BPG is committed to discovery and dissemination of knowledge
Cited by in F6Publishing
For: Amadoz A, Hidalgo MR, Çubuk C, Carbonell-Caballero J, Dopazo J. A comparison of mechanistic signaling pathway activity analysis methods. Brief Bioinform 2019;20:1655-68. [PMID: 29868818 DOI: 10.1093/bib/bby040] [Cited by in Crossref: 24] [Cited by in F6Publishing: 26] [Article Influence: 8.0] [Reference Citation Analysis]
Number Citing Articles
1 Buckler AJ, Marlevi D, Skenteris NT, Lengquist M, Kronqvist M, Matic L, Hedin U. In silico model of atherosclerosis with individual patient calibration to enable precision medicine for cardiovascular disease. Comput Biol Med 2023;152:106364. [PMID: 36525832 DOI: 10.1016/j.compbiomed.2022.106364] [Reference Citation Analysis]
2 Liu F, Heiner M, Gilbert D. Hybrid modelling of biological systems: current progress and future prospects. Brief Bioinform 2022:bbac081. [PMID: 35352101 DOI: 10.1093/bib/bbac081] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
3 Hrovatin K, Fischer DS, Theis FJ. Toward modeling metabolic state from single-cell transcriptomics. Mol Metab 2021;:101396. [PMID: 34785394 DOI: 10.1016/j.molmet.2021.101396] [Cited by in Crossref: 7] [Cited by in F6Publishing: 8] [Article Influence: 3.5] [Reference Citation Analysis]
4 Carbonell-caballero J, López-quílez A, Conesa D, Dopazo J. Deciphering Genomic Heterogeneity and the Internal Composition of Tumour Activities through a Hierarchical Factorisation Model. Mathematics 2021;9:2833. [DOI: 10.3390/math9212833] [Reference Citation Analysis]
5 Golriz Khatami S, Mubeen S, Bharadhwaj VS, Kodamullil AT, Hofmann-Apitius M, Domingo-Fernández D. Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures. NPJ Syst Biol Appl 2021;7:40. [PMID: 34707117 DOI: 10.1038/s41540-021-00199-1] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.5] [Reference Citation Analysis]
6 Rintala TJ, Federico A, Latonen L, Greco D, Fortino V. A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery. Brief Bioinform 2021:bbab314. [PMID: 34396389 DOI: 10.1093/bib/bbab314] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 0.5] [Reference Citation Analysis]
7 Romera-Giner S, Andreu Martínez Z, García-García F, Hidalgo MR. Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers. Biol Direct 2021;16:9. [PMID: 34039407 DOI: 10.1186/s13062-021-00293-8] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
8 Rian K, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Esteban-Medina M, Alamo-Alvarez I, Peña-Chilet M, Dopazo J. 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;19:2968-78. [PMID: 34136096 DOI: 10.1016/j.csbj.2021.05.022] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
9 Garrido-Rodriguez M, Lopez-Lopez D, Ortuno FM, Peña-Chilet M, Muñoz E, Calzado MA, Dopazo J. A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways. PLoS Comput Biol 2021;17:e1008748. [PMID: 33571195 DOI: 10.1371/journal.pcbi.1008748] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 2.5] [Reference Citation Analysis]
10 Rian K, Esteban-Medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M, Peña-Chilet M, Dopazo J. Mechanistic modeling of the SARS-CoV-2 disease map. BioData Min 2021;14:5. [PMID: 33478554 DOI: 10.1186/s13040-021-00234-1] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 2.5] [Reference Citation Analysis]
11 Dopazo J. Molecular Genetics in the Next Generation Sequencing Era. Mitochondrial Diseases 2021. [DOI: 10.1007/978-3-030-70147-5_9] [Reference Citation Analysis]
12 Loucera C, Esteban-Medina M, Rian K, Falco MM, Dopazo J, Peña-Chilet M. Drug repurposing for COVID-19 using machine learning and mechanistic models of signal transduction circuits related to SARS-CoV-2 infection. Signal Transduct Target Ther 2020;5:290. [PMID: 33311438 DOI: 10.1038/s41392-020-00417-y] [Cited by in Crossref: 23] [Cited by in F6Publishing: 23] [Article Influence: 7.7] [Reference Citation Analysis]
13 Khatami SG, Mubeen S, Bharadhwaj VS, Kodamullil AT, Hofmann-apitius M, Domingo-fernández D. Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures.. [DOI: 10.1101/2020.12.06.413435] [Reference Citation Analysis]
14 Çubuk C, Can FE, Peña-Chilet M, Dopazo J. Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments. Cells 2020;9:E1579. [PMID: 32610626 DOI: 10.3390/cells9071579] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 0.7] [Reference Citation Analysis]
15 Falco MM, Peña-Chilet M, Loucera C, Hidalgo MR, Dopazo J. Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscape. NAR Cancer 2020;2:zcaa011. [PMID: 34316686 DOI: 10.1093/narcan/zcaa011] [Cited by in Crossref: 8] [Cited by in F6Publishing: 8] [Article Influence: 2.7] [Reference Citation Analysis]
16 Rian K, Esteban-medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M, Peña-chilet M, Dopazo J. Mechanistic modeling of the SARS-CoV-2 disease map.. [DOI: 10.1101/2020.04.12.025577] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.3] [Reference Citation Analysis]
17 Peña-Chilet M, Esteban-Medina M, Falco MM, Rian K, Hidalgo MR, Loucera C, Dopazo J. Using mechanistic models for the clinical interpretation of complex genomic variation. Sci Rep 2019;9:18937. [PMID: 31831811 DOI: 10.1038/s41598-019-55454-7] [Cited by in Crossref: 11] [Cited by in F6Publishing: 11] [Article Influence: 2.8] [Reference Citation Analysis]
18 Falco MM, Peña-chilet M, Loucera C, Hidalgo MR, Dopazo J. Mechanistic models of signaling pathways deconvolute the functional landscape of glioblastoma at single cell resolution.. [DOI: 10.1101/858811] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.3] [Reference Citation Analysis]
19 Ravichandran S, Hartmann A, Del Sol A. SigHotSpotter: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies. Bioinformatics 2019:btz827. [PMID: 31697324 DOI: 10.1093/bioinformatics/btz827] [Cited by in Crossref: 4] [Cited by in F6Publishing: 6] [Article Influence: 1.0] [Reference Citation Analysis]
20 Esteban-Medina M, Peña-Chilet M, Loucera C, Dopazo J. Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models. BMC Bioinformatics 2019;20:370. [PMID: 31266445 DOI: 10.1186/s12859-019-2969-0] [Cited by in Crossref: 20] [Cited by in F6Publishing: 20] [Article Influence: 5.0] [Reference Citation Analysis]
21 Dugourd A, Saez-Rodriguez J. Footprint-based functional analysis of multiomic data. Curr Opin Syst Biol 2019;15:82-90. [PMID: 32685770 DOI: 10.1016/j.coisb.2019.04.002] [Cited by in Crossref: 27] [Cited by in F6Publishing: 14] [Article Influence: 6.8] [Reference Citation Analysis]
22 Esteban M, Peña-chilet M, Loucera C, Dopazo J. Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models.. [DOI: 10.1101/647735] [Reference Citation Analysis]
23 Çubuk C, Hidalgo MR, Amadoz A, Rian K, Salavert F, Pujana MA, Mateo F, Herranz C, Carbonell-Caballero J, Dopazo J. Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models. NPJ Syst Biol Appl 2019;5:7. [PMID: 30854222 DOI: 10.1038/s41540-019-0087-2] [Cited by in Crossref: 23] [Cited by in F6Publishing: 24] [Article Influence: 5.8] [Reference Citation Analysis]
24 Hidalgo MR, Amadoz A, Çubuk C, Carbonell-Caballero J, Dopazo J. Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome. Biol Direct 2018;13:16. [PMID: 30134948 DOI: 10.1186/s13062-018-0219-4] [Cited by in Crossref: 17] [Cited by in F6Publishing: 18] [Article Influence: 3.4] [Reference Citation Analysis]
25 Çubuk C, Hidalgo MR, Amadoz A, Rian K, Salavert F, Pujana MA, Mateo F, Herranz C, Carbonell-caballero J, Dopazo J. Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models.. [DOI: 10.1101/367334] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 1.0] [Reference Citation Analysis]