Publication:
Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data

Simple item page
dc.contributor.authorRian, Kinza
dc.contributor.authorHidalgo, Marta R.
dc.contributor.authorÇubuk, Cankut
dc.contributor.authorFalco, Matias M.
dc.contributor.authorLoucera, Carlos
dc.contributor.authorEsteban-Medina, Marina
dc.contributor.authorAlamo-Alvarez, Inmaculada
dc.contributor.authorPeña-Chilet, María
dc.contributor.authorDopazo, Joaquín
dc.contributor.authoraffiliation[Rian,K; Çubuk,C; Falco,MM; Loucera,C; Esteban-Medina,M; Alamo-Alvarez,I; Peña-Chilet,M; Dopazo,J] Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla, Spain. [Rian,K] Laboratory of Innovative Technologies (LTI), National School of Applied Sciences in Tangier, UAE, Morocco. [Hidalgo,MR] Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain. [Falco,MM; Peña-Chilet,M; Dopazo,J] Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain. [Loucera,C; Esteban-Medina,M; Alamo-Alvarez,I; Peña-Chilet,M; Dopazo,J] Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla, Spain. [Dopazo,J] Functional Genomics Node (INB-ELIXIR-es), Sevilla, Spain.
dc.contributor.funderThis work is supported by grants SAF2017-88908-R from the Spanish Ministry of Economy and Competitiveness and PT17/0009/0006 and PI20/01305 from the ISCIII, both co-funded with European Regional Development Funds (ERDF) as well as H2020 Programme of the European Union grants Marie Curie Inno vative Training Network ‘‘Machine Learning Frontiers in Precision Medicine” (MLFPM) (GA 813533) and ‘‘ELIXIR-EXCELERATE fast track ELIXIR implementation and drive early user exploitation across the life sciences” (GA 676559) to JD. Funding for open access charge: from the Spanish Ministry of Economy and Competitive ness / SAF2017-88908-R
dc.date.accessioned2022-08-16T11:56:54Z
dc.date.available2022-08-16T11:56:54Z
dc.date.issued2021-05-15
dc.description.abstractGenome-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.en
dc.description.versionYeses_ES
dc.identifier.citationRian 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;19:2968-2978es_ES
dc.identifier.doi10.1016/j.csbj.2021.05.022es_ES
dc.identifier.essn2001-0370
dc.identifier.pmcPMC8170118
dc.identifier.pmid34136096
dc.identifier.urihttp://hdl.handle.net/10668/3908
dc.journal.titleComputational and Structural Biotechnology Journal
dc.language.isoen
dc.page.number11 p.
dc.publisherElsevier B.Ves_ES
dc.relation.publisherversionhttps://www.sciencedirect.com/science/article/pii/S2001037021002038es_ES
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 Internacional*
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 Internacional*
dc.rights.accessRightsopen access
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.subjectSignaling pathwayes_ES
dc.subjectMathematical modellinges_ES
dc.subjectTranscriptomices_ES
dc.subjectCausalityes_ES
dc.subjectMutationses_ES
dc.subjectSistema de señalizaciónes_ES
dc.subjectCausalidades_ES
dc.subjectMutaciónes_ES
dc.subject.meshMedical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Processes::Gene Expression::Transcription, Genetic::Transcriptomees_ES
dc.subject.meshMedical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Genetics::Genomicses_ES
dc.subject.meshMedical Subject Headings::Phenomena and Processes::Genetic Phenomena::Phenotypees_ES
dc.subject.meshMedical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Variation::Mutationes_ES
dc.subject.meshMedical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Biochemical Processes::Signal Transductiones_ES
dc.subject.meshMedical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genotypees_ES
dc.titleGenome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic dataen
dc.typeresearch article
dc.type.hasVersionVoR
dspace.entity.typePublication

Files

Original bundle

Now showing 1 - 2 of 2
Thumbnail Image
Name:
Rian_GenomeScale.pdf
Size:
2.8 MB
Format:
Adobe Portable Document Format
Description:
Artículo publicado
Download
No Thumbnail Available
Name:
Rian_GenomeScale_MaterialSuplementario.docx
Size:
488.89 KB
Format:
Microsoft Word XML
Description:
Material Suplementario
Download

Collections

Fundación Pública Andaluza Progreso y Salud
Instituto de Investigación Biomédica de Sevilla (IBIS)
SAS - Hospital Universitario Virgen del Rocío

© 2023 – Repositorio Institucional de Salud de Andalucía - Fundación Pública Andaluza Progreso y Salud - Consejería de Salud y Consumo de la Junta de Andalucía