Systems pharmacology: network analysis to identify multiscale mechanisms of drug action

S Zhao, R Iyengar - Annual review of pharmacology and …, 2012 - annualreviews.org
Systems approaches have long been used in pharmacology to understand drug action at
the organ and organismal levels. The application of computational and experimental …

A review on computational systems biology of pathogen–host interactions

S Durmuş, T Çakır, A Özgür, R Guthke - Frontiers in microbiology, 2015 - frontiersin.org
Pathogens manipulate the cellular mechanisms of host organisms via pathogen–host
interactions (PHIs) in order to take advantage of the capabilities of host cells, leading to …

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

AD Rouillard, GW Gundersen, NF Fernandez… - Database, 2016 - academic.oup.com
Genomics, epigenomics, transcriptomics, proteomics and metabolomics efforts rapidly
generate a plethora of data on the activity and levels of biomolecules within mammalian …

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

EY Chen, CM Tan, Y Kou, Q Duan, Z Wang… - BMC …, 2013 - Springer
Background System-wide profiling of genes and proteins in mammalian cells produce lists of
differentially expressed genes/proteins that need to be further analyzed for their collective …

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

S Orchard, M Ammari, B Aranda, L Breuza… - Nucleic acids …, 2014 - academic.oup.com
IntAct (freely available at http://www. ebi. ac. uk/intact) is an open-source, open data
molecular interaction database populated by data either curated from the literature or from …

Global landscape of HIV–human protein complexes

S Jaeger, P Cimermancic, N Gulbahce, JR Johnson… - Nature, 2012 - nature.com
Human immunodeficiency virus (HIV) has a small genome and therefore relies heavily on
the host cellular machinery to replicate. Identifying which host proteins and complexes come …

MINT, the molecular interaction database: 2009 update

A Ceol, A Chatr Aryamontri, L Licata… - Nucleic acids …, 2010 - academic.oup.com
ABSTRACT MINT (http://mint. bio. uniroma2. it/mint) is a public repository for molecular
interactions reported in peer-reviewed journals. Since its last report, MINT has grown …

A functional map of HIV-host interactions in primary human T cells

J Hiatt, JF Hultquist, MJ McGregor… - Nature …, 2022 - nature.com
Abstract Human Immunodeficiency Virus (HIV) relies on host molecular machinery for
replication. Systematic attempts to genetically or biochemically define these host factors …

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data

T Guirimand, S Delmotte, V Navratil - Nucleic acids research, 2015 - academic.oup.com
Abstract VirHostNet release 2.0 (http://virhostnet. prabi. fr) is a knowledgebase dedicated to
the network-based exploration of virus–host protein–protein interactions. Since the previous …

VirusMentha: a new resource for virus-host protein interactions

A Calderone, L Licata, G Cesareni - Nucleic acids research, 2015 - academic.oup.com
Viral infections often cause diseases by perturbing several cellular processes in the infected
host. Viral proteins target host proteins and either form new complexes or modulate the …