Site-specific programming of the host epithelial transcriptome by the gut microbiota

Filter-Dense Multicolor Microscopy

(2015) Siavash Kijani et al.   PLoS One

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape

(2014) J. Gray Camp et al.   GENOME RESEARCH

The gut microbiota engages different signaling pathways to induce Duox2 expression in the ileum and colon epithelium

(2014) F Sommer et al.   Mucosal Immunology

Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity

(2014) Tae-Hee Kim et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

More than just a gut instinct–the potential interplay between a baby's nutrition, its gut microbiome, and the epigenome

(2013) Mona Mischke et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Gut Microbiota Regulates Bile Acid Metabolism by Reducing the Levels of Tauro-beta-muricholic Acid, a Naturally Occurring FXR Antagonist

(2013) Sama I. Sayin et al.   Cell Metabolism

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

(2013) Nicholas Arpaia et al.   NATURE

Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis

(2013) Theresa Alenghat et al.   NATURE

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

(2013) Leif Väremo et al.   NUCLEIC ACIDS RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation

(2012) Sahar El Aidy et al.   GUT

Gut bacteria–host metabolic interplay during conventionalisation of the mouse germfree colon

(2012) Sahar El Aidy et al.   ISME Journal

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets

(2012) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

Symptomatic atherosclerosis is associated with an altered gut metagenome

(2012) Fredrik H. Karlsson et al.   Nature Communications

Age-Dependent TLR3 Expression of the Intestinal Epithelium Contributes to Rotavirus Susceptibility

(2012) Johanna Pott et al.   PLoS Pathogens

Functional analysis of transcription factor binding sites in human promoters

(2012) Troy W Whitfield et al.   GENOME BIOLOGY

The Microbiome and Butyrate Regulate Energy Metabolism and Autophagy in the Mammalian Colon

(2011) Dallas R. Donohoe et al.   Cell Metabolism

Role of mucus layers in gut infection and inflammation

(2011) Gunnar C Hansson   CURRENT OPINION IN MICROBIOLOGY

Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice

(2011) Richard Kellermayer et al.   FASEB JOURNAL

Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88

(2011) Erik Larsson et al.   GUT

Intestinal Bacterial Colonization Induces Mutualistic Regulatory T Cell Responses

(2011) Markus B. Geuking et al.   IMMUNITY

Regulation of the polymeric immunoglobulin receptor by the classical and alternative NF-κB pathways in intestinal epithelial cells

(2011) M E C Bruno et al.   Mucosal Immunology

Microenvironmental regulation of stem cells in intestinal homeostasis and cancer

(2011) Jan Paul Medema et al.   NATURE

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

Aurora kinases A and B are up-regulated by Myc and are essential for maintenance of the malignant state

(2010) J. den Hollander et al.   BLOOD

Gut Microbiota in Health and Disease

(2010) Inna Sekirov et al.   PHYSIOLOGICAL REVIEWS

Probiotic and Gut Lactobacilli and Bifidobacteria: Molecular Approaches to Study Diversity and Activity

(2009) Michiel Kleerebezem et al.   Annual Review of Microbiology

Induction of MIF expression by oxidized LDL via activation of NF-κB in vascular smooth muscle cells

(2009) Lihong Chen et al.   ATHEROSCLEROSIS

The Key Role of Segmented Filamentous Bacteria in the Coordinated Maturation of Gut Helper T Cell Responses

(2009) Valérie Gaboriau-Routhiau et al.   IMMUNITY

NF-κB inhibition leads to increased synthesis and secretion of MIF in human CD4+ T cells

(2009) Mi-La Cho et al.   IMMUNOLOGY LETTERS

A CREB-C/EBP  cascade induces M2 macrophage-specific gene expression and promotes muscle injury repair

(2009) D. Ruffell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH