The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

(2020) Rachel Drysdale et al.   BIOINFORMATICS

Exploring modularity in biological networks

(2020) Maria Serban   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A paradigm shift in medicine: A comprehensive review of network-based approaches

(2019) Federica Conte et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Assessment of network module identification across complex diseases

(2019) Sarvenaz Choobdar et al.   NATURE METHODS

Co-regulation map of the human proteome enables identification of protein functions

(2019) Georg Kustatscher et al.   NATURE BIOTECHNOLOGY

The MetaCyc database of metabolic pathways and enzymes - a 2019 update

(2019) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

deepNF: deep network fusion for protein function prediction

(2018) Vladimir Gligorijević et al.   BIOINFORMATICS

Next-Generation Machine Learning for Biological Networks

(2018) Diogo M. Camacho et al.   CELL

Leveraging multiple gene networks to prioritize GWAS candidate genes via network representation learning

(2018) Mengmeng Wu et al.   METHODS

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes

(2018) Justin K. Huang et al.   Cell Systems

Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

(2018) Nadezhda T. Doncheva et al.   JOURNAL OF PROTEOME RESEARCH

Drug repurposing: progress, challenges and recommendations

(2018) Sudeep Pushpakom et al.   NATURE REVIEWS DRUG DISCOVERY

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species

(2018) Max Kotlyar et al.   NUCLEIC ACIDS RESEARCH

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes

(2018) Birgit H M Meldal et al.   NUCLEIC ACIDS RESEARCH

MitoMiner v4.0: an updated database of mitochondrial localization evidence, phenotypes and diseases

(2018) Anthony C Smith et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

HumanNet v2: human gene networks for disease research

(2018) Sohyun Hwang et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Network propagation: a universal amplifier of genetic associations

(2017) Lenore Cowen et al.   NATURE REVIEWS GENETICS

FunCoup 4: new species, data, and visualization

(2017) Christoph Ogris et al.   NUCLEIC ACIDS RESEARCH

20 years of the SMART protein domain annotation resource

(2017) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Network biology concepts in complex disease comorbidities

(2016) Jessica Xin Hu et al.   NATURE REVIEWS GENETICS

SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles

(2015) Andrea Franceschini et al.   BIOINFORMATICS

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

(2015) Aaron K. Wong et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines

(2015) Mingcong Wang et al.   PROTEOMICS

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

PubTator: a web-based text mining tool for assisting biocuration

(2013) Chih-Hsuan Wei et al.   NUCLEIC ACIDS RESEARCH

Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization

(2013) Sofie Van Landeghem et al.   PLoS One

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

(2012) Sandra Orchard et al.   NATURE METHODS

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

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach

(2011) Wangshu Zhang et al.   BMC BIOINFORMATICS

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Bayesian Inference for Genomic Data Integration Reduces Misclassification Rate in Predicting Protein-Protein Interactions

(2011) Chuanhua Xing et al.   PLoS Computational Biology

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function

(2008) Weidong Tian et al.   GENOME BIOLOGY