Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Differential abundance testing on single-cell data using k-nearest neighbor graphs

(2021) Emma Dann et al.   NATURE BIOTECHNOLOGY

Recommendations for Follow-Up After Colonoscopy and Polypectomy: A Consensus Update by the US Multi-Society Task Force on Colorectal Cancer

(2020) Samir Gupta et al.   GASTROINTESTINAL ENDOSCOPY

Pan-cancer analysis of whole genomes

(2020)   NATURE

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

(2020) Orit Rozenblatt-Rosen et al.   CELL

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Clinical significance and biological role of cancer-derived Type I collagen in lung and esophageal cancers

(2019) Shuo Fang et al.   Thoracic Cancer

Colonic CD90+ Crypt Fibroblasts Secrete Semaphorins to Support Epithelial Growth

(2019) Olga N. Karpus et al.   Cell Reports

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

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

High-dimensional cytometric analysis of colorectal cancer reveals novel mediators of antitumour immunity

(2019) Natasja L de Vries et al.   GUT

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Cancer‐associated fibroblasts secrete Wnt2 to promote cancer progression in colorectal cancer

(2019) Takashi Aizawa et al.   Cancer Medicine

Cancer-associated fibroblast-derived WNT2 increases tumor angiogenesis in colon cancer

(2019) Daniela Unterleuthner et al.   ANGIOGENESIS

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Pro-tumorigenic roles of fibroblast activation protein in cancer: back to the basics

(2018) Ellen Puré et al.   ONCOGENE

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Mesenchymal Cells in Colon Cancer

(2017) Vasiliki Koliaraki et al.   GASTROENTEROLOGY

Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer

(2017) Ludovic Barault et al.   GUT

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

Immune evasion in cancer: Mechanistic basis and therapeutic strategies

(2015) Dass S. Vinay et al.   SEMINARS IN CANCER BIOLOGY

T-cell exhaustion in the tumor microenvironment

(2015) Y Jiang et al.   Cell Death & Disease

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

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

Cancer-Associated Fibroblasts Connect Metastasis-Promoting Communication in Colorectal Cancer

(2015) Joke Tommelein et al.   Frontiers in Oncology

Twist1 Is a Key Regulator of Cancer-Associated Fibroblasts

(2014) K.-W. Lee et al.   CANCER RESEARCH

GPx2 Suppression of H2O2 Stress Links the Formation of Differentiated Tumor Mass to Metastatic Capacity in Colorectal Cancer

(2014) B. L. Emmink et al.   CANCER RESEARCH

Stroma provides an intestinal stem cell niche in the absence of epithelial Wnts

(2014) Z. Kabiri et al.   DEVELOPMENT

Inhibition of Glutathione Peroxidase Mediates the Collateral Sensitivity of Multidrug-resistant Cells to Tiopronin

(2014) Matthew D. Hall et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Cancer-Associated Fibroblasts Drive the Progression of Metastasis through both Paracrine and Mechanical Pressure on Cancer Tissue

(2012) G. S. Karagiannis et al.   MOLECULAR CANCER RESEARCH

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

TCF/LEFs and Wnt Signaling in the Nucleus

(2012) K. M. Cadigan et al.   Cold Spring Harbor Perspectives in Biology

Mesenchymal Cells of the Intestinal Lamina Propria

(2011) D.W. Powell et al.   Annual Review of Physiology

Genome-scale analysis of aberrant DNA methylation in colorectal cancer

(2011) T. Hinoue et al.   GENOME RESEARCH

Emerging actions of the nuclear receptor LRH-1 in the gut

(2010) Pablo J. Fernandez-Marcos et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Transcription Factor Achaete Scute-Like 2 Controls Intestinal Stem Cell Fate

(2009) Laurens G. van der Flier et al.   CELL

OLFM4 Is a Robust Marker for Stem Cells in Human Intestine and Marks a Subset of Colorectal Cancer Cells

(2009) Laurens G. van der Flier et al.   GASTROENTEROLOGY