Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model

Effect of starter diet supplementation on rumen epithelial morphology and expression of genes involved in cell proliferation and metabolism in pre-weaned lambs

(2018) D. M. Sun et al.   Animal

Differential regulation of ion channels function by proteolysis

(2018) Liwei Wang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose

(2018) Wenping Zhang et al.   ISME Journal

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

(2018) Rekha Seshadri et al.   NATURE BIOTECHNOLOGY

MiR-22 suppresses epithelial–mesenchymal transition in bladder cancer by inhibiting Snail and MAPK1/Slug/vimentin feedback loop

(2018) Mingjie Xu et al.   Cell Death & Disease

The hologenome concept of evolution after 10 years

(2018) Eugene Rosenberg et al.   Microbiome

Effect of Entodinium caudatum on starch intake and glycogen formation by Eudiplodinium maggii in the rumen and reticulum

(2017) Grzegorz Bełżecki et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

A High Grain Diet Dynamically Shifted the Composition of Mucosa-Associated Microbiota and Induced Mucosal Injuries in the Colon of Sheep

(2017) Yue Wang et al.   Frontiers in Microbiology

Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves

(2017) Juliana Dias et al.   Frontiers in Microbiology

RETRACTED: Twist2 promotes kidney cancer cell proliferation and invasion via regulating ITGA6 and CD44 expression in the ECM-Receptor-Interaction pathway

(2016) Hao-jie Zhang et al.   BIOMEDICINE & PHARMACOTHERAPY

Analysis of Community Structure and Species Richness of Protozoa-Enriched Rumen Metagenome from Indian Surti by Shotgun Sequencing

(2016) Ravi K. Shah et al.   CURRENT SCIENCE

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

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

Erratum: Temporal variation selects for diet–microbe co-metabolic traits in the gut of Gorilla spp

(2016) Andres Gomez et al.   ISME Journal

Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants

(2016) Junhua Liu et al.   JOURNAL OF DAIRY SCIENCE

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation

(2016) Janine Kamke et al.   Microbiome

Effects of early feeding on the host rumen transcriptome and bacterial diversity in lambs

(2016) Weimin Wang et al.   Scientific Reports

Responses in ileal and cecal bacteria to low and high amylose/amylopectin ratio diets in growing pigs

(2015) Yu-heng Luo et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Microbiome-metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model

(2015) Sheng-Yong Mao et al.   ENVIRONMENTAL MICROBIOLOGY

The influence of supplementing heifer diets with Saccharomyces cerevisiae yeast on the activity of polysaccharidases in the rumen

(2015) R. Miltko et al.   JOURNAL OF ANIMAL AND FEED SCIENCES

Control of Proliferation and Cancer Growth by the Hippo Signaling Pathway

(2015) U. Ehmer et al.   MOLECULAR CANCER RESEARCH

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Short communication: Effect of calf starter on rumen pH of Holstein dairy calves at weaning

(2015) A.H. Laarman et al.   JOURNAL OF DAIRY SCIENCE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Attenuation of TNFSF10/TRAIL-induced apoptosis by an autophagic survival pathway involving TRAF2- and RIPK1/RIP1-mediated MAPK8/JNK activation

(2012) Weiyang He et al.   Autophagy

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Characterization, metabolites and gas formation of fumarate reducing bacteria isolated from Korean native goat (Capra hircus coreanae)

(2012) Lovelia L. Mamuad et al.   JOURNAL OF MICROBIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Therapeutic Modulation of Microbiota-Host Metabolic Interactions

(2012) E. Holmes et al.   Science Translational Medicine

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

(2011) Filipa Godoy-Vitorino et al.   ISME Journal

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Heng Li et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

SNAI2/Slug promotes growth and invasion in human gliomas

(2010) Hong Wei Yang et al.   BMC CANCER

RUMINANT NUTRITION SYMPOSIUM: Role of fermentation acid absorption in the regulation of ruminal pH12

(2010) J. R. Aschenbach et al.   JOURNAL OF ANIMAL SCIENCE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols