Cells of the human intestinal tract mapped across space and time

Spatiotemporal analysis of human intestinal development at single-cell resolution

(2021) David Fawkner-Corbett et al.   CELL

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing

(2021) Luca Mazzurana et al.   CELL RESEARCH

Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics

(2021) Hamish W. King et al.   Science Immunology

A roadmap for the Human Developmental Cell Atlas

(2021) Muzlifah Haniffa et al.   NATURE

Distinct microbial and immune niches of the human colon

(2020) Kylie R. James et al.   NATURE IMMUNOLOGY

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

(2020) Mirjana Efremova et al.   Nature Protocols

High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

(2020) Joep Beumer et al.   CELL

Lymph node stromal cells: cartographers of the immune system

(2020) Akshay T. Krishnamurty et al.   NATURE IMMUNOLOGY

SARS-CoV-2 productively infects human gut enterocytes

(2020) Mart M. Lamers et al.   SCIENCE

Enteroendocrine Dynamics – New Tools Reveal Hormonal Plasticity in the Gut

(2020) Joep Beumer et al.   ENDOCRINE REVIEWS

Severe Autoinflammatory Manifestations and Antibody Deficiency Due to Novel Hypermorphic PLCG2 Mutations

(2020) Andrea Martín-Nalda et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis

(2020) Daniele Corridoni et al.   NATURE MEDICINE

Distinctive Subpopulations of Stromal Cells Are Present in Human Lymph Nodes Infiltrated with Melanoma

(2020) Jennifer Eom et al.   Cancer Immunology Research

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

(2020) Eugene Drokhlyansky et al.   CELL

Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ.

(2020) Aaron A. May-Zhang et al.   GASTROENTEROLOGY

Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses

(2020) Brigid S. Boland et al.   Science Immunology

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

Diversification of molecularly defined myenteric neuron classes revealed by single-cell RNA sequencing

(2020) Khomgrit Morarach et al.   NATURE NEUROSCIENCE

Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model

(2020) Yu-Han Hung et al.   NUCLEIC ACIDS RESEARCH

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

(2020) Matthew D Young et al.   GigaScience

Memory CD4+ T cells are generated in the human fetal intestine

(2019) Na Li et al.   NATURE IMMUNOLOGY

Two distinct interstitial macrophage populations coexist across tissues in specific subtissular niches

(2019) Svetoslav Chakarov et al.   SCIENCE

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

Comparison of Human and Murine Enteroendocrine Cells by Transcriptomic and Peptidomic Profiling

(2019) Geoffrey P. Roberts et al.   DIABETES

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

(2019) Helmuth Gehart et al.   CELL

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

(2019) Arshad Ayyaz et al.   NATURE

ILC3 function as a double-edged sword in inflammatory bowel diseases

(2019) Boning Zeng et al.   Cell Death & Disease

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

Single-Cell Survey of Human Lymphatics Unveils Marked Endothelial Cell Heterogeneity and Mechanisms of Homing for Neutrophils

(2019) Akira Takeda et al.   IMMUNITY

TCR Sequencing Reveals the Distinct Development of Fetal and Adult Human Vγ9Vδ2 T Cells

(2019) Maria Papadopoulou et al.   JOURNAL OF IMMUNOLOGY

Mucosal Profiling of Pediatric-Onset Colitis and IBD Reveals Common Pathogenics and Therapeutic Pathways

(2019) Bing Huang et al.   CELL

Decoding human fetal liver haematopoiesis

(2019) Dorin-Mirel Popescu et al.   NATURE

Mechanosensing by Peyer’s patch stroma regulates lymphocyte migration and mucosal antibody responses

(2019) Jonathan E. Chang et al.   NATURE IMMUNOLOGY

Transcription and Signaling Regulators in Developing Neuronal Subtypes of Mouse and Human Enteric Nervous System

(2018) Fatima Memic et al.   GASTROENTEROLOGY

Single-Cell RNA Sequencing of Lymph Node Stromal Cells Reveals Niche-Associated Heterogeneity

(2018) Lauren B. Rodda et al.   IMMUNITY

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

(2018) James Kinchen et al.   CELL

Identification of Genes Associated With Hirschsprung Disease, Based on Whole-Genome Sequence Analysis, and Potential Effects on Enteric Nervous System Development

(2018) Clara Sze-man Tang et al.   GASTROENTEROLOGY

Hyaluronan Receptor LYVE-1-Expressing Macrophages Maintain Arterial Tone through Hyaluronan-Mediated Regulation of Smooth Muscle Cell Collagen

(2018) Hwee Ying Lim et al.   IMMUNITY

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

High-resolution genetic mapping of putative causal interactions between regions of open chromatin

(2018) Natsuhiko Kumasaka et al.   NATURE GENETICS

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

(2017) Judith Kraiczy et al.   GUT

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

(2017) Katrina M de Lange et al.   NATURE GENETICS

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

(2017) Reena Lasrado et al.   SCIENCE

The lymphoid system: a review of species differences

(2017) Patrick J. Haley   Journal of Toxicologic Pathology

Sporadic Hirschsprung Disease: Mutational Spectrum and Novel Candidate Genes Revealed by Next-generation Sequencing

(2017) Zhen Zhang et al.   Scientific Reports

Neuropilin-1 Is Expressed on Lymphoid Tissue Residing LTi-like Group 3 Innate Lymphoid Cells and Associated with Ectopic Lymphoid Aggregates

(2017) Medya Mara Shikhagaie et al.   Cell Reports

Specification and Diversification of Pericytes and Smooth Muscle Cells from Mesenchymoangioblasts

(2017) Akhilesh Kumar et al.   Cell Reports

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

(2017) Moon Young Lee et al.   PLoS One

Mouse models of Hirschsprung disease and other developmental disorders of the enteric nervous system: Old and new players

(2016) Nadege Bondurand et al.   DEVELOPMENTAL BIOLOGY

Germinal Center B Cell Dynamics

(2016) Luka Mesin et al.   IMMUNITY

Nestin-Expressing Precursors Give Rise to Both Endothelial as well as Nonendothelial Lymph Node Stromal Cells

(2016) Jasper J. Koning et al.   JOURNAL OF IMMUNOLOGY

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Genome-wide analysis of gene expression during adipogenesis in human adipose-derived stromal cells reveals novel patterns of gene expression during adipocyte differentiation

(2016) Melvin Anyasi Ambele et al.   Stem Cell Research

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1.

(2015) Namita T. Gupta et al.   BIOINFORMATICS

Phenotypic and Morphological Properties of Germinal Center Dark ZoneCxcl12-Expressing Reticular Cells

(2015) Lauren B. Rodda et al.   JOURNAL OF IMMUNOLOGY

Trajectories of cell-cycle progression from fixed cell populations

(2015) Gabriele Gut et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Intraperitoneal Immunization with Cry1Ac Protoxin fromBacillus thuringiensisProvokes Upregulation of Fc-Gamma-II/and Fc-Gamma-III Receptors Associated with IgG in the Intestinal Epithelium of Mice

(2015) L. Moreno-Fierros et al.   SCANDINAVIAN JOURNAL OF IMMUNOLOGY

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

(2014) Jason A. Vander Heiden et al.   BIOINFORMATICS

Human Visceral-Fat-Specific Glucocorticoid Tuning of Adipogenesis

(2013) Jean Galitzky et al.   Cell Metabolism

Monogenic diseases associated with intestinal inflammation: implications for the understanding of inflammatory bowel disease

(2013) Holm H Uhlig   GUT

Germinal Center Centroblasts Transition to a Centrocyte Phenotype According to a Timed Program and Depend on the Dark Zone for Effective Selection

(2013) Oliver Bannard et al.   IMMUNITY

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

Lineage-Specific Expression of Bestrophin-2 and Bestrophin-4 in Human Intestinal Epithelial Cells

(2013) Go Ito et al.   PLoS One

Lymphatics, tertiary lymphoid organs and the granulomas of Crohn’s disease: an immunohistochemical study

(2011) R. Sura et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Voltage-Gated Na+ Channel  1B: A Secreted Cell Adhesion Molecule Involved in Human Epilepsy

(2011) G. A. Patino et al.   JOURNAL OF NEUROSCIENCE

LRRN4 and UPK3B Are Markers of Primary Mesothelial Cells

(2011) Mutsumi Kanamori-Katayama et al.   PLoS One

Human fetal lymphoid tissue–inducer cells are interleukin 17–producing precursors to RORC+ CD127+ natural killer–like cells

(2008) Tom Cupedo et al.   NATURE IMMUNOLOGY

Generation and Regeneration of Cells of the Liver and Pancreas

(2008) K. S. Zaret et al.   SCIENCE

Development of human lymph nodes and Peyer's patches

(2008) Kerim Hoorweg et al.   SEMINARS IN IMMUNOLOGY

High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation

(2008) Jean-Baptiste Veyrieras et al.   PLoS Genetics