The Features of Fecal and Ileal Mucosa-Associated Microbiota in Dairy Calves during Early Infection with Mycobacterium avium Subspecies paratuberculosis

An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms

(2015) Hooman Derakhshani et al.   JOURNAL OF BASIC MICROBIOLOGY

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

(2014) Michelle G Rooks et al.   ISME Journal

Antibody response early after experimental infection with Mycobacterium avium subspecies paratuberculosis in dairy calves

(2014) Rienske A.R. Mortier et al.   JOURNAL OF DAIRY SCIENCE

Metabolomic Profiling in Cattle Experimentally Infected with Mycobacterium avium subsp. paratuberculosis

(2014) Jeroen De Buck et al.   PLoS One

Dose-dependent interferon-gamma release in dairy calves experimentally infected with Mycobacterium avium subspecies paratuberculosis

(2014) Rienske A.R. Mortier et al.   VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY

Gene expression profiling and putative biomarkers of calves 3 months after infection with Mycobacterium avium subspecies paratuberculosis

(2014) Joel David et al.   VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY

EMerging BiomARKers in Inflammatory Bowel Disease (EMBARK) Study Identifies Fecal Calprotectin, Serum MMP9 and Serum IL-22 as a Novel Combination of Biomarkers for Crohn's Disease Activity: Role of Cross-Sectional Imaging

(2013) William A Faubion et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Intestinal microbiota: A source of novel biomarkers in inflammatory bowel diseases?

(2013) David Berry et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

(2012) Alison R. Erickson et al.   PLoS One

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

Proteomic analysis of plasma from Holstein cows testing positive for mycobacterium avium subsp. Paratuberculosis (MAP)

(2012) Qiumei You et al.   VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease

(2011) Alan W Walker et al.   BMC MICROBIOLOGY

Current perspectives onMycobacterium aviumsubsp.paratuberculosis,Johne’s disease, and Crohn’s disease: a Review

(2011) Ken Over et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives

(2011) M. Joossens et al.   GUT

Alterations in the gut microbiome of children with severe ulcerative colitis

(2011) Sonia Michail et al.   INFLAMMATORY BOWEL DISEASES

Changes in management practices and apparent prevalence on Canadian dairy farms participating in a voluntary risk assessment-based Johne's disease control program

(2011) U.S. Sorge et al.   JOURNAL OF DAIRY SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

(2010) Chin Wen Png et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes

(2010) Ben P. Willing et al.   GASTROENTEROLOGY

gp130 at the nexus of inflammation, autoimmunity, and cancer

(2010) J. S. Silver et al.   JOURNAL OF LEUKOCYTE BIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

High prevalence of viableMycobacterium aviumsubspeciesparatuberculosisin Crohn’s disease

(2010) Juan L Mendoza   WORLD JOURNAL OF GASTROENTEROLOGY

Direct sequencing of the human microbiome readily reveals community differences

(2010) Justin Kuczynski 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

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

The Relationship Between Intestinal Microbiota and the Central Nervous System in Normal Gastrointestinal Function and Disease

(2009) Stephen M. Collins et al.   GASTROENTEROLOGY

Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

(2009) Janet Jansson et al.   PLoS One

Economic evaluation of Johne's disease control programs implemented on six Michigan dairy farms

(2009) R.B. Pillars et al.   PREVENTIVE VETERINARY MEDICINE

Evidence for age susceptibility of cattle to Johne’s disease

(2009) Peter A. Windsor et al.   VETERINARY JOURNAL

Worlds within worlds: evolution of the vertebrate gut microbiota

(2008) Ruth E. Ley et al.   NATURE REVIEWS MICROBIOLOGY