Leveraging big data to transform target selection and drug discovery

Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research

(2015) Bin Chen et al.   BMC Medical Genomics

Public data and open source tools for multi-assay genomic investigation of disease

(2015) Lavanya Kannan et al.   BRIEFINGS IN BIOINFORMATICS

In Silico Prescription of Anticancer Drugs to Cohorts of 28 Tumor Types Reveals Targeting Opportunities

(2015) Carlota Rubio-Perez et al.   CANCER CELL

Elucidating Compound Mechanism of Action by Network Perturbation Analysis

(2015) Jung Hoon Woo et al.   CELL

Preclinical Mouse Cancer Models: A Maze of Opportunities and Challenges

(2015) Chi-Ping Day et al.   CELL

Drugs that reverse disease transcriptomic signatures are more effective in a mouse model of dyslipidemia

(2015) A. Wagner et al.   Molecular Systems Biology

Reproducibility crisis: Blame it on the antibodies

(2015) Monya Baker   NATURE

The support of human genetic evidence for approved drug indications

(2015) Matthew R Nelson et al.   NATURE GENETICS

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference

(2015) Rodolphe Barrangou et al.   NUCLEIC ACIDS RESEARCH

Connectivity Map-based discovery of parbendazole reveals targetable human osteogenic pathway

(2015) Andrea M. Brum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Combining genomic and network characteristics for extended capability in predicting synergistic drugs for cancer

(2015) Yi Sun et al.   Nature Communications

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

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

Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records

(2015) Hyojung Paik et al.   Scientific Reports

Predicting Drug Response in Human Prostate Cancer from Preclinical Analysis of In Vivo Mouse Models

(2015) Antonina Mitrofanova et al.   Cell Reports

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions

(2015) Francesco Iorio et al.   PLoS One

Novel Drug Candidates for the Treatment of Metastatic Colorectal Cancer through Global Inverse Gene-Expression Profiling

(2014) V. van Noort et al.   CANCER RESEARCH

HMMR Maintains the Stemness and Tumorigenicity of Glioblastoma Stem-like Cells

(2014) J. Tilghman et al.   CANCER RESEARCH

Definition of PKC-α, CDK6, and MET as Therapeutic Targets in Triple-Negative Breast Cancer

(2014) Yi-Hsin Hsu et al.   CANCER RESEARCH

A Meta-analysis of Lung Cancer Gene Expression Identifies PTK7 as a Survival Gene in Lung Adenocarcinoma

(2014) R. Chen et al.   CANCER RESEARCH

MTBP Is Overexpressed in Triple-Negative Breast Cancer and Contributes to Its Growth and Survival

(2014) B. C. Grieb et al.   MOLECULAR CANCER RESEARCH

Computational Repositioning and Preclinical Validation of Pentamidine for Renal Cell Cancer

(2014) L. F. Zerbini et al.   MOLECULAR CANCER THERAPEUTICS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

A community computational challenge to predict the activity of pairs of compounds

(2014) Mukesh Bansal et al.   NATURE BIOTECHNOLOGY

A comprehensive transcriptional portrait of human cancer cell lines

(2014) Christiaan Klijn et al.   NATURE BIOTECHNOLOGY

The Comparative Toxicogenomics Database's 10th year anniversary: update 2015

(2014) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map

(2014) Maria M. Martins et al.   Cancer Discovery

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

(2014) Glenn S Cowley et al.   Scientific Data

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

(2013) Amrita Basu et al.   CELL

Systematic Identification of Molecular Subtype-Selective Vulnerabilities in Non-Small-Cell Lung Cancer

(2013) Hyun Seok Kim et al.   CELL

Network Medicine in Disease Analysis and Therapeutics

(2013) B Chen et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Validation of the 12-Gene Colon Cancer Recurrence Score in NSABP C-07 As a Predictor of Recurrence in Patients With Stage II and III Colon Cancer Treated With Fluorouracil and Leucovorin (FU/LV) and FU/LV Plus Oxaliplatin

(2013) Greg Yothers et al.   JOURNAL OF CLINICAL ONCOLOGY

A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation

(2013) Purvesh Khatri et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Tpl2 Kinase Impacts Tumor Growth and Metastasis of Clear Cell Renal Cell Carcinoma

(2013) H. W. Lee et al.   MOLECULAR CANCER RESEARCH

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

The big challenges of big data

(2013) Vivien Marx   NATURE

Validating therapeutic targets through human genetics

(2013) Robert M. Plenge et al.   NATURE REVIEWS DRUG DISCOVERY

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Raw data from clinical trials: within reach?

(2013) Peter Doshi et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

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

(2013) Kosuke Yoshihara et al.   Nature Communications

Evaluating cell lines as tumour models by comparison of genomic profiles

(2013) Silvia Domcke et al.   Nature Communications

A Drug Repositioning Approach Identifies Tricyclic Antidepressants as Inhibitors of Small Cell Lung Cancer and Other Neuroendocrine Tumors

(2013) N. S. Jahchan et al.   Cancer Discovery

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

(2012) Jordi Barretina et al.   NATURE

Objective assessment of cancer genes for drug discovery

(2012) Mishal N. Patel et al.   NATURE REVIEWS DRUG DISCOVERY

Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes

(2012) K. Kodama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploiting drug-disease relationships for computational drug repositioning

(2011) J. T. Dudley et al.   BRIEFINGS IN BIOINFORMATICS

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

(2011) Paul B. Chapman et al.   NEW ENGLAND JOURNAL OF MEDICINE

canSAR: an integrated cancer public translational research and drug discovery resource

(2011) Mark D. Halling-Brown et al.   NUCLEIC ACIDS RESEARCH

Subtype and pathway specific responses to anticancer compounds in breast cancer

(2011) L. M. Heiser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease

(2011) J. T. Dudley et al.   Science Translational Medicine

Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data

(2011) M. Sirota et al.   Science Translational Medicine

Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells

(2011) Richard Marcotte et al.   Cancer Discovery

Loss of ATM/Chk2/p53 Pathway Components Accelerates Tumor Development and Contributes to Radiation Resistance in Gliomas

(2010) Massimo Squatrito et al.   CANCER CELL

Relationship Between Tumor Gene Expression and Recurrence in Four Independent Studies of Patients With Stage II/III Colon Cancer Treated With Surgery Alone or Surgery Plus Adjuvant Fluorouracil Plus Leucovorin

(2010) Michael J. O'Connell et al.   JOURNAL OF CLINICAL ONCOLOGY

International network of cancer genome projects

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

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Anaplastic Lymphoma Kinase Inhibition in Non–Small-Cell Lung Cancer

(2010) Eunice L. Kwak et al.   NEW ENGLAND JOURNAL OF MEDICINE

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

Discovery of drug mode of action and drug repositioning from transcriptional responses

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE