ConsensusPathDB 2022: molecular interactions update as a resource for network biology

A roadmap for the Human Developmental Cell Atlas

(2021) Muzlifah Haniffa et al.   NATURE

STAT3: A key regulator in liver fibrosis

(2020) Jie Zhao et al.   Annals of Hepatology

NetCore: a network propagation approach using node coreness

(2020) Gal Barel et al.   NUCLEIC ACIDS RESEARCH

Network integration and modelling of dynamic drug responses at multi-omics levels

(2020) Nathalie Selevsek et al.   Communications Biology

WikiPathways: connecting communities

(2020) Marvin Martens et al.   NUCLEIC ACIDS RESEARCH

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

(2020) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

miRDB: an online database for prediction of functional microRNA targets

(2019) Yuhao Chen et al.   NUCLEIC ACIDS RESEARCH

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

(2019) Sarah Mubeen et al.   Frontiers in Genetics

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

(2018) Han Chen et al.   CELL

MiR-1-3p that correlates with left ventricular function of HCM can serve as a potential target and differentiate HCM from DCM

(2018) Mengmeng Li et al.   Journal of Translational Medicine

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes

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

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

ChEMBL: towards direct deposition of bioassay data

(2018) David Mendez et al.   NUCLEIC ACIDS RESEARCH

Network propagation: a universal amplifier of genetic associations

(2017) Lenore Cowen et al.   NATURE REVIEWS GENETICS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

Understanding Tissue-Specific Gene Regulation

(2017) Abhijeet Rajendra Sonawane et al.   Cell Reports

Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer

(2016) Justin M. Drake et al.   CELL

Analyzing and interpreting genome data at the network level with ConsensusPathDB

(2016) Ralf Herwig et al.   Nature Protocols

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The H-index of a network node and its relation to degree and coreness

(2016) Linyuan Lü et al.   Nature Communications

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

(2016) Andrew D. Rouillard et al.   Database-The Journal of Biological Databases and Curation

Circulating miR-1 as a potential biomarker of doxorubicin-induced cardiotoxicity in breast cancer patients

(2016) Vagner Oliveira-Carvalho Rigaud et al.   Oncotarget

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

Fundamentals of protein interaction network mapping

(2015) J. Snider et al.   Molecular Systems Biology

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Correcting for the study bias associated with protein–protein interaction measurements reveals differences between protein degree distributions from different cancer types

(2015) Martin H. Schaefer et al.   Frontiers in Genetics

Mitochondrial form and function

(2014) Jonathan R. Friedman et al.   NATURE

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

(2014) Mark D M Leiserson et al.   NATURE GENETICS

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

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

SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks

(2013) Dávid Fazekas et al.   BMC Systems Biology

Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries

(2013) J. S. Jakobsen et al.   GENOME RESEARCH

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

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

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database

(2013) Timothy Jewison et al.   NUCLEIC ACIDS RESEARCH

Pharmacogenomics Knowledge for Personalized Medicine

(2012) M Whirl-Carrillo et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

IntScore: a web tool for confidence scoring of biological interactions

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

INOH: ontology-based highly structured database of signal transduction pathways

(2011) S. Yamamoto et al.   Database-The Journal of Biological Databases and Curation

SPIKE: a database of highly curated human signaling pathways

(2010) Arnon Paz et al.   NUCLEIC ACIDS RESEARCH

ConsensusPathDB: toward a more complete picture of cell biology

(2010) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

MicroRNA-92a Controls Angiogenesis and Functional Recovery of Ischemic Tissues in Mice

(2009) A. Bonauer et al.   SCIENCE

PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database

(2008) Chia-Ying Yang et al.   BIOINFORMATICS

PID: the Pathway Interaction Database

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

PIG--the pathogen interaction gateway

(2008) T. Driscoll et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

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