2022
PCfun: a hybrid computational framework for systematic characterization of protein complex function
Sharma V, Fossati A, Ciuffa R, Buljan M, Williams E, Chen Z, Shao W, Pedrioli P, Purcell A, Martínez M, Song J, Manica M, Aebersold R, Li C. PCfun: a hybrid computational framework for systematic characterization of protein complex function. Briefings In Bioinformatics 2022, 23: bbac239. PMID: 35724564, PMCID: PMC9310514, DOI: 10.1093/bib/bbac239.Peer-Reviewed Original ResearchConceptsProtein complex functionGO termsProtein complex databasesGene Ontology (GONatural language processing techniquesRandom forestLanguage processing techniquesNearest neighborsProtein complexesSystematic annotationCellular statesBiological functionsBiological processesQuery vectorComplex queriesWord vectorsUnsupervised approachSupervised approachChild termsProteinMolecular biologySubunit compositionComplex databasesComplex functionsComputational framework
2015
Elucidating Compound Mechanism of Action by Network Perturbation Analysis
Woo J, Shimoni Y, Yang W, Subramaniam P, Iyer A, Nicoletti P, Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell B, Bansal M, Califano A. Elucidating Compound Mechanism of Action by Network Perturbation Analysis. Cell 2015, 162: 441-451. PMID: 26186195, PMCID: PMC4506491, DOI: 10.1016/j.cell.2015.05.056.Peer-Reviewed Original ResearchConceptsGenome-wide identificationRegulatory network analysisBind target proteinsCompound's mechanism of actionNovel proteinsTarget proteinsCompound perturbationGlobal dysregulationSmall molecule compoundsCompound similarityProteinNetwork-based approachRepair activityMolecular interactionsTested compoundsCompoundsMechanism of actionNetwork analysisCompound analysisActivity modulationAnticancer drugsCompound efficacyPerturbation profilesSimilarityEffector
2007
Input–output robustness in simple bacterial signaling systems
Shinar G, Milo R, Martínez M, Alon U. Input–output robustness in simple bacterial signaling systems. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 19931-19935. PMID: 18077424, PMCID: PMC2148400, DOI: 10.1073/pnas.0706792104.Peer-Reviewed Original Research