In silico prediction of novel therapeutic targets using gene–disease association data

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

(2017) Katrina M de Lange et al.   NATURE GENETICS

Deep learning in bioinformatics

(2016) Seonwoo Min et al.   BRIEFINGS IN BIOINFORMATICS

DrugMiner: comparative analysis of machine learning algorithms for prediction of potential druggable proteins

(2016) Ali Akbar Jamali et al.   DRUG DISCOVERY TODAY

Innovation in the pharmaceutical industry: New estimates of R&D costs

(2016) Joseph A. DiMasi et al.   JOURNAL OF HEALTH ECONOMICS

Applications of Deep Learning in Biomedicine

(2016) Polina Mamoshina et al.   MOLECULAR PHARMACEUTICS

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Open Targets: a platform for therapeutic target identification and validation

(2016) Gautier Koscielny et al.   NUCLEIC ACIDS RESEARCH

Disciplined approach to drug discovery and early development

(2016) Robert M. Plenge   Science Translational Medicine

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

DISEASES: Text mining and data integration of disease–gene associations

(2015) Sune Pletscher-Frankild et al.   METHODS

Deep Learning in Drug Discovery

(2015) Erik Gawehn et al.   Molecular Informatics

The support of human genetic evidence for approved drug indications

(2015) Matthew R Nelson et al.   NATURE GENETICS

Clinical experiences with systemically administered siRNA-based therapeutics in cancer

(2015) Jonathan E. Zuckerman et al.   NATURE REVIEWS DRUG DISCOVERY

An analysis of the attrition of drug candidates from four major pharmaceutical companies

(2015) Michael J. Waring et al.   NATURE REVIEWS DRUG DISCOVERY

Using human genetics to make new medicines

(2015) Jeffrey C. Barrett et al.   NATURE REVIEWS GENETICS

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

A robust ensemble approach to learn from positive and unlabeled data using SVM base models

(2015) Marc Claesen et al.   NEUROCOMPUTING

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

(2015) J. Pinero et al.   Database-The Journal of Biological Databases and Curation

Application of high-dimensional feature selection: evaluation for genomic prediction in man

(2015) M. L. Bermingham et al.   Scientific Reports

Distinctive Behaviors of Druggable Proteins in Cellular Networks

(2015) Costas Mitsopoulos et al.   PLoS Computational Biology

TAB1: A Target of Triptolide in Macrophages

(2014) Yan Lu et al.   CHEMISTRY & BIOLOGY

Mouse BRWD1 is critical for spermatid postmeiotic transcription and female meiotic chromosome stability

(2014) Shrivatsav Pattabiraman et al.   JOURNAL OF CELL BIOLOGY

Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?

(2014) Fionn Murtagh et al.   JOURNAL OF CLASSIFICATION

Rab18 Facilitates Dengue Virus Infection by Targeting Fatty Acid Synthase to Sites of Viral Replication

(2014) W.-C. Tang et al.   JOURNAL OF VIROLOGY

Is there new hope for therapeutic matrix metalloproteinase inhibition?

(2014) Roosmarijn E. Vandenbroucke et al.   NATURE REVIEWS DRUG DISCOVERY

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

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

Targeting bromodomains: epigenetic readers of lysine acetylation

(2014) Panagis Filippakopoulos et al.   NATURE REVIEWS DRUG DISCOVERY

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   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

Strategic Applications of Gene Expression: From Drug Discovery/Development to Bedside

(2013) Jane P. F. Bai et al.   AAPS Journal

Machine learning in cell biology – teaching computers to recognize phenotypes

(2013) Christoph Sommer et al.   JOURNAL OF CELL SCIENCE

Finding the targets of a drug by integration of gene expression data with a protein interaction network

(2013) Griet Laenen et al.   Molecular BioSystems

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Phase II and Phase III attrition rates 2011–2012

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

Validating therapeutic targets through human genetics

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

The ChEMBL bioactivity database: an update

(2013) A. Patrícia Bento et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

A bagging SVM to learn from positive and unlabeled examples

(2013) F. Mordelet et al.   PATTERN RECOGNITION LETTERS

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

(2013) Dorothea Emig et al.   PLoS One

FSelector: a Ruby gem for feature selection

(2012) Tiejun Cheng et al.   BIOINFORMATICS

Positive-unlabeled learning for disease gene identification

(2012) Peng Yang et al.   BIOINFORMATICS

Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family

(2012) Panagis Filippakopoulos et al.   CELL

Resampling Methods for Meta-Model Validation with Recommendations for Evolutionary Computation

(2012) B. Bischl et al.   EVOLUTIONARY COMPUTATION

Animal models: Not close enough

(2012) Jocelyn Rice   NATURE

ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

(2011) Fantine Mordelet et al.   BMC BIOINFORMATICS

Identification and characterization of a set of conserved and new regulators of cytoskeletal organization, cell morphology and migration

(2011) Siau Bai et al.   BMC 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

Modeling sample variables with an Experimental Factor Ontology

(2010) James Malone et al.   BIOINFORMATICS

SUMOylation regulates Kv2.1 and modulates pancreatic  -cell excitability

(2009) X.-Q. Dai et al.   JOURNAL OF CELL SCIENCE

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

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Voltage-gated potassium channels as therapeutic targets

(2009) Heike Wulff et al.   NATURE REVIEWS DRUG DISCOVERY

The dual bromodomain and WD repeat-containing mouse protein BRWD1 is required for normal spermiogenesis and the oocyte–embryo transition

(2008) Dana L. Philipps et al.   DEVELOPMENTAL BIOLOGY

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

(2007) L. Yao et al.   GENOME RESEARCH