Network-based Approaches in Pharmacology

Drug combinatorics and side effect estimation on the signed human drug-target network

(2016) Núria Ballber Torres et al.   BMC Systems Biology

In silico methods to address polypharmacology: current status, applications and future perspectives

(2016) Antonio Lavecchia et al.   DRUG DISCOVERY TODAY

Providing data science support for systems pharmacology and its implications to drug discovery

(2016) Thomas Hart et al.   Expert Opinion on Drug Discovery

Lessons learned from the design of chemical space networks and opportunities for new applications

(2016) Martin Vogt et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Pharos: Collating protein information to shed light on the druggable genome

(2016) Dac-Trung Nguyen et al.   NUCLEIC ACIDS RESEARCH

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

(2016) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

PubChem BioAssay: 2017 update

(2016) Yanli Wang et al.   NUCLEIC ACIDS RESEARCH

ChemProt-3.0: a global chemical biology diseases mapping

(2016) Jens Kringelum et al.   Database-The Journal of Biological Databases and Curation

Identification of drug–target interaction from interactome network with ‘guilt-by-association’ principle and topology features

(2015) Zhan-Chao Li et al.   BIOINFORMATICS

The application of sparse estimation of covariance matrix to quadratic discriminant analysis

(2015) Jiehuan Sun et al.   BMC BIOINFORMATICS

Comparison of bioactive chemical space networks generated using substructure- and fingerprint-based measures of molecular similarity

(2015) Bijun Zhang et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Human protein interaction networks across tissues and diseases

(2015) Esti Yeger-Lotem et al.   Frontiers in Genetics

Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis

(2014) D. Carrella et al.   BIOINFORMATICS

Composition and Topology of Activity Cliff Clusters Formed by Bioactive Compounds

(2014) Dagmar Stumpfe et al.   Journal of Chemical Information and Modeling

EXPLORING COMPOUND PROMISCUITY PATTERNS AND MULTI-TARGET ACTIVITY SPACES

(2014) Ye Hu et al.   Computational and Structural Biotechnology Journal

Network-Based Approaches in Drug Discovery and Early Development

(2013) J M Harrold et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

(2013) M. Iskar et al.   Molecular Systems Biology

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

(2013) Peter Csermely et al.   PHARMACOLOGY & THERAPEUTICS

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

(2013) Dorothea Emig et al.   PLoS One

Bridging the Gap between Genotype and Phenotype via Network Approaches

(2013) Yoo-Ah Kim et al.   Frontiers in Genetics

IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis

(2012) Fan Zhang et al.   BMC BIOINFORMATICS

Sibutramine-induced mania as the first manifestation of bipolar disorder

(2012) Napoleon Waszkiewicz et al.   BMC Psychiatry

MMP-Cliffs: Systematic Identification of Activity Cliffs on the Basis of Matched Molecular Pairs

(2012) Xiaoying Hu et al.   Journal of Chemical Information and Modeling

The impact of network biology in pharmacology and toxicology

(2012) G. Panagiotou et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

Human diseases through the lens of network biology

(2012) Laura I. Furlong   TRENDS IN GENETICS

On the origins of drug polypharmacology

(2012) Xavier Jalencas et al.   MedChemComm

Chemoproteomic approaches to drug target identification and drug profiling

(2011) Marcus Bantscheff et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns

(2011) Daniel Baron et al.   BMC GENOMICS

The relationship between rational drug design and drug side effects

(2011) J. Wang et al.   BRIEFINGS IN BIOINFORMATICS

Network-based methods for human disease gene prediction

(2011) X. Wang et al.   Briefings in Functional Genomics

In Silico Predictions of hERG Channel Blockers in Drug Discovery: From Ligand-Based and Target-Based Approaches to Systems Chemical Biology

(2011) Olivier Taboureau et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

The use of phenome-wide association studies (PheWAS) for exploration of novel genotype-phenotype relationships and pleiotropy discovery

(2011) S.A. Pendergrass et al.   GENETIC EPIDEMIOLOGY

SAR Monitoring of Evolving Compound Data Sets Using Activity Landscapes

(2011) Preeti Iyer et al.   Journal of Chemical Information and Modeling

Network-Based Analysis and Characterization of Adverse Drug–Drug Interactions

(2011) Masataka Takarabe et al.   Journal of Chemical Information and Modeling

Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing

(2011) Tudor I. Oprea et al.   Molecular Informatics

Analysis of multiple compound-protein interactions reveals novel bioactive molecules

(2011) H. Yabuuchi et al.   Molecular Systems Biology

Network Neighbors of Drug Targets Contribute to Drug Side-Effect Similarity

(2011) Lucas Brouwers et al.   PLoS One

When pharmaceutical companies publish large datasets: an abundance of riches or fool's gold?

(2010) Sean Ekins et al.   DRUG DISCOVERY TODAY

Network medicine: a network-based approach to human disease

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

ChemProt: a disease chemical biology database

(2010) O. Taboureau et al.   NUCLEIC ACIDS RESEARCH

PROMISCUOUS: a database for network-based drug-repositioning

(2010) J. von Eichborn et al.   NUCLEIC ACIDS RESEARCH

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

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

Network analyses in systems pharmacology

(2009) S. I. Berger et al.   BIOINFORMATICS

Small-World Phenomena in Chemical Library Networks: Application to Fragment-Based Drug Discovery

(2009) Naoki Tanaka et al.   Journal of Chemical Information and Modeling

Identifying Network of Drug Mode of Action by Gene Expression Profiling

(2009) Francesco Iorio et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The topology of drug–target interaction networks: implicit dependence on drug properties and target families

(2009) Jordi Mestres et al.   Molecular BioSystems

Gene–disease relationship discovery based on model-driven data integration and database view definition

(2008) S. Yilmaz et al.   BIOINFORMATICS

Structure−Activity Relationship Anatomy by Network-like Similarity Graphs and Local Structure−Activity Relationship Indices

(2008) Mathias Wawer et al.   JOURNAL OF MEDICINAL CHEMISTRY

Data completeness—the Achilles heel of drug-target networks

(2008) Jordi Mestres et al.   NATURE BIOTECHNOLOGY

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

A global view of drug-therapy interactions

(2008) Jose C Nacher et al.   BMC Pharmacology & Toxicology