Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Differential methylation analysis for BS-seq data under general experimental design

(2016) Yongseok Park et al.   BIOINFORMATICS

The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin

(2016) Susanne V Schmidt et al.   CELL RESEARCH

Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues

(2016) Kimberly A. Krautkramer et al.   MOLECULAR CELL

How colonization by microbiota in early life shapes the immune system

(2016) Thomas Gensollen et al.   SCIENCE

How Our Other Genome Controls Our Epi-Genome

(2016) Antonella Celluzzi et al.   TRENDS IN MICROBIOLOGY

Epithelial Xbp1 Is Required for Cellular Proliferation and Differentiation during Mammary Gland Development

(2015) Daisuke Hasegawa et al.   MOLECULAR AND CELLULAR BIOLOGY

Assessing DNA methylation in the developing human intestinal epithelium: potential link to inflammatory bowel disease

(2015) J Kraiczy et al.   Mucosal Immunology

FNTM: a server for predicting functional networks of tissues in mouse

(2015) Jonathan Goya et al.   NUCLEIC ACIDS RESEARCH

Analysis of gene–environment interactions in postnatal development of the mammalian intestine

(2015) Seth Rakoff-Nahoum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Felix Sommer et al.   GENOME BIOLOGY

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

(2014) S. Anders et al.   BIOINFORMATICS

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Gene Body Methylation Can Alter Gene Expression and Is a Therapeutic Target in Cancer

(2014) Xiaojing Yang et al.   CANCER CELL

Identification of DNA methylation changes atcis-regulatory elements during early steps of HSC differentiation using tagmentation-based whole genome bisulfite sequencing

(2014) Daniel B Lipka et al.   CELL CYCLE

Reprogramming the Methylome: Erasing Memory and Creating Diversity

(2014) Heather J. Lee et al.   Cell Stem Cell

Tet3 and DNA Replication Mediate Demethylation of Both the Maternal and Paternal Genomes in Mouse Zygotes

(2014) Li Shen et al.   Cell Stem Cell

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

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

Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation

(2014) Jia Xue et al.   IMMUNITY

Lung microbiota promotes tolerance to allergens in neonates via PD-L1

(2014) Eva S Gollwitzer et al.   NATURE MEDICINE

Altered Mucus Glycosylation in Core 1 O-Glycan-Deficient Mice Affects Microbiota Composition and Intestinal Architecture

(2014) Felix Sommer et al.   PLoS One

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

(2013) Katja Hebestreit et al.   BIOINFORMATICS

Intestinal Microbial Diversity during Early-Life Colonization Shapes Long-Term IgE Levels

(2013) Julia Cahenzli et al.   Cell Host & Microbe

Stories of love and hate

(2013) Philip Rosenstiel   CURRENT OPINION IN GASTROENTEROLOGY

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

Paneth cells as a site of origin for intestinal inflammation

(2013) Timon E. Adolph et al.   NATURE

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

PGC7, H3K9me2 and Tet3: regulators of DNA methylation in zygotes

(2012) Jinsuk Kang et al.   CELL RESEARCH

A functional methylome map of ulcerative colitis

(2012) R. Hasler 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

Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice

(2012) Sahar El Aidy et al.   Mucosal Immunology

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function

(2012) T. Olszak et al.   SCIENCE

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

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

(2011) Richard Kellermayer et al.   FASEB JOURNAL

Hypoxia and Metabolic Factors That Influence Inflammatory Bowel Disease Pathogenesis

(2011) Louise E. Glover et al.   GASTROENTEROLOGY

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

Normal gut microbiota modulates brain development and behavior

(2011) R. D. Heijtz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Regulation of human metabolism by hypoxia-inducible factor

(2010) Federico Formenti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

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

(2009) Valérie Gaboriau-Routhiau et al.   IMMUNITY

Eukaryotic transcription factor binding sites--modeling and integrative search methods

(2008) S. Hannenhalli   BIOINFORMATICS

XBP1 Links ER Stress to Intestinal Inflammation and Confers Genetic Risk for Human Inflammatory Bowel Disease

(2008) Arthur Kaser et al.   CELL

The magic of the hypoxia-signaling cascade

(2008) E. Benizri et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Impaired Bcl3 Up-regulation Leads to Enhanced Lipopolysaccharide-induced Interleukin (IL)-23P19 Gene Expression in IL-10–/–Mice

(2008) Marcus Mühlbauer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY