New technologies to study helminth development and host-parasite interactions

Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis

(2022) Tam Vu et al.   Nature Communications

Defining the early stages of intestinal colonisation by whipworms

(2022) María A. Duque-Correa et al.   Nature Communications

Spatial transcriptomics reveals antiparasitic targets associated with essential behaviors in the human parasite Brugia malayi

(2022) Paul M. Airs et al.   PLoS Pathogens

Helminth-induced reprogramming of the stem cell compartment inhibits type 2 immunity

(2022) Danielle Karo-Atar et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Development of Bovine Gastric Organoids as a Novel In Vitro Model to Study Host-Parasite Interactions in Gastrointestinal Nematode Infections

(2022) Marc N. Faber et al.   Frontiers in Cellular and Infection Microbiology

Genetic engineering in organoids

(2021) Isaree Teriyapirom et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Single-cell analysis of Schistosoma mansoni identifies a conserved genetic program controlling germline stem cell fate

(2021) Pengyang Li et al.   Nature Communications

Comprehensive characterization of tissue-specific chromatin accessibility in L2 C. elegans nematodes

(2021) Timothy J Durham et al.   GENOME RESEARCH

Whole-organism eQTL mapping at cellular resolution with single-cell sequencing

(2021) Eyal Ben-David et al.   eLife

Molecular topography of an entire nervous system

(2021) Seth R. Taylor et al.   CELL

Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing

(2021) Emma M. Briggs et al.   Nature Communications

Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoire

(2021) Ivy K. Brown et al.   PLoS Pathogens

The Development of Ovine Gastric and Intestinal Organoids for Studying Ruminant Host-Pathogen Interactions

(2021) David Smith et al.   Frontiers in Cellular and Infection Microbiology

Biobanking of human gut organoids for translational research

(2021) Francesca Perrone et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Intestinal epithelial tuft cell induction is negated by a murine helminth and its secreted products

(2021) Claire Drurey et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Tuft Cells Increase Following Ovine Intestinal Parasite Infections and Define Evolutionarily Conserved and Divergent Responses

(2021) Katie A. Hildersley et al.   Frontiers in Immunology

Fast and efficient generation of knock-in human organoids using homology-independent CRISPR–Cas9 precision genome editing

(2020) Benedetta Artegiani et al.   NATURE CELL BIOLOGY

Single-cell RNA sequencing of Trypanosoma brucei from tsetse salivary glands unveils metacyclogenesis and identifies potential transmission blocking antigens

(2020) Aurélien Vigneron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation

(2020) Alan Selewa et al.   Scientific Reports

FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells

(2020) Noudjoud Attaf et al.   Frontiers in Immunology

Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance

(2020) Till Ringel et al.   Cell Stem Cell

Development of caecaloids to study host–pathogen interactions: new insights into immunoregulatory functions of Trichuris muris extracellular vesicles in the caecum

(2020) María A. Duque-Correa et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Infection by the parasitic helminthTrichinella spiralisactivates a Tas2r-mediated signaling pathway in intestinal tuft cells

(2019) Xiao-Cui Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Derivation of adult canine intestinal organoids for translational research in gastroenterology

(2019) Lawrance Chandra et al.   BMC BIOLOGY

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

(2019) Geng Chen et al.   Frontiers in Genetics

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

(2019) Jonathan S. Packer et al.   SCIENCE

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

(2018) Kelly Street et al.   BMC GENOMICS

A Metabolite-Triggered Tuft Cell-ILC2 Circuit Drives Small Intestinal Remodeling

(2018) Christoph Schneider et al.   CELL

Transcriptomic profiling of nematode parasites surviving vaccine exposure

(2018) Guillaume Sallé et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Cell type transcriptome atlas for the planarianSchmidtea mediterranea

(2018) Christopher T. Fincher et al.   SCIENCE

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

(2018) Mireya Plass et al.   SCIENCE

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

Current Status of 3-D Organoids as Pre-Clinical Models

(2018) Garima Kaushik et al.   STEM CELLS

Stem cell heterogeneity drives the parasitic life cycle of Schistosoma mansoni

(2018) Bo Wang et al.   eLife

Hookworm Secreted Extracellular Vesicles Interact With Host Cells and Prevent Inducible Colitis in Mice

(2018) Ramon M. Eichenberger et al.   Frontiers in Immunology

Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche

(2018) Ysbrand M. Nusse et al.   NATURE

Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis

(2018) Haojia Wu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

(2018) Trygve E. Bakken et al.   PLoS One

A Single-Cell Sequencing Guide for Immunologists

(2018) Peter See et al.   Frontiers in Immunology

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

A primary human macrophage-enteroid co-culture model to investigate mucosal gut physiology and host-pathogen interactions

(2017) Gaelle Noel et al.   Scientific Reports

Conservation of a microRNA cluster in parasitic nematodes and profiling of miRNAs in excretory-secretory products and microvesicles of Haemonchus contortus

(2017) Henry Y. Gu et al.   PLoS Neglected Tropical Diseases

A Transcriptional Lineage of the Early C. elegans Embryo

(2016) Sophia C. Tintori et al.   DEVELOPMENTAL CELL

Identification of new markers for the Schistosoma mansoni vitelline lineage

(2016) Jipeng Wang et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

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

(2016) François Gerbe et al.   NATURE

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

(2016) M. R. Howitt et al.   SCIENCE

A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians

(2015) Omri Wurtzel et al.   DEVELOPMENTAL CELL

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

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

(2015) Jakob von Moltke et al.   NATURE

Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer

(2014) Tamar Hashimshony et al.   NATURE

Adult somatic stem cells in the human parasite Schistosoma mansoni

(2013) James J. Collins III et al.   NATURE

Method of the Year 2013

(2013)   NATURE METHODS

It's No Fluke: The Planarian as a Model for Understanding Schistosomes

(2013) James J. Collins et al.   PLoS Pathogens

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

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

(2011) Toshiro Sato et al.   GASTROENTEROLOGY

Increased production through parasite control: can ancient breeds of sheep teach us new lessons?

(2010) David Piedrafita et al.   TRENDS IN PARASITOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS