Genetic and transcriptional evolution alters cancer cell line drug response

Patient-derived xenografts undergo mouse-specific tumor evolution

(2017) Uri Ben-David et al.   NATURE GENETICS

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

(2017) Julia Joung et al.   Nature Protocols

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

(2017) Shashikant Pujar et al.   NUCLEIC ACIDS RESEARCH

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

(2017) Andrew S. Venteicher et al.   SCIENCE

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

(2017) Viktor A. Adalsteinsson et al.   Nature Communications

CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets

(2016) David Dao et al.   BIOINFORMATICS

High-throughput Phenotyping of Lung Cancer Somatic Mutations

(2016) Alice H. Berger et al.   CANCER CELL

Reproducible pharmacogenomic profiling of cancer cell line panels

(2016) Peter M. Haverty et al.   NATURE

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

(2016) Mark-Anthony Bray et al.   Nature Protocols

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

MCF-7 Cells--Changing the Course of Breast Cancer Research and Care for 45 Years

(2015) A. V. Lee et al.   JNCI-Journal of the National Cancer Institute

Correlating chemical sensitivity and basal gene expression reveals mechanism of action

(2015) Matthew G Rees et al.   Nature Chemical Biology

In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer

(2015) Michalina Janiszewska et al.   NATURE GENETICS

Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

(2015) Hyo-eun C Bhang et al.   NATURE MEDICINE

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

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

The Economics of Reproducibility in Preclinical Research

(2015) Leonard P. Freedman et al.   PLOS BIOLOGY

MCF-7 Cells--Changing the Course of Breast Cancer Research and Care for 45 Years

(2015) A. V. Lee et al.   JNCI-Journal of the National Cancer Institute

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

(2014) Peter Eirew et al.   NATURE

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers

(2014) Ryan P. Abo et al.   NUCLEIC ACIDS RESEARCH

A Genomic Instability Score in Discriminating Nonequivalent Outcomes of BRCA1/2 Mutations and in Predicting Outcomes of Ovarian Cancer Treated with Platinum-Based Chemotherapy

(2014) Shaojun Zhang et al.   PLoS One

An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules

(2013) Amrita Basu et al.   CELL

Inconsistency in large pharmacogenomic studies

(2013) Benjamin Haibe-Kains et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Virtual karyotyping of pluripotent stem cells on the basis of their global gene expression profiles

(2013) Uri Ben-David et al.   Nature Protocols

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

(2012) G. Ha et al.   GENOME RESEARCH

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells

(2012) Wanjuan Yang et al.   NUCLEIC ACIDS RESEARCH

Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells

(2011) Piyush B. Gupta et al.   CELL

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Believe it or not: how much can we rely on published data on potential drug targets?

(2011) Florian Prinz et al.   NATURE REVIEWS DRUG DISCOVERY

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE