2020
Inferring clonal composition from multiple tumor biopsies
Manica M, Kim H, Mathis R, Chouvarine P, Rutishauser D, De Vargas Roditi L, Szalai B, Wagner U, Oehl K, Saba K, Pati A, Saez-Rodriguez J, Roy A, Parsons D, Wild P, Martínez M, Sumazin P. Inferring clonal composition from multiple tumor biopsies. Npj Systems Biology And Applications 2020, 6: 27. PMID: 32843649, PMCID: PMC7447821, DOI: 10.1038/s41540-020-00147-5.Peer-Reviewed Original ResearchConceptsCopy number alterationsEffects of copy number alterationsGenetic instabilityClonal evolutionClonal compositionDrug-resistant prostate cancerAcquisition of mutationsDrug-resistant subclonesPhylogeny reconstructionTumor phylogeniesRelative abundanceTumor biopsiesWilms tumorProstate cancerGenetic alterationsGenetic profileMultiple biopsiesTumor profilingHepatocellular carcinomaPhylogenyTumorSubclonesAnalysis of simulated dataMutationsBiopsyPan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries
Pinoli P, Stamoulakatou E, Nguyen A, Martínez M, Ceri S. Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries. PLOS ONE 2020, 15: e0227180. PMID: 31945090, PMCID: PMC6964824, DOI: 10.1371/journal.pone.0227180.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsBinding SitesCCCTC-Binding FactorChromosomes, Human, Pair 11DNA Copy Number VariationsDNA MethylationDNA Mutational AnalysisEpigenesis, GeneticExonsFemaleGene Expression Regulation, NeoplasticGenome, HumanHumansInsulator ElementsMutation RateNeoplasmsPoint MutationPromoter Regions, GeneticConceptsCTCF motifsCopy number alterationsSomatic mutationsAbnormal methylationCTCF binding sitesCopy number alteration eventsAnalysis of somatic mutationsMatched normal samplesCancer typesCTCF bindingOncogene dysregulationMutation enrichmentPan-cancer analysisPositive selectionEpigenetic alterationsIn-boundaryGenomic alterationsMotifMutational signaturesBinding sitesMutationsCTCFPan-cancerCopyNormal samples
2019
Network-based Biased Tree Ensembles (NetBiTE) for Drug Sensitivity Prediction and Drug Sensitivity Biomarker Identification in Cancer
Oskooei A, Manica M, Mathis R, Martínez M. Network-based Biased Tree Ensembles (NetBiTE) for Drug Sensitivity Prediction and Drug Sensitivity Biomarker Identification in Cancer. Scientific Reports 2019, 9: 15918. PMID: 31685861, PMCID: PMC6828742, DOI: 10.1038/s41598-019-52093-w.Peer-Reviewed Original ResearchConceptsMembrane receptor pathwayDrug sensitivity predictionProtein-protein interaction networkDrug sensitivityGenomics of Drug SensitivityDrug targetsGene expression dataIGFR signaling pathwaysAssignment of high weightsBiomarker identificationExpression dataInteraction networkSensitivity predictionSignaling pathwaySignaling pathway inhibitorsReceptor pathwayTree ensemblesPathway inhibitorPathwayGenomeGenesGDSCNeighborhoods of influenceIdentificationSynthetic datasets
2018
The number of titrated microRNA species dictates ceRNA regulation
Chiu H, Martínez M, Komissarova E, Llobet-Navas D, Bansal M, Paull E, Silva J, Yang X, Sumazin P, Califano A. The number of titrated microRNA species dictates ceRNA regulation. Nucleic Acids Research 2018, 46: gky286-. PMID: 29684207, PMCID: PMC5961349, DOI: 10.1093/nar/gky286.Peer-Reviewed Original ResearchConceptsCo-regulationPrediction of gene expressionMiRNA speciesTumor suppressor PTENCeRNA regulationGene expressionCeRNA interactionsMicroRNA speciesBiochemical assaysMultiple miRNAsSpeciesOncogene CCND1Non-tumour contextsRegulating microRNAsMiRNAsInteraction kineticsEndogenous RNAIndependent tumorsCeRNA networkHIF1AInteractomeCeRNAGenesRNAOncogene
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