Colonic mucosal and exfoliome transcriptomic profiling and fecal microbiome response to a flaxseed lignan extract intervention in humans

Generalized Hotelling's test for paired compositional data with application to human microbiome studies

(2018) Ni Zhao et al.   GENETIC EPIDEMIOLOGY

Association of gut microbial communities with plasma lipopolysaccharide-binding protein (LBP) in premenopausal women

(2018) Jessica S Citronberg et al.   ISME Journal

Gut cell metabolism shapes the microbiome

(2017) Patrice D. Cani   SCIENCE

Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion

(2017) Mariana X. Byndloss et al.   SCIENCE

The non-invasive exfoliated transcriptome (exfoliome) reflects the tissue-level transcriptome in a mouse model of NSAID enteropathy

(2017) Canaan M. Whitfield-Cargile et al.   Scientific Reports

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

Comprehensive site-specific whole genome profiling of stromal and epithelial colonic gene signatures in human sigmoid colon and rectal tissue

(2016) Jason M. Knight et al.   PHYSIOLOGICAL GENOMICS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test

(2015) Ni Zhao et al.   AMERICAN JOURNAL OF HUMAN GENETICS

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application

(2015) Mattia D'Antonio et al.   BMC GENOMICS

Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men

(2015) Ilias Lagkouvardos et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Fat, fibre and cancer risk in African Americans and rural Africans

(2015) Stephen J. D. O’Keefe et al.   Nature Communications

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

(2014) S. Anders et al.   BIOINFORMATICS

Enterolignan-Producing Phenotypes Are Associated with Increased Gut Microbial Diversity and Altered Composition in Premenopausal Women in the United States

(2014) M. A. J. Hullar et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production

(2014) Gary D Wu et al.   GUT

Low serum enterolactone concentration is associated with low colonic Lactobacillus–Enterococcus counts in men but is not affected by a synbiotic mixture in a randomised, placebo-controlled, double-blind, cross-over intervention study

(2013) Reetta Holma et al.   BRITISH JOURNAL OF NUTRITION

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

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

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

Genome-wide analysis of the rat colon reveals proximal-distal differences in histone modifications and proto-oncogene expression

(2013) Karen Triff et al.   PHYSIOLOGICAL GENOMICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Inflamed gut mucosa: downstream of interleukin-10

(2011) Gregor Paul et al.   EUROPEAN JOURNAL OF CLINICAL INVESTIGATION

Inflammation meets cancer, with NF-κB as the matchmaker

(2011) Yinon Ben-Neriah et al.   NATURE IMMUNOLOGY

Noninvasive stool-based detection of infant gastrointestinal development using gene expression profiles from exfoliated epithelial cells

(2010) Robert S. Chapkin et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

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

Recent Advances on the Roles of NO in Cancer and Chronic Inflammatory Disorders

(2009) Jagat Kanwar et al.   CURRENT MEDICINAL CHEMISTRY

Changes in Gut Microbiota Control Metabolic Endotoxemia-Induced Inflammation in High-Fat Diet-Induced Obesity and Diabetes in Mice

(2008) P. D. Cani et al.   DIABETES