Heterogeneous pathway activation and drug response modelled in colorectal-tumor-derived 3D cultures

The role of TGF-β/SMAD4 signaling in cancer

(2018) Ming Zhao et al.   International Journal of Biological Sciences

Patient-derived organoids model treatment response of metastatic gastrointestinal cancers

(2018) Georgios Vlachogiannis et al.   SCIENCE

Intra-tumour diversification in colorectal cancer at the single-cell level

(2018) Sophie F. Roerink et al.   NATURE

Drugging RAS: Know the enemy

(2017) Bjoern Papke et al.   SCIENCE

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

(2017) Moritz Schütte et al.   Nature Communications

DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer

(2017) Soulafa Mamlouk et al.   Nature Communications

Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine

(2017) Chantal Pauli et al.   Cancer Discovery

Non-Canonical Hedgehog Signaling Is a Positive Regulator of the WNT Pathway and Is Required for the Survival of Colon Cancer Stem Cells

(2017) Joseph L. Regan et al.   Cell Reports

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

(2016) Belinda Phipson et al.   Annals of Applied Statistics

The Role of Cetuximab in the Induction of Anticancer Immune Response in Colorectal Cancer Treatment

(2016) LUBOS HOLUBEC et al.   ANTICANCER RESEARCH

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

BRAF V600E Mutant Colorectal Cancer Subtypes Based on Gene Expression

(2016) David Barras et al.   CLINICAL CANCER RESEARCH

Loss of SMAD4 Promotes Lung Metastasis of Colorectal Cancer by Accumulation of CCR1 + Tumor-Associated Neutrophils through CCL15-CCR1 Axis

(2016) Takamasa Yamamoto et al.   CLINICAL CANCER RESEARCH

Organoids: A historical perspective of thinking in three dimensions

(2016) Marina Simian et al.   JOURNAL OF CELL BIOLOGY

Comparison of Next-Generation Sequencing Panels and Platforms for Detection and Verification of Somatic Tumor Variants for Clinical Diagnostics

(2016) Maksym Misyura et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

From tumour heterogeneity to advances in precision treatment of colorectal cancer

(2016) Cornelis J. A. Punt et al.   Nature Reviews Clinical Oncology

A bead-based western for high-throughput cellular signal transduction analyses

(2016) Fridolin Treindl et al.   Nature Communications

Targeting mutant RAS in patient-derived colorectal cancer organoids by combinatorial drug screening

(2016) Carla S Verissimo et al.   eLife

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

(2015) Marc van de Wetering et al.   CELL

A Big Bang model of human colorectal tumor growth

(2015) Andrea Sottoriva et al.   NATURE GENETICS

The consensus molecular subtypes of colorectal cancer

(2015) Justin Guinney et al.   NATURE MEDICINE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

(2015) Ruijie Liu et al.   NUCLEIC ACIDS RESEARCH

Tumor Heterogeneity and Lesion-Specific Response to Targeted Therapy in Colorectal Cancer

(2015) M. Russo et al.   Cancer Discovery

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The developing story of Sprouty and cancer

(2014) Samar Masoumi-Moghaddam et al.   CANCER AND METASTASIS REVIEWS

Rapidly derived colorectal cancer cultures recapitulate parental cancer characteristics and enable personalized therapeutic assays

(2014) Neil Ashley et al.   JOURNAL OF PATHOLOGY

MutationTaster2: mutation prediction for the deep-sequencing age

(2014) Jana Marie Schwarz et al.   NATURE METHODS

Timing and heterogeneity of mutations associated with drug resistance in metastatic cancers

(2014) Ivana Bozic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DUSP6 regulates drug sensitivity by modulating DNA damage response

(2013) T V Bagnyukova et al.   BRITISH JOURNAL OF CANCER

Routine use of the Ion Torrent AmpliSeq™ Cancer Hotspot Panel for identification of clinically actionable somatic mutations

(2013) Gregory J. Tsongalis et al.   CLINICAL CHEMISTRY AND LABORATORY MEDICINE

Tumour heterogeneity in the clinic

(2013) Philippe L. Bedard et al.   NATURE

Panitumumab–FOLFOX4 Treatment and RAS Mutations in Colorectal Cancer

(2013) Jean-Yves Douillard et al.   NEW ENGLAND JOURNAL OF MEDICINE

Amplification of the MET Receptor Drives Resistance to Anti-EGFR Therapies in Colorectal Cancer

(2013) Alberto Bardelli et al.   Cancer Discovery

Clinical application of amplicon-based next-generation sequencing in cancer

(2013) Fengqi Chang et al.   Cancer Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Dynamic Reprogramming of the Kinome in Response to Targeted MEK Inhibition in Triple-Negative Breast Cancer

(2012) James S. Duncan et al.   CELL

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

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

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Direct and immune mediated antibody targeting of ERBB receptors in a colorectal cancer cell-line panel

(2012) S. Q. Ashraf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer

(2012) A. Kreso et al.   SCIENCE

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

(2011) Toshiro Sato et al.   GASTROENTEROLOGY

Activation of ERBB2 Signaling Causes Resistance to the EGFR-Directed Therapeutic Antibody Cetuximab

(2011) K. Yonesaka et al.   Science Translational Medicine

A Molecularly Annotated Platform of Patient-Derived Xenografts ("Xenopatients") Identifies HER2 as an Effective Therapeutic Target in Cetuximab-Resistant Colorectal Cancer

(2011) A. Bertotti et al.   Cancer Discovery

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

An Optimized Pentaplex PCR for Detecting DNA Mismatch Repair-Deficient Colorectal Cancers

(2010) Ajay Goel et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts

(2009) Nils Blüthgen et al.   FEBS Journal

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Implications of EGFR inhibition in ovarian cancer cell proliferation

(2008) Shawna L. Bull Phelps et al.   GYNECOLOGIC ONCOLOGY