4.8 Article

Systematic integration of biomedical knowledge prioritizes drugs for repurposing

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks

Irina Balaur et al.

BIOINFORMATICS (2017)

Article Biochemistry & Molecular Biology

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

Christopher J. Mungall et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

DrugCentral: online drug compendium

Oleg Ursu et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

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

Janet Pinero et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

Jacqueline MacArthur et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biotechnology & Applied Microbiology

Reproducibility of computational workflows is automated using continuous analysis

Brett K. Beaulieu-Jones et al.

NATURE BIOTECHNOLOGY (2017)

Article Mathematical & Computational Biology

Toward a comprehensive drug ontology: extraction of drug-indication relations from diverse information sources

Mark E. Sharp

JOURNAL OF BIOMEDICAL SEMANTICS (2017)

Article Multidisciplinary Sciences

Precision annotation of digital samples in NCBI's gene expression omnibus

Dexter Hadley et al.

SCIENTIFIC DATA (2017)

Article Multidisciplinary Sciences

A standard database for drug repositioning

Adam S. Brown et al.

SCIENTIFIC DATA (2017)

Article Biochemistry & Molecular Biology

WikiPathways: capturing the full diversity of pathway knowledge

Martina Kutmon et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

Michael K. Gilson et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

The SIDER database of drugs and side effects

Michael Kuhn et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

The Reactome pathway Knowledgebase

Antonio Fabregat et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Medicine, General & Internal

Mining Retrospective Data for Virtual Prospective Drug Repurposing: L-DOPA and Age-related Macular Degeneration

Murray H. Brilliant et al.

AMERICAN JOURNAL OF MEDICINE (2016)

Article Biochemical Research Methods

The Network Library: a framework to rapidly integrate network biology resources

Georg Summer et al.

BIOINFORMATICS (2016)

Review Behavioral Sciences

Proconvulsant effects of antidepressants - What is the current evidence?

Cecilie Johannessen Landmark et al.

EPILEPSY & BEHAVIOR (2016)

Article Economics

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

Joseph A. DiMasi et al.

JOURNAL OF HEALTH ECONOMICS (2016)

News Item Multidisciplinary Sciences

Legal maze threatens to slow data science

Simon Oxenham

NATURE (2016)

Editorial Material Multidisciplinary Sciences

A tragedy of errors

David B. Allison et al.

NATURE (2016)

News Item Multidisciplinary Sciences

THE WAITING GAME

Kendall Powell

NATURE (2016)

Editorial Material Multidisciplinary Sciences

Enhancing reproducibility for computational methods

Victoria Stodden et al.

SCIENCE (2016)

Article Medicine, Research & Experimental

In silico methods for drug repurposing and pharmacology

Rachel A. Hodos et al.

WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE (2016)

Article Multidisciplinary Sciences

Network-based in silico drug efficacy screening

Emre Guney et al.

NATURE COMMUNICATIONS (2016)

Editorial Material Biochemical Research Methods

Ten Simple Rules for Selecting a Bio-ontology

James Malone et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Review Mathematical & Computational Biology

Representing and querying disease networks using graph databases

Artem Lysenko et al.

BIODATA MINING (2016)

Article Biology

How open science helps researchers succeed

Erin C. McKiernan et al.

ELIFE (2016)

Article Computer Science, Artificial Intelligence

Computational drug repositioning based on side-effects mined from social media

Timothy Nugent et al.

PEERJ COMPUTER SCIENCE (2016)

Article Computer Science, Information Systems

A method for systematic discovery of adverse drug events from clinical notes

Guan Wang et al.

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION (2015)

Review Multidisciplinary Sciences

Methods for biological data integration: perspectives and challenges

Vladimir Gligorijevic et al.

JOURNAL OF THE ROYAL SOCIETY INTERFACE (2015)

Article Biochemical Research Methods

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

Sune Pletscher-Frankild et al.

METHODS (2015)

News Item Multidisciplinary Sciences

Why we are teaching science wrong, and how to make it right

M. Mitchell Waldrop

NATURE (2015)

Article Genetics & Heredity

The support of human genetic evidence for approved drug indications

Matthew R. Nelson et al.

NATURE GENETICS (2015)

Article Multidisciplinary Sciences

Accelerating scientific publication in biology

Ronald D. Vale

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

Uncovering disease-disease relationships through the incomplete interactome

Joerg Menche et al.

SCIENCE (2015)

Article Mathematical & Computational Biology

Scaling drug indication curation through crowdsourcing

Ritu Khare et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2015)

Article Mathematical & Computational Biology

Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis

Tsung-Jung Wu et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2015)

Article Mathematical & Computational Biology

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

Janet Pinero et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2015)

Article Biochemical Research Methods

Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes

Daniel S. Himmelstein et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Article Multidisciplinary Sciences

Comprehensive comparison of large-scale tissue expression datasets

Alberto Santos et al.

PEERJ (2015)

Editorial Material Biology

Bioboxes: standardised containers for interchangeable bioinformatics software

Peter Belmann et al.

GIGASCIENCE (2015)

Article Computer Science, Information Systems

Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality

Hua Xu et al.

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION (2015)

Article Biochemistry & Molecular Biology

The GOA database: Gene Ontology annotation updates for 2015

Rachael P. Huntley et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Clinical Neurology

Anticonvulsant-induced downbeat nystagmus in epilepsy

Dongyan Wu et al.

EPILEPSY & BEHAVIOR CASE REPORTS (2015)

Article Biochemistry & Molecular Biology

A Proteome-Scale Map of the Human Interactome Network

Thomas Rolland et al.

Article Computer Science, Interdisciplinary Applications

LabeledIn: Cataloging labeled indications for human drugs

Ritu Khare et al.

JOURNAL OF BIOMEDICAL INFORMATICS (2014)

Article Biochemistry & Molecular Biology

Pathway-based Bayesian inference of drug-disease interactions

Naruemon Pratanwanich et al.

MOLECULAR BIOSYSTEMS (2014)

Article Biotechnology & Applied Microbiology

Clinical development success rates for investigational drugs

Michael Hay et al.

NATURE BIOTECHNOLOGY (2014)

Article Medicine, General & Internal

Cytisine versus Nicotine for Smoking Cessation

Natalie Walker et al.

NEW ENGLAND JOURNAL OF MEDICINE (2014)

Article Biochemistry & Molecular Biology

DrugBank 4.0: shedding new light on drug metabolism

Vivian Law et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

Human symptoms-disease network

XueZhong Zhou et al.

NATURE COMMUNICATIONS (2014)

Article Chemistry, Multidisciplinary

UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers

Jon Chambers et al.

JOURNAL OF CHEMINFORMATICS (2014)

Article Genetics & Heredity

Systematic evaluation of connectivity map for disease indications

Jie Cheng et al.

GENOME MEDICINE (2014)

Article Mathematics, Interdisciplinary Applications

Multilayer networks

Mikko Kivela et al.

JOURNAL OF COMPLEX NETWORKS (2014)

Editorial Material Biochemical Research Methods

Are graph databases ready for bioinformatics?

Christian Theil Have et al.

BIOINFORMATICS (2013)

Review Pharmacology & Pharmacy

Computational Drug Repositioning: From Data to Therapeutics

M. R. Hurle et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2013)

Review Pharmacology & Pharmacy

In silico drug repositioning - what we need to know

Zhichao Liu et al.

DRUG DISCOVERY TODAY (2013)

Review Pharmacology & Pharmacy

Transcriptional data: a new gateway to drug repositioning?

Francesco Iorio et al.

DRUG DISCOVERY TODAY (2013)

Article Computer Science, Information Systems

Development and evaluation of an ensemble resource linking medications to their indications

Wei-Qi Wei et al.

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION (2013)

Article Biochemistry & Molecular Biology

NCBI GEO: archive for functional genomics data sets-update

Tanya Barrett et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Chemistry, Multidisciplinary

UniChem: a unified chemical structure cross-referencing and identifier tracking system

Jon Chambers et al.

JOURNAL OF CHEMINFORMATICS (2013)

Review Chemistry, Multidisciplinary

InChI - the worldwide chemical structure identifier standard

Stephen Heller et al.

JOURNAL OF CHEMINFORMATICS (2013)

Article Multidisciplinary Sciences

Data reuse and the open data citation advantage

Heather A. Piwowar et al.

PEERJ (2013)

Review Biochemical Research Methods

Drug discovery in the age of systems biology: the rise of computational approaches for data integration

Murat Iskar et al.

CURRENT OPINION IN BIOTECHNOLOGY (2012)

Review Pharmacology & Pharmacy

Applications of Connectivity Map in drug discovery and development

Xiaoyan A. Qu et al.

DRUG DISCOVERY TODAY (2012)

Article Computer Science, Information Systems

Development and evaluation of a crowdsourcing methodology for knowledge base construction: identifying relationships between clinical problems and medications

Allison B. McCoy et al.

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION (2012)

News Item Multidisciplinary Sciences

THE DIGITAL LAB

Jim Giles

NATURE (2012)

Letter Biotechnology & Applied Microbiology

Use of genome-wide association studies for drug repositioning

Philippe Sanseau et al.

NATURE BIOTECHNOLOGY (2012)

Article Biotechnology & Applied Microbiology

Diagnosing the decline in pharmaceutical R&D efficiency

Jack W. Scannell et al.

NATURE REVIEWS DRUG DISCOVERY (2012)

Review Substance Abuse

Development of Novel Pharmacotherapeutics for Tobacco Dependence: Progress and Future Directions

Dympna Harmey et al.

NICOTINE & TOBACCO RESEARCH (2012)

Article Biochemistry & Molecular Biology

Disease Ontology: a backbone for disease semantic integration

Lynn Marie Schriml et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

A Framework for Annotating Human Genome in Disease Context

Wei Xu et al.

PLOS ONE (2012)

Article Cell Biology

Data-Driven Prediction of Drug Effects and Interactions

Nicholas P. Tatonetti et al.

SCIENCE TRANSLATIONAL MEDICINE (2012)

Article Biotechnology & Applied Microbiology

Uberon, an integrative multi-species anatomy ontology

Christopher J. Mungall et al.

GENOME BIOLOGY (2012)

Article Biochemical Research Methods

Molecular signatures database (MSigDB) 3.0

Arthur Liberzon et al.

BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

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

Assaf Gottlieb et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Biochemical Research Methods

Next-generation sequencing to generate interactome datasets

Haiyuan Yu et al.

NATURE METHODS (2011)

Article Biotechnology & Applied Microbiology

How were new medicines discovered?

David C. Swinney et al.

NATURE REVIEWS DRUG DISCOVERY (2011)

Article Medicine, General & Internal

Placebo-Controlled Trial of Cytisine for Smoking Cessation

Robert West et al.

NEW ENGLAND JOURNAL OF MEDICINE (2011)

Article Biochemistry & Molecular Biology

Pathway Commons, a web resource for biological pathway data

Ethan G. Cerami et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

Entrez Gene: gene-centered information at NCBI

Donna Maglott et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Clinical Neurology

Gastrointestinal adverse effects of antiepileptic drugs in intractable epileptic patients

Soodeh Razeghi Jahromi et al.

SEIZURE-EUROPEAN JOURNAL OF EPILEPSY (2011)

Editorial Material Biochemistry & Molecular Biology

The Open Knowledge Foundation: Open Data Means Better Science

Jennifer C. Molloy

PLOS BIOLOGY (2011)

Article Pharmacology & Pharmacy

Antiepileptic Drug Interactions - Principles and Clinical Implications

Svein I. Johannessen et al.

Current Neuropharmacology (2010)

Article Chemistry, Medicinal

Extended-Connectivity Fingerprints

David Rogers et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)

Letter Multidisciplinary Sciences

Disclose all data in publications

Keith Baggerly

NATURE (2010)

Article Pharmacology & Pharmacy

Systematic Evaluation of Drug-Disease Relationships to Identify Leads for Novel Drug Uses

A. P. Chiang et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2009)

Editorial Material Cell Biology

This revolution will be digitized: online tools for radical collaboration

Chris Patil et al.

