Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Characterization of All Family-9 Glycoside Hydrolases Synthesized by the Cellulosome-producing BacteriumClostridium cellulolyticum

(2014) Julie Ravachol et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identifying the core microbial community in the gut of fungus-growing termites

(2014) Saria Otani et al.   MOLECULAR ECOLOGY

Origins of major archaeal clades correspond to gene acquisitions from bacteria

(2014) Shijulal Nelson-Sathi et al.   NATURE

Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor

(2014) M. W. Baldwin et al.   SCIENCE

Determining the culturability of the rumen bacterial microbiome

(2014) Christopher J. Creevey et al.   Microbial Biotechnology

Rumen Methanogenic Genotypes Differ in Abundance According to Host Residual Feed Intake Phenotype and Diet Type

(2013) CIara A. Carberry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

(2013) Anthony G Doran et al.   BMC BIOINFORMATICS

Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen

(2013) Morten Poulsen et al.   Nature Communications

Community Structure Analysis of Methanogens Associated with Rumen Protozoa Reveals Bias in Universal Archaeal Primers

(2012) Lisa D. Tymensen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effect of Phenotypic Residual Feed Intake and Dietary Forage Content on the Rumen Microbial Community of Beef Cattle

(2012) Ciara A. Carberry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomics: microbial diversity through a scratched lens

(2012) Ben Temperton et al.   CURRENT OPINION IN MICROBIOLOGY

Arabinose is metabolized via a phosphoketolase pathway in Clostridium acetobutylicum ATCC 824

(2012) M. D. Servinsky et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Functional Consequence of Positive Selection Revealed through Rational Mutagenesis of Human Myeloperoxidase

(2012) Noeleen B. Loughran et al.   MOLECULAR BIOLOGY AND EVOLUTION

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

As yet uncultured bacteria phylogenetically classified asPrevotella,Lachnospiraceaeincertae sedis and unclassifiedBacteroidales,ClostridialesandRuminococcaceaemay play a predominant role in ruminal biohydrogenation

(2011) Sharon A. Huws et al.   ENVIRONMENTAL MICROBIOLOGY

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

Ecologically and Evolutionarily Important SNPs Identified in Natural Populations

(2011) L. M. Williams et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Meng Qi et al.   PLoS One

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

(2011) Christopher J. Creevey et al.   PLoS One

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Metatranscriptome Analysis for Insight into Whole-Ecosystem Gene Expression during Spontaneous Wheat and Spelt Sourdough Fermentations

(2010) Stefan Weckx et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence

(2010) Nuria Fonknechten et al.   BMC GENOMICS

Antimicrobial Effect of Red Clover (Trifolium pratense) Phenolic Extract on the Ruminal Hyper Ammonia-Producing Bacterium, Clostridium sticklandii

(2010) Michael Flythe et al.   CURRENT MICROBIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Comparative Genome Analysis of Prevotella ruminicola and Prevotella bryantii: Insights into Their Environmental Niche

(2010) Janaki Purushe et al.   MICROBIAL ECOLOGY

Evolutionary microbial genomics: insights into bacterial host adaptation

(2010) Christina Toft et al.   NATURE REVIEWS GENETICS

Succession of microbial consortia in the developing infant gut microbiome

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

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Effect of divergence in residual feed intake on feeding behavior, blood metabolic variables, and body composition traits in growing beef heifers1

(2009) A. K. Kelly et al.   JOURNAL OF ANIMAL SCIENCE

The genomic basis of trophic strategy in marine bacteria

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

Phylogenetic Comparison of the Methanogenic Communities from an Acidic, Oligotrophic Fen and an Anaerobic Digester Treating Municipal Wastewater Sludge

(2008) L. M. Steinberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Structure of the Archaeal Community of the Rumen

(2008) P. H. Janssen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Aspects of rumen microbiology central to mechanistic modelling of methane production in cattle

(2008) J. L. ELLIS et al.   JOURNAL OF AGRICULTURAL SCIENCE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Metagenomics and the niche concept

(2008) Diana Marco   THEORY IN BIOSCIENCES