Systematic interrogation of diverse Omic data reveals interpretable, robust, and generalizable transcriptomic features of clinically successful therapeutic targets

Are Topological Properties of Drug Targets Based on Protein-Protein Interaction Network Ready to Predict Potential Drug Targets?

(2016) Shiliang Li et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Reflection of successful anticancer drug development processes in the literature

(2016) Fabian Heinemann et al.   DRUG DISCOVERY TODAY

Phase II and phase III failures: 2013–2015

(2016) Richard K. Harrison   NATURE REVIEWS DRUG DISCOVERY

Impact of genetically supported target selection on R&D productivity

(2016) Mark R. Hurle et al.   NATURE REVIEWS DRUG DISCOVERY

The 2016 database issue ofNucleic Acids Researchand an updated molecular biology database collection

(2016) Daniel J. Rigden 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

Systematic Analysis of Drug Targets Confirms Expression in Disease-Relevant Tissues

(2016) Vinod Kumar et al.   Scientific Reports

Large-scale identification of potential drug targets based on the topological features of human protein–protein interaction network

(2015) Zhan-Chao Li et al.   ANALYTICA CHIMICA ACTA

A comparative study of disease genes and drug targets in the human protein interactome

(2015) Jingchun Sun et al.   BMC BIOINFORMATICS

Network-based prediction and knowledge mining of disease genes

(2015) Matthew B Carson et al.   BMC Medical Genomics

Reprint of “Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction”

(2015) Andrew D. Rouillard et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Know your target, know your molecule

(2015) Mark E Bunnage et al.   Nature Chemical Biology

The support of human genetic evidence for approved drug indications

(2015) Matthew R Nelson et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Targets of drugs are generally and targets of drugs having side effects are specifically good spreaders of human interactome perturbations

(2015) Áron R. Perez-Lopez et al.   Scientific Reports

Distinctive Behaviors of Druggable Proteins in Cellular Networks

(2015) Costas Mitsopoulos et al.   PLoS Computational Biology

A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome

(2015) Susan Dina Ghiassian et al.   PLoS Computational Biology

Prediction of Druggable Proteins Using Machine Learning and Systems Biology: A Mini-Review

(2015) Gaurav Kandoi et al.   Frontiers in Physiology

Comprehensive comparison of large-scale tissue expression datasets

(2015) Alberto Santos et al.   PeerJ

Properties of Protein Drug Target Classes

(2015) Simon C. Bull et al.   PLoS One

Lessons learned from the fate of AstraZeneca's drug pipeline: a five-dimensional framework

(2014) David Cook et al.   NATURE REVIEWS DRUG DISCOVERY

Genenames.org: the HGNC resources in 2015

(2014) Kristian A. Gray et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

Ensemble Positive Unlabeled Learning for Disease Gene Identification

(2014) Peng Yang et al.   PLoS One

A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening

(2014) Jouhyun Jeon et al.   Genome Medicine

Gene set bagging for estimating the probability a statistically significant result will replicate

(2013) Andrew E Jaffe et al.   BMC BIOINFORMATICS

Inferring protein domains associated with drug side effects based on drug-target interaction network

(2013) Hiroaki Iwata et al.   BMC Systems Biology

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Phase II and Phase III attrition rates 2011–2012

(2013) John Arrowsmith et al.   NATURE REVIEWS DRUG DISCOVERY

Drug Target Prediction and Repositioning Using an Integrated Network-Based Approach

(2013) Dorothea Emig et al.   PLoS One

Comparison of Profile Similarity Measures for Genetic Interaction Networks

(2013) Raamesh Deshpande et al.   PLoS One

Target Essentiality and Centrality Characterize Drug Side Effects

(2013) Xiujuan Wang et al.   PLoS Computational Biology

A Permutation Procedure to Correct for Confounders in Case-Control Studies, Including Tests of Rare Variation

(2012) Michael P. Epstein et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction

(2012) Antonio Mora et al.   BMC BIOINFORMATICS

Computational approaches to disease-gene prediction: rationale, classification and successes

(2012) Rosario M. Piro et al.   FEBS Journal

Making do with what we have: use your bootstraps

(2012) Guillaume Calmettes et al.   JOURNAL OF PHYSIOLOGY-LONDON

Network-based characterization of drug-regulated genes, drug targets, and toxicity

(2012) Max Kotlyar et al.   METHODS

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

Computational tools for prioritizing candidate genes: boosting disease gene discovery

(2012) Yves Moreau et al.   NATURE REVIEWS GENETICS

Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

(2012) Susan M. Sunkin et al.   NUCLEIC ACIDS RESEARCH

Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks

(2012) Oded Magger et al.   PLoS Computational Biology

A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data

(2011) Pedro R Costa et al.   BMC GENOMICS

Structure-based druggability assessment—identifying suitable targets for small molecule therapeutics

(2011) Eric B Fauman et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

What makes a good drug target?

(2011) Isabella Gashaw et al.   DRUG DISCOVERY TODAY

Selection Bias and Information Bias in Clinical Research

(2010) Giovanni Tripepi et al.   NEPHRON CLINICAL PRACTICE

Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn

(2010) Belinda Phipson et al.   Statistical Applications in Genetics and Molecular Biology

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets

(2010) Silpa Suthram et al.   PLoS Computational Biology

Properties and identification of human protein drug targets

(2009) Tala M. Bakheet et al.   BIOINFORMATICS

The analysis of the drug–targets based on the topological properties in the human protein–protein interaction network

(2009) Mingzhu Zhu et al.   JOURNAL OF DRUG TARGETING

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

(2008) K. Lage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative systems-level determinants of human genes targeted by successful drugs

(2007) L. Yao et al.   GENOME RESEARCH