Rian, KinzaHidalgo, Marta R.Çubuk, CankutFalco, Matias M.Loucera, CarlosEsteban-Medina, MarinaAlamo-Alvarez, InmaculadaPeña-Chilet, MaríaDopazo, Joaquín2022-08-162022-08-162021-05-15Rian K, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Esteban-Medina M, et al. Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. Comput Struct Biotechnol J. 2021 May 15;19:2968-2978http://hdl.handle.net/10668/3908Genome-scale mechanistic models of pathways are gaining importance for genomic data interpretation because they provide a natural link between genotype measurements (transcriptomics or genomics data) and the phenotype of the cell (its functional behavior). Moreover, mechanistic models can be used to predict the potential effect of interventions, including drug inhibitions. Here, we present the implementation of a mechanistic model of cell signaling for the interpretation of transcriptomic data as an R/Bioconductor package, a Cytoscape plugin and a web tool with enhanced functionality which includes building interpretable predictors, estimation of the effect of perturbations and assessment of the effect of mutations in complex scenarios.enAttribution-NonCommercial-NoDerivatives 4.0 InternacionalAttribution-NonCommercial-NoDerivatives 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc-nd/4.0/Signaling pathwayMathematical modellingTranscriptomicCausalityMutationsSistema de señalizaciónCausalidadMutaciónMedical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Processes::Gene Expression::Transcription, Genetic::TranscriptomeMedical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Genetics::GenomicsMedical Subject Headings::Phenomena and Processes::Genetic Phenomena::PhenotypeMedical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Variation::MutationMedical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Biochemical Processes::Signal TransductionMedical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genotyperesearch article34136096open access10.1016/j.csbj.2021.05.0222001-0370PMC8170118