Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality

Optimization of miRNA-seq data preprocessing

(2015) S. Tam et al.   BRIEFINGS IN BIOINFORMATICS

Pectin Induces an In Vitro Rumen Microbial Population Shift Attributed to the Pectinolytic Treponema Group

(2014) Jing Liu et al.   CURRENT MICROBIOLOGY

16S rDNA Pyrosequencing Analysis of Bacterial Community in Heavy Metals Polluted Soils

(2014) Marcin Gołębiewski et al.   MICROBIAL ECOLOGY

Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation

(2014) Albi Celaj et al.   Microbiome

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

(2014) Andrew D Fernandes et al.   Microbiome

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation

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

Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling

(2013) Brett J Baker et al.   ISME Journal

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Correction: Macrophage Migration Inhibitory Factor Inhibits the Migration of Cartilage End Plate-Derived Stem Cells by Reacting with CD74

(2013) Cheng-jie Xiong et al.   PLoS One

A Metagenomics Transect into the Deepest Point of the Baltic Sea Reveals Clear Stratification of Microbial Functional Capacities

(2013) Petter Thureborn et al.   PLoS One

Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity

(2013) J. G. M. Markle et al.   SCIENCE

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer

(2013) Shun’ichi Ishii et al.   Nature Communications

Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen

(2013) Morten Poulsen et al.   Nature Communications

Transcriptome sequencing of neonatal thymic epithelial cells

(2013) Charles St-Pierre et al.   Scientific Reports

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

(2012) Ryan A Lesniewski et al.   ISME Journal

Genome Sequence of the Alkaliphilic Bacterium Nitritalea halalkaliphila Type Strain LW7, Isolated from Lonar Lake, India

(2012) P. K. Jangir et al.   JOURNAL OF BACTERIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

The genes and enzymes of phosphonate metabolism by bacteria, and their distribution in the marine environment

(2012) Juan F. Villarreal-Chiu   Frontiers in Microbiology

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

(2011) Suparna Mitra et al.   BMC BIOINFORMATICS

Microbiome analysis of dairy cows fed pasture or total mixed ration diets

(2011) Alexandre B. de Menezes et al.   FEMS MICROBIOLOGY ECOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

DETECT—a Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum

(2010) Stacy S. Hung et al.   BIOINFORMATICS

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads

(2010) G. L. Rosen et al.   BIOINFORMATICS

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Toward defining the autoimmune microbiome for type 1 diabetes

(2010) Adriana Giongo et al.   ISME Journal

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Unlocking Short Read Sequencing for Metagenomics

(2010) Sébastien Rodrigue et al.   PLoS One

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

What Is the Metabolic Role of Phosphoenolpyruvate Carboxykinase?

(2009) Jianqi Yang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

(2009) M. A. Mahowald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones

(2009) D. A. Walsh et al.   SCIENCE

The Modular Organization of Protein Interactions in Escherichia coli

(2009) José M. Peregrín-Alvarez et al.   PLoS Computational Biology

The conservation and evolutionary modularity of metabolism

(2009) José M Peregrín-Alvarez et al.   GENOME BIOLOGY

Innate immunity and intestinal microbiota in the development of Type 1 diabetes

(2008) Li Wen et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH