutations and dramatic changes in mRNA and protein expression

(2013) De Chang et al.   BMC MICROBIOLOGY

IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology

(2013) Henry C.M. Leung et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Transcriptome Sequence and Plasmid Copy Number Analysis of the Brewery Isolate Pediococcus claussenii ATCC BAA-344T during Growth in Beer

(2013) Vanessa Pittet et al.   PLoS One

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

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Dietary protein – its role in satiety, energetics, weight loss and health

(2012) Margriet S. Westerterp-Plantenga et al.   BRITISH JOURNAL OF NUTRITION

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

(2012) C. Lozupone et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Xuejian Xiong et al.   PLoS One

Dietary Protein Affects Gene Expression and Prevents Lipid Accumulation in the Liver in Mice

(2012) Jessica Schwarz et al.   PLoS One

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont 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

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Obesity, Diabetes, and Gut Microbiota: The hygiene hypothesis expanded?

(2010) G. Musso et al.   DIABETES CARE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Do nutrient-gut-microbiota interactions play a role in human obesity, insulin resistance and type 2 diabetes?

(2010) M. Diamant et al.   Obesity Reviews

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 Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME 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