Charting human development using a multi-endodermal organ atlas and organoid models

Spatiotemporal analysis of human intestinal development at single-cell resolution

(2021) David Fawkner-Corbett et al.   CELL

Novel variants in the stem cell niche factor WNT2B define the disease phenotype as a congenital enteropathy with ocular dysgenesis

(2021) Yanjia Jason Zhang et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Dysregulation of the NRG1/ERBB pathway causes a developmental disorder with gastrointestinal dysmotility in humans

(2021) Thuy-Linh Le et al.   JOURNAL OF CLINICAL INVESTIGATION

Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient

(2020) Neil McCarthy et al.   Cell Stem Cell

In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution

(2020) Alyssa J. Miller et al.   DEVELOPMENTAL CELL

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

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

(2020) Thierry Jardé et al.   Cell Stem Cell

AXL Is a Potential Target for the Treatment of Intestinal Fibrosis

(2020) Calen A Steiner et al.   INFLAMMATORY BOWEL DISEASES

Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution

(2020) Cameron S. Cowan et al.   CELL

Differentiation of Human Intestinal Organoids with Endogenous Vascular Endothelial Cells

(2020) Emily M. Holloway et al.   DEVELOPMENTAL CELL

Cellular and molecular architecture of the intestinal stem cell niche

(2020) Neil McCarthy et al.   NATURE CELL BIOLOGY

Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis

(2020) Lu Han et al.   Nature Communications

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

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

Novel ACTG2 variants disclose allelic heterogeneity and bi‐allelic inheritance in pediatric chronic intestinal pseudo‐obstruction

(2020) Ivana Matera et al.   CLINICAL GENETICS

Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease

(2020) Rasa Elmentaite et al.   DEVELOPMENTAL CELL

Generation of lung organoids from human pluripotent stem cells in vitro

(2019) Alyssa J. Miller et al.   Nature Protocols

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

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

Flow-enhanced vascularization and maturation of kidney organoids in vitro

(2019) Kimberly A. Homan et al.   NATURE METHODS

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution

(2019) Deanne M. Taylor et al.   DEVELOPMENTAL CELL

The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development

(2019) Namit Kumar et al.   DEVELOPMENT

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

(2019) Christopher S. Smillie et al.   CELL

Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts

(2019) Carlo C. Campa et al.   NATURE METHODS

Mapping human cell phenotypes to genotypes with single-cell genomics

(2019) J. Gray Camp et al.   SCIENCE

Organoid single-cell genomic atlas uncovers human-specific features of brain development

(2019) Sabina Kanton et al.   NATURE

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

Multiplexed activation of endogenous genes by CRISPRa elicits potent antitumor immunity

(2019) Guangchuan Wang et al.   NATURE IMMUNOLOGY

Recent advances in deriving human endodermal tissues from pluripotent stem cells

(2019) Daniel O Kechele et al.   CURRENT OPINION IN CELL BIOLOGY

Neonatal-Onset Chronic Diarrhea Caused by Homozygous Nonsense WNT2B Mutations

(2018) Amy E. O’Connell et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

In Vitro Induction and In Vivo Engraftment of Lung Bud Tip Progenitor Cells Derived from Human Pluripotent Stem Cells

(2018) Alyssa J. Miller et al.   Stem Cell Reports

Mechanically induced development and maturation of human intestinal organoids in vivo

(2018) Holly M. Poling et al.   Nature Biomedical Engineering

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

(2018) James Kinchen et al.   CELL

Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis

(2018) Andreas E. Moor et al.   CELL

Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification

(2018) Stephen L. Trisno et al.   Cell Stem Cell

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

(2018) Michal Shoshkes-Carmel et al.   NATURE

Progress and potential in organoid research

(2018) Giuliana Rossi et al.   NATURE REVIEWS GENETICS

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

(2018) Hui Hu et al.   NUCLEIC ACIDS RESEARCH

The Intestinal Stem Cell Niche: Homeostasis and Adaptations

(2018) António J.M. Santos et al.   TRENDS IN CELL BIOLOGY

Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics

(2018) Haojia Wu et al.   Cell Stem Cell

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

Wnt/β-catenin promotes gastric fundus specification in mice and humans

(2017) Kyle W. McCracken et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

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

Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium

(2017) David R Hill et al.   eLife

Human embryonic lung epithelial tips are multipotent progenitors that can be expanded in vitro as long-term self-renewing organoids

(2017) Marko Z Nikolić et al.   eLife

Neural Crest Cell Implantation Restores Enteric Nervous System Function and Alters the Gastrointestinal Transcriptome in Human Tissue-Engineered Small Intestine

(2017) Christopher R. Schlieve et al.   Stem Cell Reports

Engineered human pluripotent-stem-cell-derived intestinal tissues with a functional enteric nervous system

(2016) Michael J Workman et al.   NATURE MEDICINE

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

Intestinal organoids: A model of intestinal fibrosis for evaluating anti-fibrotic drugs

(2015) Eva S. Rodansky et al.   EXPERIMENTAL AND MOLECULAR PATHOLOGY

Interaction of Salmonella enterica Serovar Typhimurium with Intestinal Organoids Derived from Human Induced Pluripotent Stem Cells

(2015) Jessica L. Forbester et al.   INFECTION AND IMMUNITY

In vitro generation of human pluripotent stem cell derived lung organoids

(2015) Briana R Dye et al.   eLife

Generation of tissue-engineered small intestine using embryonic stem cell-derived human intestinal organoids

(2015) S. R. Finkbeiner et al.   Biology Open

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

Role Played by Prx1-Dependent Extracellular Matrix Properties in Vascular Smooth Muscle Development in Embryonic Lungs

(2015) Kaori Ihida-Stansbury et al.   Pulmonary Circulation

NANOG and CDX2 Pattern Distinct Subtypes of Human Mesoderm during Exit from Pluripotency

(2014) Sasha Mendjan et al.   Cell Stem Cell

How to make an intestine

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

Persistence and Toxin Production by Clostridium difficile within Human Intestinal Organoids Result in Disruption of Epithelial Paracellular Barrier Function

(2014) Jhansi L. Leslie et al.   INFECTION AND IMMUNITY

Modelling human development and disease in pluripotent stem-cell-derived gastric organoids

(2014) Kyle W. McCracken et al.   NATURE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

An in vivo model of human small intestine using pluripotent stem cells

(2014) Carey L Watson et al.   NATURE MEDICINE

The EGFR Family: Not So Prototypical Receptor Tyrosine Kinases

(2014) M. A. Lemmon et al.   Cold Spring Harbor Perspectives in Biology

Abrogation of Eya1/Six1 disrupts the saccular phase of lung morphogenesis and causes remodeling

(2013) Karol Lu et al.   DEVELOPMENTAL BIOLOGY

Endothelial PAS Domain Protein 1 Activates the Inflammatory Response in the Intestinal Epithelium to Promote Colitis in Mice

(2013) Xiang Xue et al.   GASTROENTEROLOGY

Production of an aminoterminally truncated, stable type of bioactive mouse fibroblast growth factor 4 in Escherichia coli

(2013) Saiko Sugawara et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

ER Stress Causes Rapid Loss of Intestinal Epithelial Stemness through Activation of the Unfolded Protein Response

(2013) Jarom Heijmans et al.   Cell Reports

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

(2012) Aiping Du et al.   DEVELOPMENTAL BIOLOGY

Stem Cell-Derived Human Intestinal Organoids as an Infection Model for Rotaviruses

(2012) S. R. Finkbeiner et al.   mBio

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

BRACHYURY and CDX2 Mediate BMP-Induced Differentiation of Human and Mouse Pluripotent Stem Cells into Embryonic and Extraembryonic Lineages

(2011) Andreia S. Bernardo et al.   Cell Stem Cell

Cdx2 determines the fate of postnatal intestinal endoderm

(2011) E. J. Stringer et al.   DEVELOPMENT

Six1 transcription factor is critical for coordination of epithelial, mesenchymal and vascular morphogenesis in the mammalian lung

(2011) Ahmed H.K. El-Hashash et al.   DEVELOPMENTAL BIOLOGY

Generating human intestinal tissue from pluripotent stem cells in vitro

(2011) Kyle W McCracken et al.   Nature Protocols

Cdx2 regulates patterning of the intestinal epithelium

(2010) Stephanie Grainger et al.   DEVELOPMENTAL BIOLOGY

Differentiation-Specific Histone Modifications Reveal Dynamic Chromatin Interactions and Partners for the Intestinal Transcription Factor CDX2

(2010) Michael P. Verzi et al.   DEVELOPMENTAL CELL

Indian Hedgehog Regulates Intestinal Stem Cell Fate Through Epithelial−Mesenchymal Interactions During Development

(2010) Cynthia Kosinski et al.   GASTROENTEROLOGY

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

(2010) Jason R. Spence et al.   NATURE

Onecut-2 knockout mice fail to thrive during early postnatal period and have altered patterns of gene expression in small intestine

(2010) Mary R. Dusing et al.   PHYSIOLOGICAL GENOMICS

Matrigel: A complex protein mixture required for optimal growth of cell culture

(2010) Chris S. Hughes et al.   PROTEOMICS

Vertebrate Endoderm Development and Organ Formation

(2009) Aaron M. Zorn et al.   Annual Review of Cell and Developmental Biology

Establishment of Intestinal Identity and Epithelial-Mesenchymal Signaling by Cdx2

(2009) Nan Gao et al.   DEVELOPMENTAL CELL

Sox17 Regulates Organ Lineage Segregation of Ventral Foregut Progenitor Cells

(2009) Jason R. Spence et al.   DEVELOPMENTAL CELL

Overlapping functions of Cdx1, Cdx2, and Cdx4 in the development of the amphibian Xenopus tropicalis

(2009) Laura Faas et al.   DEVELOPMENTAL DYNAMICS

OLFM4 Is a Robust Marker for Stem Cells in Human Intestine and Marks a Subset of Colorectal Cancer Cells

(2009) Laurens G. van der Flier et al.   GASTROENTEROLOGY

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

(2009) Akifumi Ootani et al.   NATURE MEDICINE

Increased Cdx protein dose effects upon axial patterning in transgenic lines of mice

(2008) S. J. Gaunt et al.   DEVELOPMENT

Functional selectivity of EGF family peptide growth factors: Implications for cancer

(2008) Kristy J. Wilson et al.   PHARMACOLOGY & THERAPEUTICS