Clump sequencing exposes the spatial expression programs of intestinal secretory cells

Lgr5+ telocytes are a signaling source at the intestinal villus tip

(2020) Keren Bahar Halpern et al.   Nature Communications

A molecular cell atlas of the human lung from single-cell RNA sequencing

(2020) Kyle J. Travaglini et al.   NATURE

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

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

(2019) Helmuth Gehart et al.   CELL

Intra-Tumoral Metabolic Zonation and Resultant Phenotypic Diversification Are Dictated by Blood Vessel Proximity

(2019) Saran Kumar et al.   Cell Metabolism

MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing

(2019) Hadas Keren-Shaul et al.   Nature Protocols

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Enteroendocrine cells switch hormone expression along the crypt-to-villus BMP signalling gradient

(2018) Joep Beumer et al.   NATURE CELL BIOLOGY

Activation of intestinal tuft cell-expressed Sucnr1 triggers type 2 immunity in the mouse small intestine

(2018) Weiwei Lei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Intestinal Epithelium: Central Coordinator of Mucosal Immunity

(2018) Joannie M. Allaire et al.   TRENDS IN IMMUNOLOGY

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs

(2018) Swati Parekh et al.   GigaScience

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

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

(2018) Andreas E. Moor et al.   CELL

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

(2018) Keren Bahar Halpern et al.   NATURE BIOTECHNOLOGY

Transcriptional Heterogeneity of Beta Cells in the Intact Pancreas

(2018) Lydia Farack et al.   DEVELOPMENTAL CELL

Sox4 Promotes Atoh1-Independent Intestinal Secretory Differentiation Toward Tuft and Enteroendocrine Fates

(2018) Adam D. Gracz et al.   GASTROENTEROLOGY

Tales from the crypt: new insights into intestinal stem cells

(2018) Helmuth Gehart et al.   Nature Reviews Gastroenterology & Hepatology

Transmembrane Mucins: Signaling Receptors at the Intersection of Inflammation and Cancer

(2017) Jos P.M. van Putten et al.   Journal of Innate Immunity

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

Intestinal epithelial tuft cells initiate type 2 mucosal immunity to helminth parasites

(2016) François Gerbe et al.   NATURE

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

A sentinel goblet cell guards the colonic crypt by triggering Nlrp6-dependent Muc2 secretion

(2016) G. M. H. Birchenough et al.   SCIENCE

Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut

(2016) M. R. Howitt et al.   SCIENCE

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Tuft-cell-derived IL-25 regulates an intestinal ILC2–epithelial response circuit

(2015) Jakob von Moltke et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

RIG-I in RNA virus recognition

(2015) Alison M. Kell et al.   VIROLOGY

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

The mucus and mucins of the goblet cells and enterocytes provide the first defense line of the gastrointestinal tract and interact with the immune system

(2014) Thaher Pelaseyed et al.   IMMUNOLOGICAL REVIEWS

A promoter-level mammalian expression atlas

(2014)   NATURE

The integrin adhesome: from genes and proteins to human disease

(2014) Sabina E. Winograd-Katz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single-molecule mRNA detection and counting in mammalian tissue

(2013) Anna Lyubimova et al.   Nature Protocols

The intestinal epithelium tuft cells: specification and function

(2012) François Gerbe et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

(2012) Johannes Schindelin et al.   NATURE METHODS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Indoleamine 2,3-dioxygenase in intestinal immunity and inflammation

(2009) Bobby J. Cherayil   INFLAMMATORY BOWEL DISEASES