TGFB1 induces fetal reprogramming and enhances intestinal regeneration

Aberrant cell state plasticity mediated by developmental reprogramming precedes colorectal cancer initiation

(2023) Pratyusha Bala et al.   Science Advances

Transplantation of intestinal organoids into a mouse model of colitis

(2022) Satoshi Watanabe et al.   Nature Protocols

Lymphatics and fibroblasts support intestinal stem cells in homeostasis and injury

(2022) Norihiro Goto et al.   Cell Stem Cell

Establishment of intestinal organoid cultures modeling injury-associated epithelial regeneration

(2021) Molong Qu et al.   CELL RESEARCH

Interferon b drives intestinal regeneration after radiation

(2021) Brian J. Leibowitz et al.   Science Advances

Injury-Induced Cellular Plasticity Drives Intestinal Regeneration

(2021) Anne R. Meyer et al.   Cellular and Molecular Gastroenterology and Hepatology

Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient

(2020) Neil McCarthy et al.   Cell Stem Cell

Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells

(2020) Kazutaka Murata 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

Organoid-based regenerative medicine for inflammatory bowel disease

(2020) Ryuichi Okamoto et al.   Regenerative Therapy

Paracrine orchestration of intestinal tumorigenesis by a mesenchymal niche

(2020) Manolis Roulis et al.   NATURE

LIF is essential for ISC function and protects against radiation-induced gastrointestinal syndrome

(2020) Huaying Wang et al.   Cell Death & Disease

Lineage reversion drives WNT independence in intestinal cancer

(2020) Teng Han et al.   Cancer Discovery

Cycling Stem Cells Are Radioresistant and Regenerate the Intestine

(2020) Xiaole Sheng et al.   Cell Reports

At the Forefront of the Mucosal Barrier: The Role of Macrophages in the Intestine

(2020) Barbara Ruder et al.   Cells

Mapping Development of the Human Intestinal Niche at Single-Cell Resolution

(2020) Emily M. Holloway et al.   Cell Stem Cell

Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell

(2019) Arshad Ayyaz et al.   NATURE

A reinforcing HNF4–SMAD4 feed-forward module stabilizes enterocyte identity

(2019) Lei Chen et al.   NATURE GENETICS

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Long-Term Culture Captures Injury-Repair Cycles of Colonic Stem Cells

(2019) Yi Wang et al.   CELL

R-spondin 3 promotes stem cell recovery and epithelial regeneration in the colon

(2019) Christine Harnack et al.   Nature Communications

Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements

(2018) Luca Pinello et al.   BIOINFORMATICS

Paneth Cell Multipotency Induced by Notch Activation following Injury

(2018) Shiyan Yu et al.   Cell Stem Cell

YAP/TAZ-Dependent Reprogramming of Colonic Epithelium Links ECM Remodeling to Tissue Regeneration

(2018) Shiro Yui et al.   Cell Stem Cell

PDGFRα+pericryptal stromal cells are the critical source of Wnts and RSPO3 for murine intestinal stem cells in vivo

(2018) Gediminas Greicius et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

YAP and TAZ regulate adherens junction dynamics and endothelial cell distribution during vascular development

(2018) Filipa Neto et al.   eLife

Phospho-regulation of ATOH1 Is Required for Plasticity of Secretory Progenitors and Tissue Regeneration

(2018) Goran Tomic et al.   Cell Stem Cell

Neutrophils Promote Amphiregulin Production in Intestinal Epithelial Cells through TGF-β and Contribute to Intestinal Homeostasis

(2018) Feidi Chen et al.   JOURNAL OF IMMUNOLOGY

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche

(2018) Ysbrand M. Nusse et al.   NATURE

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

(2018) Michal Shoshkes-Carmel et al.   NATURE

GLI1-expressing mesenchymal cells form the essential Wnt-secreting niche for colon stem cells

(2018) Bahar Degirmenci et al.   NATURE

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation

(2018) Moshe Biton et al.   CELL

CD34+mesenchymal cells are a major component of the intestinal stem cells niche at homeostasis and after injury

(2017) Igor Stzepourginski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

YAP regulates cell mechanics by controlling focal adhesion assembly

(2017) Giorgia Nardone et al.   Nature Communications

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

(2016) Paul W. Tetteh et al.   Cell Stem Cell

Prostaglandin E2 promotes intestinal repair through an adaptive cellular response of the epithelium

(2016) Hiroyuki Miyoshi et al.   EMBO JOURNAL

Msi RNA-binding proteins control reserve intestinal stem cell quiescence

(2016) Maryam Yousefi et al.   JOURNAL OF CELL BIOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

Macrophage-derived extracellular vesicle-packaged WNTs rescue intestinal stem cells and enhance survival after radiation injury

(2016) Subhrajit Saha et al.   Nature Communications

SOX9 Maintains Reserve Stem Cells and Preserves Radioresistance in Mouse Small Intestine

(2015) Kyle C. Roche et al.   GASTROENTEROLOGY

Yap-dependent reprogramming of Lgr5+ stem cells drives intestinal regeneration and cancer

(2015) Alex Gregorieff et al.   NATURE

Persistent cell migration and adhesion rely on retrograde transport of β1 integrin

(2015) Massiullah Shafaq-Zadah et al.   NATURE CELL BIOLOGY

Mapping early fate determination in Lgr5+ crypt stem cells using a novel Ki67-RFP allele

(2014) O. Basak et al.   EMBO JOURNAL

Lgr5+ Stem Cells Are Indispensable for Radiation-Induced Intestinal Regeneration

(2013) Ciara Metcalfe et al.   Cell Stem Cell

Mechanotransduction and YAP-dependent matrix remodelling is required for the generation and maintenance of cancer-associated fibroblasts

(2013) Fernando Calvo et al.   NATURE CELL BIOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Identification of Lgr5-Independent Spheroid-Generating Progenitors of the Mouse Fetal Intestinal Epithelium

(2013) Roxana C. Mustata et al.   Cell Reports

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers

(2012) Javier Muñoz et al.   EMBO JOURNAL

Dll1+ secretory progenitor cells revert to stem cells upon crypt damage

(2012) Johan H. van Es et al.   NATURE CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Wnt5a Potentiates TGF-  Signaling to Promote Colonic Crypt Regeneration After Tissue Injury

(2012) H. Miyoshi et al.   SCIENCE

The limitations of simple gene set enrichment analysis assuming gene independence

(2012) Pablo Tamayo et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Amphiregulin Promotes Intestinal Epithelial Regeneration: Roles of Intestinal Subepithelial Myofibroblasts

(2010) Jinyi Shao et al.   ENDOCRINOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

YAP-dependent induction of amphiregulin identifies a non-cell-autonomous component of the Hippo pathway

(2009) Jianmin Zhang et al.   NATURE CELL BIOLOGY

TEAD mediates YAP-dependent gene induction and growth control

(2008) B. Zhao et al.   GENES & DEVELOPMENT

Wound repair and regeneration

(2008) Geoffrey C. Gurtner et al.   NATURE

Efficient colonic mucosal wound repair requires Trem2 signaling

(2008) H. Seno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY