B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing

Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity

(2022) Mathieu Uzzan et al.   NATURE MEDICINE

The spatial transcriptomic landscape of the healing mouse intestine following damage

(2022) Sara M. Parigi et al.   Nature Communications

DRGquant: A new modular AI-based pipeline for 3D analysis of the DRG

(2022) Matthew A. Hunt et al.   JOURNAL OF NEUROSCIENCE METHODS

Human gut-associated lymphoid tissues (GALT); diversity, structure, and function

(2021) Urs M. Mörbe et al.   Mucosal Immunology

TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data

(2021) Li Song et al.   NATURE METHODS

Optimization and expansion of non-negative matrix factorization

(2020) Xihui Lin et al.   BMC BIOINFORMATICS

Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient

(2020) Neil McCarthy et al.   Cell Stem Cell

Single cell and genetic analyses reveal conserved populations and signaling mechanisms of gastrointestinal stromal niches

(2020) Ji-Eun Kim et al.   Nature Communications

Elastin is a key factor of tumor development in colorectal cancer

(2020) Jinzhi Li et al.   BMC CANCER

FADD and Caspase-8 Regulate Gut Homeostasis and Inflammation by Controlling MLKL- and GSDMD-Mediated Death of Intestinal Epithelial Cells

(2020) Robin Schwarzer et al.   IMMUNITY

Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity

(2020) Thomas M. Fenton et al.   IMMUNITY

Resolution of Inflammation and Gut Repair in IBD: Translational Steps Towards Complete Mucosal Healing

(2020) Gwo-tzer Ho et al.   INFLAMMATORY BOWEL DISEASES

Z-nucleic-acid sensing triggers ZBP1-dependent necroptosis and inflammation

(2020) Huipeng Jiao et al.   NATURE

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

(2020) Simon Cabello-Aguilar et al.   NUCLEIC ACIDS RESEARCH

Liver X receptor regulates Th17 and RORγt+ Treg cells by distinct mechanisms

(2020) Sara M. Parigi et al.   Mucosal Immunology

Cellular and molecular architecture of the intestinal stem cell niche

(2020) Neil McCarthy et al.   NATURE CELL BIOLOGY

Colonic epithelial cell diversity in health and inflammatory bowel disease

(2019) Kaushal Parikh et al.   NATURE

De Novo Colitis Associated With Rituximab in 21 Patients at a Tertiary Center

(2019) Jason D. Eckmann et al.   Clinical Gastroenterology and Hepatology

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

Conserved transcriptomic profile between mouse and human colitis allows unsupervised patient stratification

(2019) Paulo Czarnewski et al.   Nature Communications

Transfer of regulatory knowledge from human to mouse for functional genomic analysis

(2019) Christian H. Holland et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

(2019) José L. McFaline-Figueroa et al.   NATURE GENETICS

Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging

(2019) Ziming Du et al.   Nature Protocols

Impact of Fibroblast-Derived SPARC on Invasiveness of Colorectal Cancer Cells

(2019) Daniel Drev et al.   Cancers

No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population

(2019) Luisa W Hugerth et al.   GUT

Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses

(2019) Heping Xu et al.   IMMUNITY

Chronic Inflammation: A Common Promoter in Tertiary Lymphoid Organ Neogenesis

(2019) Shanshan Luo et al.   Frontiers in Immunology

Unveiling skin macrophage dynamics explains both tattoo persistence and strenuous removal

(2018) Anna Baranska et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Transcription profiling of peripheral B cells in antibody-positive primary Sjögren's syndrome reveals upregulated expression of CX3CR1 and a type I and type II interferon signature

(2018) J. Imgenberg-Kreuz et al.   SCANDINAVIAN JOURNAL OF IMMUNOLOGY

Obesity exacerbates colitis-associated cancer via IL-6-regulated macrophage polarisation and CCL-20/CCR-6-mediated lymphocyte recruitment

(2018) Claudia M. Wunderlich et al.   Nature Communications

Perturbation-response genes reveal signaling footprints in cancer gene expression

(2018) Michael Schubert et al.   Nature Communications

A presentation of ulcerative colitis after rituximab therapy in a patient with multiple sclerosis and literature review

(2018) Sareh Shahmohammadi et al.   Multiple Sclerosis and Related Disorders

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

(2018) James Kinchen et al.   CELL

Subepithelial telocytes are an important source of Wnts that supports intestinal crypts

(2018) Michal Shoshkes-Carmel et al.   NATURE

Two to Tango: Dialog between Immunity and Stem Cells in Health and Disease

(2018) Shruti Naik et al.   CELL

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Alarmin S100A11 initiates a chemokine response to the human pathogen Toxoplasma gondii

(2018) Alexandra Safronova et al.   NATURE IMMUNOLOGY

B Cells Produce the Tissue-Protective Protein RELMα during Helminth Infection, which Inhibits IL-17 Expression and Limits Emphysema

(2018) Fei Chen et al.   Cell Reports

The regulation of gut mucosal IgA B-cell responses: recent developments

(2017) N Y Lycke et al.   Mucosal Immunology

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Rituximab-induced Crohn’s disease

(2017) Poornima Varma et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Mature B cells accelerate wound healing after acute and chronic diabetic skin lesions

(2017) Ruxandra F. Sîrbulescu et al.   WOUND REPAIR AND REGENERATION

Intestinal Stem Cell Niche: The Extracellular Matrix and Cellular Components

(2017) Laween Meran et al.   Stem Cells International

Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures

(2017) Moon Young Lee et al.   PLoS One

QuPath: Open source software for digital pathology image analysis

(2017) Peter Bankhead et al.   Scientific Reports

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data

(2016) David A. duVerle et al.   BMC BIOINFORMATICS

B cell IFN-γ receptor signaling promotes autoimmune germinal centers via cell-intrinsic induction of BCL-6

(2016) Shaun W. Jackson et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The human intestinal B-cell response

(2016) J Spencer et al.   Mucosal Immunology

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Ectopic Tertiary Lymphoid Tissue in Inflammatory Bowel Disease: Protective or Provocateur?

(2016) Eóin N. McNamee et al.   Frontiers in Immunology

T regulatory cells and B cells cooperate to form a regulatory loop that maintains gut homeostasis and suppresses dextran sulfate sodium-induced colitis

(2015) L Wang et al.   Mucosal Immunology

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Interleukin-22 promotes intestinal-stem-cell-mediated epithelial regeneration

(2015) Caroline A. Lindemans et al.   NATURE

PD-L1hi B cells are critical regulators of humoral immunity

(2015) Adnan R. Khan et al.   Nature Communications

DUOX2 and DUOXA2 Form the Predominant Enzyme System Capable of Producing the Reactive Oxygen Species H2O2 in Active Ulcerative Colitis and are Modulated by 5-Aminosalicylic Acid

(2014) Tammie S. MacFie et al.   INFLAMMATORY BOWEL DISEASES

Plasma Cells in the Mucosa of Patients with Inflammatory Bowel Disease Produce Granzyme B and Possess Cytotoxic Activities

(2014) M. L. Cupi et al.   JOURNAL OF IMMUNOLOGY

Mesenchymal Stromal Cells: Sensors and Switchers of Inflammation

(2013) Maria Ester Bernardo et al.   Cell Stem Cell

Efficient B Cell Depletion via Diphtheria Toxin in CD19-Cre/iDTR Mice

(2013) Filiz Demircik et al.   PLoS One

Interleukin-22 Protects Intestinal Stem Cells from Immune-Mediated Tissue Damage and Regulates Sensitivity to Graft versus Host Disease

(2012) Alan M. Hanash et al.   IMMUNITY

Intestinal stromal cells in mucosal immunity and homeostasis

(2012) B M J Owens et al.   Mucosal Immunology

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Lymphatics, tertiary lymphoid organs and the granulomas of Crohn’s disease: an immunohistochemical study

(2011) R. Sura et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Distinct Developmental Requirements for Isolated Lymphoid Follicle Formation in the Small and Large Intestine

(2011) Kathryn A. Knoop et al.   AMERICAN JOURNAL OF PATHOLOGY

B Lymphocyte intestinal homing in inflammatory bowel disease

(2011) Caterina Defendenti et al.   BMC IMMUNOLOGY

MyD88 and Retinoic Acid Signaling Pathways Interact to Modulate Gastrointestinal Activities of Dendritic Cells

(2011) Eduardo J. Villablanca et al.   GASTROENTEROLOGY

Randomised placebo-controlled trial of rituximab (anti-CD20) in active ulcerative colitis

(2011) K. Leiper et al.   GUT

B Cells Exposed to Enterobacterial Components Suppress Development of Experimental Colitis

(2011) Esben Gjerlff Wedebye Schmidt et al.   INFLAMMATORY BOWEL DISEASES

Microbiota-induced tertiary lymphoid tissues aggravate inflammatory disease in the absence of RORγt and LTi cells

(2010) Matthias Lochner et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Cutting Edge: Hierarchy of Maturity of Murine Memory B Cell Subsets

(2010) M. M. Tomayko et al.   JOURNAL OF IMMUNOLOGY

Regulatory role of B-1 B cells in chronic colitis

(2008) Y. Shimomura et al.   INTERNATIONAL IMMUNOLOGY

A unique B2 B cell subset in the intestine

(2008) Yasuyo Shimomura et al.   JOURNAL OF EXPERIMENTAL MEDICINE