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

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

Mesenchymal Niche-Derived Neuregulin-1 Drives Intestinal Stem Cell Proliferation and Regeneration of Damaged Epithelium

(2020) Thierry Jardé et al.   Cell Stem Cell

Single-cell analysis uncovers fibroblast heterogeneity and criteria for fibroblast and mural cell identification and discrimination

(2020) Lars Muhl et al.   Nature Communications

Nonadhesive Alginate Hydrogels Support Growth of Pluripotent Stem Cell-Derived Intestinal Organoids

(2019) Meghan M. Capeling et al.   Stem Cell Reports

Colonic epithelial cell diversity in health and inflammatory bowel disease

(2019) Kaushal Parikh et al.   NATURE

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping

(2019) Helmuth Gehart et al.   CELL

Self-organization and symmetry breaking in intestinal organoid development

(2019) Denise Serra et al.   NATURE

The emergent landscape of the mouse gut endoderm at single-cell resolution

(2019) Sonja Nowotschin et al.   NATURE

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

(2019) Christopher S. Smillie et al.   CELL

Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

(2019) Jerome C. Martin et al.   CELL

Enteroendocrine and tuft cells support Lgr5 stem cells on Paneth cell depletion

(2019) Johan H. van Es et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification, isolation and characterization of human LGR5-positive colon adenoma cells

(2018) Michael K. Dame et al.   DEVELOPMENT

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

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

(2018) James Kinchen et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

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

(2018) Michal Shoshkes-Carmel et al.   NATURE

Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition

(2018) Masayuki Fujii et al.   Cell Stem Cell

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development

(2017) Judith Kraiczy et al.   GUT

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Synthetic hydrogels for human intestinal organoid generation and colonic wound repair

(2017) Ricardo Cruz-Acuña et al.   NATURE CELL BIOLOGY

Morphogenesis and maturation of the embryonic and postnatal intestine

(2017) Alana M. Chin et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Organoids: Modeling Development and the Stem Cell Niche in a Dish

(2016) Kai Kretzschmar et al.   DEVELOPMENTAL CELL

Organoid Models of Human Gastrointestinal Development and Disease

(2016) Priya H. Dedhia et al.   GASTROENTEROLOGY

Designer matrices for intestinal stem cell and organoid culture

(2016) Nikolce Gjorevski et al.   NATURE

Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo

(2015) Stacy R. Finkbeiner et al.   Stem Cell Reports

How to make an intestine

(2014) J. M. Wells et al.   DEVELOPMENT

Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays

(2014) Kelli L VanDussen et al.   GUT

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Transplantation of Expanded Fetal Intestinal Progenitors Contributes to Colon Regeneration after Injury

(2013) Robert P. Fordham et al.   Cell Stem Cell

In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture

(2013) Hiroyuki Miyoshi et al.   Nature Protocols

Arx is required for normal enteroendocrine cell development in mice and humans

(2012) Aiping Du et al.   DEVELOPMENTAL BIOLOGY

The Homeodomain-Containing Transcription Factors Arx and Pax4 Control Enteroendocrine Subtype Specification in Mice

(2012) Anthony Beucher 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

Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts

(2010) Toshiro Sato et al.   NATURE

Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro

(2010) Jason R. Spence et al.   NATURE

SAM pointed domain ETS factor (SPDEF) regulates terminal differentiation and maturation of intestinal goblet cells

(2009) Taeko K. Noah et al.   EXPERIMENTAL CELL RESEARCH

The Ets-Domain Transcription Factor Spdef Promotes Maturation of Goblet and Paneth Cells in the Intestinal Epithelium

(2009) Alex Gregorieff et al.   GASTROENTEROLOGY

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

(2009) Toshiro Sato et al.   NATURE

Sustained in vitro intestinal epithelial culture within a Wnt-dependent stem cell niche

(2009) Akifumi Ootani et al.   NATURE MEDICINE

Requirement of Notch activation during regeneration of the intestinal epithelia

(2008) Ryuichi Okamoto et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY