Colonic epithelial cell diversity in health and inflammatory bowel disease

Dietary and Microbial Oxazoles Induce Intestinal Inflammation by Modulating Aryl Hydrocarbon Receptor Responses

(2018) Shankar S. Iyer et al.   CELL

Guanylate cyclase-C as a therapeutic target in gastrointestinal disorders

(2018) Scott A Waldman et al.   GUT

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing

(2018) Shuai Gao et al.   NATURE CELL BIOLOGY

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

An evolutionarily conserved gene family encodes proton-selective ion channels

(2018) Yu-Hsiang Tu et al.   SCIENCE

Inflammasome, Inflammation, and Tissue Homeostasis

(2018) Vijay A.K. Rathinam et al.   TRENDS IN MOLECULAR MEDICINE

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

(2018) James Kinchen et al.   CELL

Interactions Between Autophagy and the Unfolded Protein Response: Implications for Inflammatory Bowel Disease

(2018) Kirsty M Hooper et al.   INFLAMMATORY BOWEL DISEASES

Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range

(2017) Malte Sielaff et al.   JOURNAL OF PROTEOME RESEARCH

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

(2017) Katrina M de Lange et al.   NATURE GENETICS

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

SCnorm: robust normalization of single-cell RNA-seq data

(2017) Rhonda Bacher et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Guanylin and uroguanylin are produced by mouse intestinal epithelial cells of columnar and secretory lineage

(2016) Pauline T. Ikpa et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Claudin-7 indirectly regulates the integrin/FAK signaling pathway in human colon cancer tissue

(2016) Lei Ding et al.   JOURNAL OF HUMAN GENETICS

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci

(2016) David Ellinghaus et al.   NATURE GENETICS

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

Reg4+deep crypt secretory cells function as epithelial niche for Lgr5+stem cells in colon

(2016) Nobuo Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Mucosal Immune System and Its Regulation by Autophagy

(2016) Agnieszka M. Kabat et al.   Frontiers in Immunology

Strong Upregulation of AIM2 and IFI16 Inflammasomes in the Mucosa of Patients with Active Inflammatory Bowel Disease

(2015) Wiebe Vanhove et al.   INFLAMMATORY BOWEL DISEASES

Matrix Metalloproteinases in Inflammatory Bowel Disease: An Update

(2015) Shane O’Sullivan et al.   MEDIATORS OF INFLAMMATION

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Three cheers for the goblet cell: maintaining homeostasis in mucosal epithelia

(2015) Heather A. McCauley et al.   TRENDS IN MOLECULAR MEDICINE

SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci

(2014) Kamil Slowikowski et al.   BIOINFORMATICS

Ultrasensitive proteome analysis using paramagnetic bead technology

(2014) C. S. Hughes et al.   Molecular Systems Biology

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Heparin-binding epidermal growth factor-like growth factor restores Wnt/β-catenin signaling in intestinal stem cells exposed to ischemia/reperfusion injury

(2014) Chun-Liang Chen et al.   SURGERY

Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis

(2013) Malin E V Johansson et al.   GUT

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Lineage-Specific Expression of Bestrophin-2 and Bestrophin-4 in Human Intestinal Epithelial Cells

(2013) Go Ito et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

The mammalian gene function resource: the international knockout mouse consortium

(2012) Allan Bradley et al.   MAMMALIAN GENOME

Goblet cells deliver luminal antigen to CD103+ dendritic cells in the small intestine

(2012) Jeremiah R. McDole et al.   NATURE

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Fast Renewal of the Distal Colonic Mucus Layers by the Surface Goblet Cells as Measured by In Vivo Labeling of Mucin Glycoproteins

(2012) Malin E. V. Johansson   PLoS One

Human Epididymis Protein-4 (HE-4): A Novel Cross-Class Protease Inhibitor

(2012) Nirmal Chhikara et al.   PLoS One

Long-term Expansion of Epithelial Organoids From Human Colon, Adenoma, Adenocarcinoma, and Barrett's Epithelium

(2011) Toshiro Sato et al.   GASTROENTEROLOGY

A conditional knockout resource for the genome-wide study of mouse gene function

(2011) William C. Skarnes et al.   NATURE

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

(2011) Carl A Anderson et al.   NATURE GENETICS

A simple, versatile and efficient method to genetically modify human monocyte-derived dendritic cells with HIV-1–derived lentiviral vectors

(2011) Grégory Berger et al.   Nature Protocols

Dysregulation of laminins in intestinal inflammation

(2011) C. Spenlé et al.   PATHOLOGIE BIOLOGIE

Normal colon epithelium: a dataset for the analysis of gene expression and alternative splicing events in colon disease

(2010) Wilfrido Mojica et al.   BMC GENOMICS

Bacteria Penetrate the Inner Mucus Layer before Inflammation in the Dextran Sulfate Colitis Model

(2010) Malin E. V. Johansson et al.   PLoS One

The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions

(2010) M. E. V. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Agouti C57BL/6N embryonic stem cells for mouse genetic resources

(2009) Stephen J Pettitt et al.   NATURE METHODS

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria

(2008) M. E. V. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA