Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

Chr20q amplification defines a distinct molecular subtype of microsatellite stable colorectal cancer

(2021) Baoyi Zhang et al.   CANCER RESEARCH

Pan-cancer analysis of ligand-receptor crosstalk in the tumor microenvironment

(2021) Umesh Ghoshdastider et al.   CANCER RESEARCH

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Spatially organized multicellular immune hubs in human colorectal cancer

(2021) Karin Pelka et al.   CELL

Clinical Value of Consensus Molecular Subtypes in Colorectal Cancer: A Systematic Review and Meta-Analysis

(2021) Sanne ten Hoorn et al.   JNCI-Journal of the National Cancer Institute

NOTUM from Apc-mutant cells biases clonal competition to initiate cancer

(2021) Dustin J. Flanagan et al.   NATURE

Apc-mutant cells act as supercompetitors in intestinal tumour initiation

(2021) Sanne M. van Neerven et al.   NATURE

Oncogenic BRAF, unrestrained by TGFβ-receptor signalling, drives right-sided colonic tumorigenesis

(2021) Joshua D. G. Leach et al.   Nature Communications

Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps

(2021) Bob Chen et al.   CELL

DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data

(2021) Bobby Ranjan et al.   Nature Communications

Immune checkpoint signaling and cancer immunotherapy

(2020) Xing He et al.   CELL RESEARCH

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer

(2020) Hae-Ock Lee et al.   NATURE GENETICS

Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities

(2020) Caitlin A. Nichols et al.   Nature Communications

Predicting cell-to-cell communication networks using NATMI

(2020) Rui Hou et al.   Nature Communications

SMuRF: Portable and accurate ensemble prediction of somatic mutations

(2019) Weitai Huang et al.   BIOINFORMATICS

Immunotherapy for Colorectal Cancer: A Review of Current and Novel Therapeutic Approaches

(2019) Aaron J Franke et al.   JNCI-Journal of the National Cancer Institute

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

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

Exploiting differential Wnt target gene expression to generate a molecular biomarker for colorectal cancer stratification

(2019) Sam O Kleeman et al.   GUT

Targeting Oncogenic BRAF: Past, Present, and Future

(2019) Zaman et al.   Cancers

Pathways of Colorectal Carcinogenesis

(2019) Long H. Nguyen et al.   GASTROENTEROLOGY

De novo compartment deconvolution and weight estimation of tumor samples using DECODER

(2019) Xianlu Laura Peng et al.   Nature Communications

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

Tumor Cell-Intrinsic Factors Underlie Heterogeneity of Immune Cell Infiltration and Response to Immunotherapy

(2018) Jinyang Li et al.   IMMUNITY

Genetic Mechanisms of Immune Evasion in Colorectal Cancer

(2018) Catherine S. Grasso et al.   Cancer Discovery

The Intestinal Stem Cell Niche: Homeostasis and Adaptations

(2018) António J.M. Santos et al.   TRENDS IN CELL BIOLOGY

Identification of the predictive genes for the response of colorectal cancer patients to FOLFOX therapy

(2018) Hengjun Lin et al.   OncoTargets and Therapy

TissueEnrich: Tissue-specific gene enrichment analysis

(2018) Ashish Jain et al.   BIOINFORMATICS

Author Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2018) Huipeng Li et al.   NATURE GENETICS

Mesenchymal Cells in Colon Cancer

(2017) Vasiliki Koliaraki et al.   GASTROENTEROLOGY

A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy

(2017) Marta Łuksza et al.   NATURE

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Oncogenic KRAS-associated gene signature defines co-targeting of CDK4/6 and MEK as a viable therapeutic strategy in colorectal cancer

(2017) M Pek et al.   ONCOGENE

Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors

(2017) Moritz Schütte et al.   Nature Communications

Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer

(2017) Claudio Isella et al.   Nature Communications

Molecular-Subtype-Specific Biomarkers Improve Prediction of Prognosis in Colorectal Cancer

(2017) Jesper Bertram Bramsen et al.   Cell Reports

BRAF V600E Mutant Colorectal Cancer Subtypes Based on Gene Expression

(2016) David Barras et al.   CLINICAL CANCER RESEARCH

Immune and Stromal Classification of Colorectal Cancer Is Associated with Molecular Subtypes and Relevant for Precision Immunotherapy

(2016) Etienne Becht et al.   CLINICAL CANCER RESEARCH

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

(2016) Andrew D. Rouillard et al.   Database-The Journal of Biological Databases and Curation

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

The consensus molecular subtypes of colorectal cancer

(2015) Justin Guinney et al.   NATURE MEDICINE

Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset

(2015) B. Seashore-Ludlow et al.   Cancer Discovery

Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post-chemotherapy tissues

(2015) Mengsha Tong et al.   Oncotarget

Fibroblast surface-associated FGF-2 promotes contact-dependent colorectal cancer cell migration and invasion through FGFR-SRC signaling and integrin αvβ5-mediated adhesion

(2015) Sarah Knuchel et al.   Oncotarget

AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data

(2014) Lei Bao et al.   BIOINFORMATICS

PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data

(2013) Nicholas B. Larson et al.   BIOINFORMATICS

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions

(2013) Felipe De Sousa E Melo et al.   NATURE MEDICINE

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Dependency of Colorectal Cancer on a TGF-β-Driven Program in Stromal Cells for Metastasis Initiation

(2012) Alexandre Calon et al.   CANCER CELL

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

A combined oncogenic pathway signature ofBRAF,KRASandPI3KCAmutation improves colorectal cancer classification and cetuximab treatment prediction

(2012) Sun Tian et al.   GUT

Identification of a Poor-PrognosisBRAF-Mutant–Like Population of Patients With Colon Cancer

(2012) Vlad Popovici et al.   JOURNAL OF CLINICAL ONCOLOGY

IL-1β promotes stemness and invasiveness of colon cancer cells through Zeb1 activation

(2012) Yijing Li et al.   Molecular Cancer

β-Catenin signaling dosage dictates tissue-specific tumor predisposition in Apc-driven cancer

(2012) E R M Bakker et al.   ONCOGENE

Different APC genotypes in proximal and distal sporadic colorectal cancers suggest distinct WNT/β-catenin signalling thresholds for tumourigenesis

(2012) M Christie et al.   ONCOGENE

Tcf7 Is an Important Regulator of the Switch of Self-Renewal and Differentiation in a Multipotential Hematopoietic Cell Line

(2012) Jia Qian Wu et al.   PLoS Genetics

Differential gene expression signatures between colorectal cancers with and without KRAS mutations: Crosstalk between the KRAS pathway and other signalling pathways

(2011) Toshiaki Watanabe et al.   EUROPEAN JOURNAL OF CANCER

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA