Spatiotemporal analysis of human intestinal development at single-cell resolution

Single-Cell Transcriptome Atlas of Murine Endothelial Cells

(2020) Joanna Kalucka et al.   CELL

Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient

(2020) Neil McCarthy et al.   Cell Stem Cell

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

(2020) Lei Zhang et al.   CELL

High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

(2020) Joep Beumer et al.   CELL

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

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

The Human and Mouse Enteric Nervous System at Single-Cell Resolution

(2020) Eugene Drokhlyansky et al.   CELL

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

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

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

(2020) Rasa Elmentaite et al.   DEVELOPMENTAL CELL

Anti-LRP5/6 VHHs promote differentiation of Wnt-hypersensitive intestinal stem cells

(2019) Nicola Fenderico et al.   Nature Communications

Colonic epithelial cell diversity in health and inflammatory bowel disease

(2019) Kaushal Parikh et al.   NATURE

Human Fetal TNF-α-Cytokine-Producing CD4+ Effector Memory T Cells Promote Intestinal Development and Mediate Inflammation Early in Life

(2019) Renée R.C.E. Schreurs et al.   IMMUNITY

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

(2019) Helmuth Gehart et al.   CELL

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

Discovery of a CD10-negative B-progenitor in human fetal life identifies unique ontogeny-related developmental programs

(2019) Sorcha O’Byrne et al.   BLOOD

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

Intestinal epithelial cells: at the interface of the microbiota and mucosal immunity

(2019) Amelia T. Soderholm et al.   IMMUNOLOGY

Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine

(2019) Yalong Wang et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Decoding human fetal liver haematopoiesis

(2019) Dorin-Mirel Popescu et al.   NATURE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Endothelial specific deletion of FOXO1 alters pericyte coverage in the developing retina

(2019) Kenta Niimi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Intestinal Neurod1 expression impairs paneth cell differentiation and promotes enteroendocrine lineage specification

(2019) Hui Joyce Li et al.   Scientific Reports

WNT Signaling Perturbations Underlie the Genetic Heterogeneity of Robinow Syndrome

(2018) Janson J. White et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

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

Hirschsprung disease — integrating basic science and clinical medicine to improve outcomes

(2018) Robert O. Heuckeroth   Nature Reviews Gastroenterology & Hepatology

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

Iron Promotes Intestinal Development in Neonatal Piglets

(2018) Yutian Pu et al.   Nutrients

Stereotypic Immune System Development in Newborn Children

(2018) Axel Olin et al.   CELL

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

The Human Cell Atlas Bone Marrow Single-Cell Interactive Web Portal

(2018) Stuart Hay et al.   EXPERIMENTAL HEMATOLOGY

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

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

(2018) Bahar Degirmenci et al.   NATURE

Necrotizing enterocolitis leads to disruption of tight junctions and increase in gut permeability in a mouse model

(2018) Srikanth Ravisankar et al.   BMC Pediatrics

SPINT2 (HAI-2) missense variants identified in congenital sodium diarrhea/tufting enteropathy affect the ability of HAI-2 to inhibit prostasin but not matriptase

(2018) Lasse Holt-Danborg et al.   HUMAN MOLECULAR GENETICS

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

(2018) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

Origin, Differentiation, and Function of Intestinal Macrophages

(2018) Calum C. Bain et al.   Frontiers in Immunology

Upregulation of PD-L1 by SPP1 mediates macrophage polarization and facilitates immune escape in lung adenocarcinoma

(2017) Yan Zhang et al.   EXPERIMENTAL CELL RESEARCH

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Lineage-dependent spatial and functional organization of the mammalian enteric nervous system

(2017) Reena Lasrado et al.   SCIENCE

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

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

(2017) Moon Young Lee et al.   PLoS One

Identification of blood vascular endothelial stem cells by the expression of protein C receptor

(2016) Qing Cissy Yu et al.   CELL RESEARCH

Transcriptome of the inner circular smooth muscle of the developing mouse intestine: Evidence for regulation of visceral smooth muscle genes by the hedgehog target gene,cJun

(2016) Katherine Gurdziel et al.   DEVELOPMENTAL DYNAMICS

Fibroblasts and myofibroblasts of the intestinal lamina propria in physiology and disease

