Drug repositioning by applying ‘expression profiles’ generated by integrating chemical structure similarity and gene semantic similarity

A sensitive method for computing GO-based functional similarities among genes with ‘shallow annotation’

(2012) Xiujie Chen et al.   GENE

Old friends in new guise: repositioning of known drugs with structural bioinformatics

(2011) V. J. Haupt et al.   BRIEFINGS IN BIOINFORMATICS

The Effects of Ethanol on the Bioavailability of Oxymorphone Extended-Release Tablets and Oxymorphone Crush-Resistant Extended-Release Tablets

(2011) William D. Fiske et al.   JOURNAL OF PAIN

PREDICT: a method for inferring novel drug indications with application to personalized medicine

(2011) A. Gottlieb et al.   Molecular Systems Biology

Identification of Candidate Small-Molecule Therapeutics to Cancer by Gene-Signature Perturbation in Connectivity Mapping

(2011) Darragh G. McArt et al.   PLoS One

Modulatory profiling identifies mechanisms of small molecule-induced cell death

(2011) A. J. Wolpaw et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Identification of small molecules enhancing autophagic function from drug network analysis

(2010) Francesco Iorio et al.   Autophagy

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work

(2010) Gregor Warsow et al.   BMC Systems Biology

A Systematic Review of Oxymorphone in the Management of Chronic Pain

(2010) Fadia Mayyas et al.   JOURNAL OF PAIN AND SYMPTOM MANAGEMENT

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

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

A Network of Cancer Genes with Co-Occurring and Anti-Co-Occurring Mutations

(2010) Qinghua Cui   PLoS One

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

Unveiling the role of network and systems biology in drug discovery

(2010) Albert Pujol et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks

(2010) Joel T. Dudley et al.   Journal of Cardiovascular Translational Research

Human Disease-Drug Network Based on Genomic Expression Profiles

(2009) Guanghui Hu et al.   PLoS One

Semantic Similarity in Biomedical Ontologies

(2009) Catia Pesquita et al.   PLoS Computational Biology

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology