Cell-type-specific signaling networks in heterocellular organoids

Cancer modeling meets human organoid technology

(2019) David Tuveson et al.   SCIENCE

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Patient-derived organoids model treatment response of metastatic gastrointestinal cancers

(2018) Georgios Vlachogiannis et al.   SCIENCE

CellCycleTRACER accounts for cell cycle and volume in mass cytometry data

(2018) Maria Anna Rapsomaniki et al.   Nature Communications

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry

(2018) Stéphane Chevrier et al.   Cell Systems

Generation of Tumor-Reactive T Cells by Co-culture of Peripheral Blood Lymphocytes and Tumor Organoids

(2018) Krijn K. Dijkstra et al.   CELL

Tellurium-based mass cytometry barcode for live and fixed cells

(2018) Lisa M. Willis et al.   CYTOMETRY PART A

Metal-isotope-tagged monoclonal antibodies for high-dimensional mass cytometry

(2018) Guojun Han et al.   Nature Protocols

Organoid Modeling of the Tumor Immune Microenvironment

(2018) James T. Neal et al.   CELL

Tales from the crypt: new insights into intestinal stem cells

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

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Transplantation of engineered organoids enables rapid generation of metastatic mouse models of colorectal cancer

(2017) Kevin P O'Rourke et al.   NATURE BIOTECHNOLOGY

Synthetic hydrogels for human intestinal organoid generation and colonic wound repair

(2017) Ricardo Cruz-Acuña et al.   NATURE CELL BIOLOGY

In Situ Fixation Redefines Quiescence and Early Activation of Skeletal Muscle Stem Cells

(2017) Léo Machado et al.   Cell Reports

Rapid monoisotopic cisplatin based barcoding for multiplexed mass cytometry

(2017) Ryan L. McCarthy et al.   Scientific Reports

Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation

(2016) Christopher J. Tape et al.   CELL

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

Modeling Development and Disease with Organoids

(2016) Hans Clevers   CELL

Earth Mover’s Distance (EMD): A True Metric for Comparing Biomarker Expression Levels in Cell Populations

(2016) Darya Y. Orlova et al.   PLoS One

Systems Biology Analysis of Heterocellular Signaling

(2016) Christopher J. Tape   TRENDS IN BIOTECHNOLOGY

Three-Dimensional Gastrointestinal Organoid Culture in Combination with Nerves or Fibroblasts: A Method to Characterize the Gastrointestinal Stem Cell Niche

(2016) Agnieszka Pastuła et al.   Stem Cells International

Apc Restoration Promotes Cellular Differentiation and Reestablishes Crypt Homeostasis in Colorectal Cancer

(2015) Lukas E. Dow et al.   CELL

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

(2015) Marc van de Wetering et al.   CELL

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF- -induced apoptosis in vivo

(2015) A. J. Simmons et al.   Molecular Systems Biology

Stromal gene expression defines poor-prognosis subtypes in colorectal cancer

(2015) Alexandre Calon et al.   NATURE GENETICS

Stromal contribution to the colorectal cancer transcriptome

(2015) Claudio Isella et al.   NATURE GENETICS

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm

(2015) Eli R Zunder et al.   Nature Protocols

An interactive reference framework for modeling a dynamic immune system

(2015) M. H. Spitzer et al.   SCIENCE

Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity

(2014) Tae-Hee Kim et al.   NATURE

Conditional density-based analysis of T cell signaling in single-cell data

(2014) S. Krishnaswamy et al.   SCIENCE

Normalization of mass cytometry data with bead standards

(2013) Rachel Finck et al.   CYTOMETRY PART A

Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny

(2013) Xiaolei Yin et al.   NATURE METHODS

Isolation of Primary Myofibroblasts from Mouse and Human Colon Tissue

(2013) Hassan Khalil et al.   Jove-Journal of Visualized Experiments

A platinum-based covalent viability reagent for single-cell mass cytometry

(2012) Harris G. Fienberg et al.   CYTOMETRY PART A

Single-cell mass cytometry adapted to measurements of the cell cycle

(2012) Gregory K. Behbehani et al.   CYTOMETRY PART A

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

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

(2012) Johannes Schindelin et al.   NATURE METHODS

TGFβ signalling in context

(2012) Joan Massagué   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

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

(2009) Toshiro Sato et al.   NATURE