Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen

Analysis by RNA-seq of transcriptomic changes elicited by heat shock in Leishmania major

(2019) Alberto Rastrojo et al.   Scientific Reports

The Ruminal Microbiome and Metabolome Alterations Associated with Diet-Induced Milk Fat Depression in Dairy Cows

(2019) Hongbo Zeng et al.   Metabolites

Conversion of Branched-Chain Amino Acids to Corresponding Isoacids - An in vitro Tool for Estimating Ruminal Protein Degradability

(2019) Juha Apajalahti et al.   Frontiers in Veterinary Science

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

New Insights Into the Mechanisms and Biological Roles of D-Amino Acids in Complex Eco-Systems

(2018) Alena Aliashkevich et al.   Frontiers in Microbiology

Assessment of Rumen Microbiota from a Large Dairy Cattle Cohort Reveals the Pan and Core Bacteriomes Contributing to Varied Phenotypes

(2018) Mingyuan Xue et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data

(2018) Tiago F Jesus et al.   NUCLEIC ACIDS RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Biological Functions of ilvC in Branched-Chain Fatty Acid Synthesis and Diffusible Signal Factor Family Production in Xanthomonas campestris

(2017) Kai-Huai Li et al.   Frontiers in Microbiology

Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure

(2017) Rebecca Danielsson et al.   Frontiers in Microbiology

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

(2016) Imchang Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants

(2016) Sheerli Kruger Ben Shabat et al.   ISME Journal

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Insights into Abundant Rumen Ureolytic Bacterial Community Using Rumen Simulation System

(2016) Di Jin et al.   Frontiers in Microbiology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle

(2015) Matthew Sean McCabe et al.   PLoS One

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

(2014) S. Anders et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes

(2014) Corey M. Hudson et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq-Based Analysis of Cold Shock Response in Thermoanaerobacter tengcongensis, a Bacterium Harboring a Single Cold Shock Protein Encoding Gene

(2014) Bo Liu et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Effects of Branched-chain Amino Acids on <italic>In vitro</italic> Ruminal Fermentation of Wheat Straw

(2013) Hui Ling Zhang et al.   ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES

Effects of Synchronicity of Carbohydrate and Protein Degradation on Rumen Fermentation Characteristics and Microbial Protein Synthesis

(2013) J. K. Seo et al.   ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES

Infernal 1.1: 100-fold faster RNA homology searches

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

HTQC: a fast quality control toolkit for Illumina sequencing data

(2013) Xi Yang et al.   BMC BIOINFORMATICS

Growth Rates Made Easy

(2013) B. G. Hall et al.   MOLECULAR BIOLOGY AND EVOLUTION

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Carbohydrate utilization by enterohaemorrhagicEscherichia coliO157:H7 in bovine intestinal content

(2012) Yolande Bertin et al.   ENVIRONMENTAL MICROBIOLOGY

Direct Regulation of GTP Homeostasis by (p)ppGpp: A Critical Component of Viability and Stress Resistance

(2012) Allison Kriel et al.   MOLECULAR CELL

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

Impact of Feed Efficiency and Diet on Adaptive Variations in the Bacterial Community in the Rumen Fluid of Cattle

(2011) Emma Hernandez-Sanabria et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Purification, Characterization, and Expression of Multiple Glutamine Synthetases from Prevotella ruminicola 23

(2011) J. N. Kim et al.   JOURNAL OF BACTERIOLOGY

Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies

(2011) P. B. Pope et al.   SCIENCE

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Rumen Microbiome Composition Determined Using Two Nutritional Models of Subacute Ruminal Acidosis

(2009) E. Khafipour et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

D-Amino Acids Govern Stationary Phase Cell Wall Remodeling in Bacteria

(2009) H. Lam et al.   SCIENCE

Effects of Limiting Amino Acids on Rumen Fermentation and Microbial Community In vitro

(2008) Meng-zhi WANG et al.   Agricultural Sciences in China

Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes

(2008) J. A. Frank et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY