IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis

Model-based analysis uncovers mutations altering autophagy selectivity in human cancer

(2021) Zhu Han et al.   Nature Communications

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D

(2020) Susan A. Kennedy et al.   Nature Communications

A reference map of the human binary protein interactome

(2020) Katja Luck et al.   NATURE

Molecular networks in Network Medicine: Development and applications

(2020) Edwin K. Silverman et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Split Intein-Mediated Protein Ligation for detecting protein-protein interactions and their inhibition

(2020) Zhong Yao et al.   Nature Communications

Precision medicine — networks to the rescue

(2020) Anupama Yadav et al.   CURRENT OPINION IN BIOTECHNOLOGY

Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing

(2020) Sepideh Sadegh et al.   Nature Communications

Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19

(2020) Ting Shu et al.   IMMUNITY

The BioGRID database: A comprehensive biomedical resource of curated protein, genetic and chemical interactions

(2020) Rose Oughtred et al.   PROTEIN SCIENCE

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

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

(2020) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Towards a unified open access dataset of molecular interactions

(2020) Pablo Porras et al.   Nature Communications

TP53 mutations in high grade serous ovarian cancer and impact on clinical outcomes: a comparison of next generation sequencing and bioinformatics analyses

(2019) Victoria Mandilaras et al.   INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER

APID database: redefining protein–protein interaction experimental evidences and binary interactomes

(2019) Diego Alonso-López et al.   Database-The Journal of Biological Databases and Curation

Interleukin-17 receptor D constitutes an alternative receptor for interleukin-17A important in psoriasis-like skin inflammation

(2019) Yang Su et al.   Science Immunology

Protein-protein interactions of drug uptake transporters that are important for liver and kidney

(2019) Yuchen Zhang et al.   BIOCHEMICAL PHARMACOLOGY

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

MatrixDB: integration of new data with a focus on glycosaminoglycan interactions

(2018) Olivier Clerc et al.   NUCLEIC ACIDS RESEARCH

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   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

15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms

(2018) Peter V Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

(2018) N. del-Toro et al.   Nature Communications

Architecture of the human interactome defines protein communities and disease networks

(2017) Edward L. Huttlin et al.   NATURE

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

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model

(2016) Hyundoo Jeong et al.   BMC BIOINFORMATICS

Developmental transcription factor NFIB is a putative target of oncofetal miRNAs and is associated with tumour aggressiveness in lung adenocarcinoma

(2016) Daiana D Becker-Santos et al.   JOURNAL OF PATHOLOGY

The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues

(2016) Omer Basha et al.   NUCLEIC ACIDS RESEARCH

HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks

(2016) Gregorio Alanis-Lobato et al.   NUCLEIC ACIDS RESEARCH

PaxtoolsR: pathway analysis in R using Pathway Commons

(2015) Augustin Luna et al.   BIOINFORMATICS

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts

(2015) Omer Basha et al.   NUCLEIC ACIDS RESEARCH

Drug target prioritization by perturbed gene expression and network information

(2015) Zerrin Isik et al.   Scientific Reports

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

In silico prediction of physical protein interactions and characterization of interactome orphans

(2014) Max Kotlyar et al.   NATURE METHODS

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

HINT: High-quality protein interactomes and their applications in understanding human disease

(2012) Jishnu Das et al.   BMC Systems Biology

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Blockade of Phosphatidylinositol 3-Kinase (PI3K)δ or PI3Kγ Reduces IL-17 and Ameliorates Imiquimod-Induced Psoriasis-like Dermatitis

(2012) Anne Roller et al.   JOURNAL OF IMMUNOLOGY

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Combining many interaction networks to predict gene function and analyze gene lists

(2012) Sara Mostafavi et al.   PROTEOMICS

Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes

(2012) Yuanfang Guan et al.   PLoS Computational Biology

Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks

(2012) Oded Magger et al.   PLoS Computational Biology

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

(2011) I. Lee et al.   GENOME RESEARCH

Large-scaleDe NovoPrediction of Physical Protein-Protein Association

(2011) Antigoni Elefsinioti et al.   MOLECULAR & CELLULAR PROTEOMICS

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

(2011) B. Turner et al.   Database-The Journal of Biological Databases and Curation

The power of protein interaction networks for associating genes with diseases

(2010) Saket Navlakha et al.   BIOINFORMATICS

Lung cancer: Developmental networks gone awry?

(2010) Jie Dong et al.   CANCER BIOLOGY & THERAPY

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species

(2010) D. Xie et al.   GENOME RESEARCH

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

(2009) Kevin R. Brown et al.   BIOINFORMATICS

Tissue specificity and the human protein interaction network

(2009) Alice Bossi et al.   Molecular Systems Biology

Information Flow Analysis of Interactome Networks

(2009) Patrycja Vasilyev Missiuro et al.   PLoS Computational Biology

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

PID: the Pathway Interaction Database

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

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad 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