2022
Attention-Based Interpretable Regression of Gene Expression in Histology
Graziani M, Marini N, Deutschmann N, Janakarajan N, Müller H, Martínez M. Attention-Based Interpretable Regression of Gene Expression in Histology. Lecture Notes In Computer Science 2022, 13611: 44-60. DOI: 10.1007/978-3-031-17976-1_5.Peer-Reviewed Original ResearchCancer molecular subtypesGene expressionPredicting RNA structureMolecular subtypesTreatment responsePatient stratificationColorectal cancerGene expression profilesCancer tissuesRNA structurePathology UnitMicroscopic appearancePatient recommendationsHistologyCancerGenesExpression profilesExpression values
2020
Convergent network effects along the axis of gene expression during prostate cancer progression
Charmpi K, Guo T, Zhong Q, Wagner U, Sun R, Toussaint N, Fritz C, Yuan C, Chen H, Rupp N, Christiansen A, Rutishauser D, Rüschoff J, Fankhauser C, Saba K, Poyet C, Hermanns T, Oehl K, Moore A, Beisel C, Calzone L, Martignetti L, Zhang Q, Zhu Y, Martínez M, Manica M, Haffner M, Aebersold R, Wild P, Beyer A. Convergent network effects along the axis of gene expression during prostate cancer progression. Genome Biology 2020, 21: 302. PMID: 33317623, PMCID: PMC7737297, DOI: 10.1186/s13059-020-02188-9.Peer-Reviewed Original ResearchConceptsHigh-throughput genomic measurementsProstate cancer progressionGene expressionMolecular networksCopy number alterationsCancer progressionComplex genomic alterationsTumor phenotypePrediction of recurrence-free survivalGenomic measurementsRecurrence-free survivalProstate cancer patientsProteomic alterationsGenomic aberrationsAggressive tumor phenotypeGenomic alterationsDownstream proteinsGenomic effectsNetwork-based approachProstate samplesTumor siteBiochemical stateMalignant tumorsProtein levelsTumor tissues
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