Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection

Trajectory-based differential expression analysis for single-cell sequencing data

(2020) Koen Van den Berge et al.   Nature Communications

Retinoic Acid and Lymphotoxin Signaling Promote Differentiation of Human Intestinal M Cells

(2020) Siyuan Ding et al.   GASTROENTEROLOGY

Transcriptional and Spatial Resolution of Cell Types in the Mammalian Habenula

(2020) Yoshiko Hashikawa et al.   NEURON

SARS-CoV-2 productively infects human gut enterocytes

(2020) Mart M. Lamers et al.   SCIENCE

Astrovirus infects actively secreting goblet cells and alters the gut mucus barrier

(2020) Valerie Cortez et al.   Nature Communications

Critical Role of Type III Interferon in Controlling SARS-CoV-2 Infection in Human Intestinal Epithelial Cells

(2020) Megan L. Stanifer et al.   Cell Reports

Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection

(2020) Jiayi Sun et al.   PLoS Pathogens

West Nile virus-inclusive single-cell RNA sequencing reveals heterogeneity in the type I interferon response within single cells

(2019) Justin T. O’Neal et al.   JOURNAL OF VIROLOGY

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

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

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

Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program

(2019) Emanuel Wyler et al.   Nature Communications

Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape

(2019) Abimbola O. Kolawole et al.   PLoS Pathogens

Asymmetric distribution of TLR3 leads to a polarized immune response in human intestinal epithelial cells

(2019) Megan L. Stanifer et al.   Nature Microbiology

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Intrinsic Immunity Shapes Viral Resistance of Stem Cells

(2018) Xianfang Wu et al.   CELL

Human Pancreatic Tumor Organoids Reveal Loss of Stem Cell Niche Factor Dependence during Disease Progression

(2018) Takashi Seino et al.   Cell Stem Cell

Viral gastroenteritis

(2018) Krisztián Bányai et al.   LANCET

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

Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier

(2018) Eric C. Martens et al.   NATURE REVIEWS MICROBIOLOGY

Extreme heterogeneity of influenza virus infection in single cells

(2018) Alistair B Russell et al.   eLife

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

(2018) Masayuki Fujii et al.   Cell Stem Cell

Mouse fetal intestinal organoids: new model to study epithelial maturation from suckling to weaning

(2018) Marit Navis et al.   EMBO REPORTS

Tales from the crypt: new insights into intestinal stem cells

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

Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue

(2018) Fabio Zanini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential induction of interferon stimulated genes between type I and type III interferons is independent of interferon receptor abundance

(2018) Kalliopi Pervolaraki et al.   PLoS Pathogens

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Astrovirus Biology and Pathogenesis

(2017) Valerie Cortez et al.   Annual Review of Virology

Interferon-Lambda: A Potent Regulator of Intestinal Viral Infections

(2017) Sanghyun Lee et al.   Frontiers in Immunology

Type I and Type III Interferons Display Different Dependency on Mitogen-Activated Protein Kinases to Mount an Antiviral State in the Human Gut

(2017) Kalliopi Pervolaraki et al.   Frontiers in Immunology

In vitropatterning of pluripotent stem cell-derived intestine recapitulatesin vivohuman development

(2016) Yu-Hwai Tsai et al.   DEVELOPMENT

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

(2016) Kai Kretzschmar et al.   DEVELOPMENTAL CELL

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Development of Functional Microfold (M) Cells from Intestinal Stem Cells in Primary Human Enteroids

(2016) Joshua D. Rouch et al.   PLoS One

Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units

(2015) Marine Combe et al.   Cell Host & Microbe

Stem cell and progenitor fate in the mammalian intestine: Notch and lateral inhibition in homeostasis and disease

(2015) R. Sancho et al.   EMBO REPORTS

Type I Interferon Response Limits Astrovirus Replication and Protects against Increased Barrier PermeabilityIn VitroandIn Vivo

(2015) Shauna A. Marvin et al.   JOURNAL OF VIROLOGY

Type I Interferon Response Is Delayed in Human Astrovirus Infections

(2015) Susana Guix et al.   PLoS One

Leukocyte-Derived IFN-α/β and Epithelial IFN-λ Constitute a Compartmentalized Mucosal Defense System that Restricts Enteric Virus Infections

(2015) Tanel Mahlakõiv et al.   PLoS Pathogens

Human Cytomegalovirus Infection of Human Embryonic Stem Cell-Derived Primitive Neural Stem Cells Is Restricted at Several Steps but Leads to the Persistence of Viral DNA

(2014) J.-P. Belzile et al.   JOURNAL OF VIROLOGY

Interferon-  cures persistent murine norovirus infection in the absence of adaptive immunity

(2014) T. J. Nice et al.   SCIENCE

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

(2012) Johannes Schindelin et al.   NATURE METHODS

Long-term Expansion of Epithelial Organoids From Human Colon, Adenoma, Adenocarcinoma, and Barrett's Epithelium

(2011) Toshiro Sato et al.   GASTROENTEROLOGY

IFN-  determines the intestinal epithelial antiviral host defense

(2011) J. Pott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Embryonic stem cells use ZFP809 to silence retroviral DNAs

(2009) Daniel Wolf et al.   NATURE

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

(2009) Toshiro Sato et al.   NATURE