DISEASE MODELS & MECHANISMS (2009)

Article Biochemical Research Methods

An empirical framework for binary interactome mapping

Kavitha Venkatesan et al.

NATURE METHODS (2009)

Review Genetics & Heredity

Bayesian statistical methods for genetic association studies

Matthew Stephens et al.

NATURE REVIEWS GENETICS (2009)

Article Biochemistry & Molecular Biology

PID: the Pathway Interaction Database

Carl F. Schaefer et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Medicine, General & Internal

Efficacy and safety of varenicline for smoking cessation

J. Taylor Hays et al.

AMERICAN JOURNAL OF MEDICINE (2008)

Article Multidisciplinary Sciences

A variant associated with nicotine dependence, lung cancer and peripheral arterial disease

Thorgeir E. Thorgeirsson et al.

NATURE (2008)

Review Biochemistry & Molecular Biology

Network pharmacology: the next paradigm in drug discovery

Andrew L. Hopkins

NATURE CHEMICAL BIOLOGY (2008)

Article Psychology, Biological

Acamprosate attenuates the handling induced convulsions during alcohol withdrawal in Swiss Webster mice

Justin M. Farook et al.

PHYSIOLOGY & BEHAVIOR (2008)

Article Multidisciplinary Sciences

Drug target identification using side-effect similarity

Monica Campillos et al.

SCIENCE (2008)

Editorial Material Biochemistry & Molecular Biology

WikiPathways: Pathway editing for the people

Alexander R. Pico et al.

PLOS BIOLOGY (2008)

Article Clinical Neurology

Movement disorders in patients taking anticonvulsants

C. Zadikoff et al.

JOURNAL OF NEUROLOGY NEUROSURGERY AND PSYCHIATRY (2007)

Article Oncology

Innovation - The Connectivity Map: a new tool for biomedical research

Justin Lamb

NATURE REVIEWS CANCER (2007)

Article Pharmacology & Pharmacy

Varenicline is a partial agonist at α4β2 and a full agonist at α7 neuronal nicotinic receptors

Karla B. Mihalak et al.

MOLECULAR PHARMACOLOGY (2006)

Article Biochemistry & Molecular Biology

DrugBank: a comprehensive resource for in silico drug discovery and exploration

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Multidisciplinary Sciences

Towards a proteome-scale map of the human protein-protein interaction network

JF Rual et al.

NATURE (2005)

Article Information Science & Library Science

Who owns scientific data? The impact of intellectual property rights on the scientific publication chain

R Elliott

LEARNED PUBLISHING (2005)

Article Biotechnology & Applied Microbiology

Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia

BL Roth et al.

NATURE REVIEWS DRUG DISCOVERY (2004)

Review Clinical Neurology

The effect of antiepileptic drugs on visual performance

EJR Hilton et al.

SEIZURE-EUROPEAN JOURNAL OF EPILEPSY (2004)

Article Biotechnology & Applied Microbiology

Drug repositioning: Identifying and developing new uses for existing drugs

TT Ashburn et al.

NATURE REVIEWS DRUG DISCOVERY (2004)

Review Neurosciences

The neurobiology of antiepileptic drugs

MA Rogawski et al.

NATURE REVIEWS NEUROSCIENCE (2004)

Article Biochemistry & Molecular Biology

The Unified Medical Language System (UMLS): integrating biomedical terminology

O Bodenreider

NUCLEIC ACIDS RESEARCH (2004)

Review Biotechnology & Applied Microbiology

Trends in development and approval times for new therapeutics in the United States

JM Reichert

NATURE REVIEWS DRUG DISCOVERY (2003)

Article Biochemistry & Molecular Biology

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

R Edgar et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Clinical Neurology

Effect of antiepileptic drugs on sleep

F Placidi et al.

CLINICAL NEUROPHYSIOLOGY (2000)