(2016) Manolis Roulis et al.   DIFFERENTIATION

Zinc finger transcription factor Casz1 expression is regulated by homeodomain transcription factor Prrxl1 in embryonic spinal dorsal horn late-born excitatory interneurons

(2016) César B. Monteiro et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Bending Gradients: How the Intestinal Stem Cell Gets Its Home

(2015) Amy E. Shyer et al.   CELL

PRRX1- and PRRX2-positive mesenchymal stem/progenitor cells are involved in vasculogenesis during rat embryonic pituitary development

(2015) Masashi Higuchi et al.   CELL AND TISSUE RESEARCH

Villification in the mouse: Bmp signals control intestinal villus patterning

(2015) Katherine D. Walton et al.   DEVELOPMENT

Forkhead Box F2 Regulation of Platelet-derived Growth Factor and Myocardin/Serum Response Factor Signaling Is Essential for Intestinal Development

(2015) Craig Bolte et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Malrotation and intestinal atresias

(2014) Stephen D. Adams et al.   EARLY HUMAN DEVELOPMENT

Dynamic Interactions between Intermediate Neurogenic Progenitors and Radial Glia in Embryonic Mouse Neocortex: Potential Role in Dll1-Notch Signaling

(2013) B. R. Nelson et al.   JOURNAL OF NEUROSCIENCE

Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration

(2013) Nick Barker   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Villification: How the Gut Gets Its Villi

(2013) A. E. Shyer et al.   SCIENCE

The UCSC genome browser and associated tools

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

Regulation of endodermal differentiation of human embryonic stem cells through integrin-ECM interactions

(2012) D A Brafman et al.   CELL DEATH AND DIFFERENTIATION

DGAT1 mutation is linked to a congenital diarrheal disorder

(2012) Joel T. Haas et al.   JOURNAL OF CLINICAL INVESTIGATION

Identification and prospective isolation of a mesothelial precursor lineage giving rise to smooth muscle cells and fibroblasts for mammalian internal organs and their vasculature

(2012) Yuval Rinkevich et al.   NATURE CELL BIOLOGY

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

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

Novel functional roles for enteric glia in the gastrointestinal tract

(2012) Brian D. Gulbransen et al.   Nature Reviews Gastroenterology & Hepatology

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

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

Intestinal myofibroblasts: targets for stem cell therapy

(2011) R. C. Mifflin et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Targeted deletion of Hand2 in enteric neural precursor cells affects its functions in neurogenesis, neurotransmitter specification and gangliogenesis, causing functional aganglionosis

(2011) J. Lei et al.   DEVELOPMENT

Vertebrate intestinal endoderm development

(2011) Jason R. Spence et al.   DEVELOPMENTAL DYNAMICS

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

Pulsatile shear and Gja5 modulate arterial identity and remodeling events during flow-driven arteriogenesis

(2010) I. Buschmann et al.   DEVELOPMENT

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

Establishment of Intestinal Identity and Epithelial-Mesenchymal Signaling by Cdx2

(2009) Nan Gao et al.   DEVELOPMENTAL CELL

Refinement of the 12q14 microdeletion syndrome: primordial dwarfism and developmental delay with or without osteopoikilosis

(2009) Francesca Mari et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

The Role of the Visceral Mesoderm in the Development of the Gastrointestinal Tract

(2009) Valérie A. McLin et al.   GASTROENTEROLOGY

Foxa1 and Foxa2 Control the Differentiation of Goblet and Enteroendocrine L- and D-Cells in Mice

(2009) Diana Z. Ye et al.   GASTROENTEROLOGY

Mortality of necrotizing enterocolitis expressed by birth weight categories

(2009) Shimae Cross Fitzgibbons et al.   JOURNAL OF PEDIATRIC SURGERY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Wnt6 signaling regulates heart muscle development during organogenesis

(2008) Danielle L. Lavery et al.   DEVELOPMENTAL BIOLOGY

Transcriptional dynamics of endodermal organ formation

(2008) Richard I. Sherwood et al.   DEVELOPMENTAL DYNAMICS

Interferon-γ Induces X-linked Inhibitor of Apoptosis-associated Factor-1 and Noxa Expression and Potentiates Human Vascular Smooth Muscle Cell Apoptosis by STAT3 Activation

(2008) Yalai Bai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Novel insights into the relationships between dendritic cell subsets in human and mouse revealed by genome-wide expression profiling

(2008) Scott H Robbins et al.   GENOME BIOLOGY