FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity

Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro

(2020) Manli Wang et al.   CELL RESEARCH

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

(2020) Alexandra C. Walls et al.   CELL

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

(2020) Jun Lan et al.   NATURE

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

(2020) David E. Gordon et al.   NATURE

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

(2020) Waradon Sungnak et al.   NATURE MEDICINE

The Quest for Orthologs benchmark service and consensus calls in 2020

(2020) Adrian M Altenhoff et al.   NUCLEIC ACIDS RESEARCH

Breakthrough: Chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies

(2020) Jianjun Gao et al.   BioScience Trends

Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV

(2020) Xiuyuan Ou et al.   Nature Communications

Distribution of ACE2, CD147, CD26 and other SARS‐CoV‐2 associated molecules in tissues and immune cells in health and in asthma, COPD, obesity, hypertension, and COVID‐19 risk factors

(2020) U. Radzikowska et al.   ALLERGY

COVID-19 and cardiovascular disease: from basic mechanisms to clinical perspectives

(2020) Masataka Nishiga et al.   Nature Reviews Cardiology

Pathway-specific model estimation for improved pathway annotation by network crosstalk

(2020) Miguel Castresana-Aguirre et al.   Scientific Reports

Molecular pathogenesis of secondary bacterial infection associated to viral infections including SARS-CoV-2

(2020) Sounik Manna et al.   Journal of Infection and Public Health

COVID-19, Renin-Angiotensin System and Endothelial Dysfunction

(2020) Razie Amraei et al.   Cells

Tissue-specificity in cancer: The rule, not the exception

(2019) Kevin M. Haigis et al.   SCIENCE

The DisGeNET knowledge platform for disease genomics: 2019 update

(2019) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

GIANT 2.0: genome-scale integrated analysis of gene networks in tissues

(2018) Aaron K Wong et al.   NUCLEIC ACIDS RESEARCH

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes

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

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

HumanNet v2: human gene networks for disease research

(2018) Sohyun Hwang et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

FunCoup 4: new species, data, and visualization

(2017) Christoph Ogris et al.   NUCLEIC ACIDS RESEARCH

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Analyzing and interpreting genome data at the network level with ConsensusPathDB

(2016) Ralf Herwig et al.   Nature Protocols

PathwAX: a web server for network crosstalk based pathway annotation

(2016) Christoph Ogris et al.   NUCLEIC ACIDS RESEARCH

Tissue Specificity of Human Disease Module

(2016) Maksim Kitsak et al.   Scientific Reports

Comparison of microarray and RNA-Seq analysis of mRNA expression in dermal mesenchymal stem cells

(2015) Junqin Li et al.   BIOTECHNOLOGY LETTERS

RNA-Seq identifies novel myocardial gene expression signatures of heart failure

(2015) Yichuan Liu et al.   GENOMICS

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

Integrated interactions database: tissue-specific view of the human and model organism interactomes

(2015) Max Kotlyar et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

(2015) Zhi-Ping Liu et al.   Database-The Journal of Biological Databases and Curation

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

(2014) Charles Wang et al.   NATURE BIOTECHNOLOGY

Comparative Analysis of Human Tissue Interactomes Reveals Factors Leading to Tissue-Specific Manifestation of Hereditary Diseases

(2014) Ruth Barshir et al.   PLoS Computational Biology

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

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

FunCoup 3.0: database of genome-wide functional coupling networks

(2013) Thomas Schmitt et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles

(2011) Chao Cheng et al.   BIOINFORMATICS

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

ODB: a database for operon organizations, 2011 update

(2010) S. Okuda et al.   NUCLEIC ACIDS RESEARCH

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

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

Global networks of functional coupling in eukaryotes from comprehensive data integration

(2009) A. Alexeyenko et al.   GENOME RESEARCH

Precision and recall estimates for two-hybrid screens

(2008) Hailiang Huang et al.   BIOINFORMATICS

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS