The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

Identification of GPR83 as the receptor for the neuroendocrine peptide PEN

(2016) Ivone Gomes et al.   Science Signaling

Identification of GPR83 as the receptor for the neuroendocrine peptide PEN

(2016) Ivone Gomes et al.   Science Signaling

Dynamics of the discovery process of protein-protein interactions from low content studies

(2015) Zichen Wang et al.   BMC Systems Biology

Ten things you should know about protein kinases: IUPHAR Review 14

(2015) Doriano Fabbro et al.   BRITISH JOURNAL OF PHARMACOLOGY

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

Thematic Minireview Series: New Directions in G Protein-coupled Receptor Pharmacology

(2015) Henrik G. Dohlman   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2015) Sune Pletscher-Frankild et al.   METHODS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65

(2015) Xi-Ping Huang et al.   NATURE

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

(2015) et al.   SCIENCE

FDA-approved small-molecule kinase inhibitors

(2015) Peng Wu et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Advancements in therapeutically targeting orphan GPCRs

(2015) Jennifer A. Stockert et al.   Frontiers in Pharmacology

Comprehensive comparison of large-scale tissue expression datasets

(2015) Alberto Santos et al.   PeerJ

Sorafenib and irinotecan (NEXIRI) as second- or later-line treatment for patients with metastatic colorectal cancer and KRAS-mutated tumours: a multicentre Phase I/II trial

(2014) E Samalin et al.   BRITISH JOURNAL OF CANCER

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

A comprehensive transcriptional portrait of human cancer cell lines

(2014) Christiaan Klijn et al.   NATURE BIOTECHNOLOGY

The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease

(2014) Janan T. Eppig et al.   NUCLEIC ACIDS RESEARCH

The human DEPhOsphorylation database DEPOD: a 2015 update

(2014) Guangyou Duan et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

(2014) Qiaonan Duan et al.   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

The Comparative Toxicogenomics Database's 10th year anniversary: update 2015

(2014) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

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

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Lean Big Data integration in systems biology and systems pharmacology

(2014) Avi Ma’ayan et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

COMPARTMENTS: unification and visualization of protein subcellular localization evidence

(2014) J. X. Binder et al.   Database-The Journal of Biological Databases and Curation

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

(2014) Glenn S Cowley et al.   Scientific Data

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Inconsistency in large pharmacogenomic studies

(2013) Benjamin Haibe-Kains et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse

(2013) Judith A. Blake et al.   NUCLEIC ACIDS RESEARCH

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

(2013) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands

(2013) Adam J. Pawson et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

(2013) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

NCBI’s Database of Genotypes and Phenotypes: dbGaP

(2013) Kimberly A. Tryka et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells

(2013) Huilei Xu et al.   Database-The Journal of Biological Databases and Curation

GO-Elite: a flexible solution for pathway and ontology over-representation

(2012) Alexander C. Zambon et al.   BIOINFORMATICS

Genes2FANs: connecting genes through functional association networks

(2012) Ruth Dannenfelser et al.   BMC BIOINFORMATICS

Sets2Networks: network inference from repeated observations of sets

(2012) Neil R Clark et al.   BMC Systems Biology

Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?

(2012) W. G. Touw et al.   BRIEFINGS IN BIOINFORMATICS

Ion Channels as Therapeutic Targets: A Drug Discovery Perspective

(2012) Sharan K. Bagal et al.   JOURNAL OF MEDICINAL CHEMISTRY

The International Mouse Phenotyping Consortium: past and future perspectives on mouse phenotyping

(2012) Steve D. M. Brown et al.   MAMMALIAN GENOME

The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data

(2012) Cynthia L. Smith et al.   MAMMALIAN GENOME

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

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

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

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

HMDB 3.0—The Human Metabolome Database in 2013

(2012) David S. Wishart et al.   NUCLEIC ACIDS RESEARCH

The Allen Human Brain Atlas

(2012) Elaine H. Shen et al.   TRENDS IN NEUROSCIENCES

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Analysis of the Human Endogenous Coregulator Complexome

(2011) Anna Malovannaya et al.   CELL

Phase I Study of Bosutinib, a Src/Abl Tyrosine Kinase Inhibitor, Administered to Patients with Advanced Solid Tumors

(2011) A. I. Daud et al.   CLINICAL CANCER RESEARCH

Too many roads not taken

(2011) Aled M. Edwards et al.   NATURE

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

(2011) Bruno Aranda et al.   NATURE METHODS

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

(2011) David M Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GeneWeaver: a web-based system for integrative functional genomics

(2011) Erich J. Baker et al.   NUCLEIC ACIDS RESEARCH

GWASdb: a database for human genetic variants identified by genome-wide association studies

(2011) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

(2011) A. C. Culhane et al.   NUCLEIC ACIDS RESEARCH

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification

(2011) N. Juty et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Subtype and pathway specific responses to anticancer compounds in breast cancer

(2011) L. M. Heiser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer

(2011) H. W. Cheung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards BioDBcore: a community-defined information specification for biological databases

(2011) P. Gaudet et al.   Database-The Journal of Biological Databases and Curation

The Biomolecular Interaction Network Database in PSI-MI 2.5

(2011) Ruth Isserlin et al.   Database-The Journal of Biological Databases and Curation

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

SKI-606 (Bosutinib) Blocks Prostate Cancer Invasion, Growth, and Metastasis In vitro and In vivo through Regulation of Genes Involved in Cancer Growth and Skeletal Metastasis

(2010) S. A. Rabbani et al.   MOLECULAR CANCER THERAPEUTICS

Towards patient-based cancer therapeutics

(2010) Stuart L Schreiber et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

miRTarBase: a database curates experimentally validated microRNA–target interactions

(2010) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Prediction of the human membrane proteome

(2010) Linn Fagerberg et al.   PROTEOMICS

GeneCards Version 3: the human gene integrator

(2010) M. Safran et al.   Database-The Journal of Biological Databases and Curation

KEA: kinase enrichment analysis

(2009) A. Lachmann et al.   BIOINFORMATICS

Src activation in melanoma and Src inhibitors as therapeutic agents in melanoma

(2009) Jade Homsi et al.   MELANOMA RESEARCH

Disease signatures are robust across tissues and experiments

(2009) Joel T Dudley et al.   Molecular Systems Biology

The Allen Brain Atlas: 5 years and beyond

(2009) Allan R. Jones et al.   NATURE REVIEWS NEUROSCIENCE

GeneSigDB—a curated database of gene expression signatures

(2009) Aedín C. Culhane et al.   NUCLEIC ACIDS RESEARCH

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer

(2009) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

'Omics Data Sharing

(2009) D. Field et al.   SCIENCE

The mammalian phenotype ontology: enabling robust annotation and comparative analysis

(2009) Cynthia L. Smith et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

A wiki for the life sciences where authorship matters

(2008) Robert Hoffmann   NATURE GENETICS

A navigator for human genome epidemiology

(2008) Wei Yu et al.   NATURE GENETICS

Structural diversity of G protein-coupled receptors and significance for drug discovery

(2008) Malin C. Lagerström et al.   NATURE REVIEWS DRUG DISCOVERY

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks

(2008) A. P. Davis et al.   NUCLEIC ACIDS RESEARCH

VirusMINT: a viral protein interaction database

(2008) A. Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH