Research

Research Projects as Principal Investigator

• PID2024-156297OB-I00. Diagnosis and monitoring of autoimmune diseases through analysis of single-cell transcriptional signatures: new bioinformatics methods and predictive models. Ministry of Science, Innovation and Universities, 2025–2028. PI: Pedro Carmona Sáez.
• PIN-0004-2026. Caracterización genómica avanzada y desarrollo de herramientas diagnósticas para el Mieloma Múltiple. Junta de Andalucía, 2026–2029.IPs: Pedro Carmona Sáez & Mónica Bernal
• PID2020-119032RB-I00. Integration of omics data for biomarker discovery and network inference. Ministry of Science, Innovation and Universities, 2021–2025. PI: Pedro Carmona Sáez.
• P20_00335. Precision genomic medicine in autoimmune diseases: network inference and personalized treatments. Junta de Andalucía, 2021–2023. PI: Pedro Carmona Sáez.
• PP2024PP-07. New data-driven approaches for the diagnosis of complex diseases. University of Granada (UGR), 2025. PI: Pedro Carmona Sáez.
• PPJIA2022-14. Novel artificial intelligence method for predictive models using single-cell gene expression data. University of Granada (UGR), 2023. PI: Pedro Carmona Sáez.
• B-CTS-40-UGR20. Development of a centralized omics data platform for autoimmune diseases for biomarker discovery and therapeutic target identification. Junta de Andalucía (FEDER), 2021–2023. PI: Pedro Carmona Sáez & Marta Alarcón-Riquelme.
• CV20-36723 (DatAC – Data Against COVID-19). Data integration and modeling of the COVID-19 pandemic. Junta de Andalucía, 2020–2022. PI: Pedro Carmona Sáez.
• PI-0173-2017. Identification of biomarkers in systemic lupus erythematosus through integrated transcriptome and methylome analysis. Junta de Andalucía, 2017–2021. PI: Pedro Carmona Sáez.

Selected Publications

For a complete and updated publication list please visit Google Scholar, PubMed or the UGR Research Portal.

• Vargas-Fernández M, Luna JD, Martorell-Marugán J, Carmona-Sáez P. Network analysis of longitudinal electronic health records using linear mixed models. BioData Mining. 2026;19(1):7. DOI: 10.1186/s13040-025-00508-y
• Villatoro-Garcia JA, Jurado-Bascon PP, Carmona-Saez P. Effect Size-Driven Pathway Meta-Analysis for Gene Expression Data. IEEE Transactions on Computational Biology and Bioinformatics. 2026;23(1):101-111. DOI: 10.1109/TCBBIO.2025.3635882
• Martorell-Marugán J, López-Domínguez R, Villatoro-García JA, Toro-Domínguez D, Chierici M, Jurman G, Carmona-Sáez P. Explainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics. Briefings in Bioinformatics. 2024;26(1):bbae673. DOI: 10.1093/bib/bbae673
• Asenjo HG, Alcazar-Fabra M, Espinosa-Martínez M, Lopez-Onieva L, Gallardo A, Dimitrova E, Feldmann A, Pachano T, Martorell-Marugán J, Carmona-Sáez P, Sanchez-Pozo A, Rada-Iglesias Á, Klose RJ, Landeira D. Changes in PRC1 activity during interphase modulate lineage transition in pluripotent cells. Nature Communications. 2023;14(1):180. DOI: 10.1038/s41467-023-35859-9
• Toro-Domínguez D, Martorell-Marugán J, Martinez-Bueno M, López-Domínguez R, Carnero-Montoro E, Barturen G, Goldman D, Petri M, Carmona-Sáez P, Alarcón-Riquelme ME. Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression. Briefings in Bioinformatics. 2022;23(5):bbac332. DOI: 10.1093/bib/bbac332
• Toro-Domínguez D, Villatoro-García JA, Martorell-Marugán J, Román-Montoya Y, Alarcón-Riquelme ME, Carmona-Sáez P. A survey of gene expression meta-analysis: methods and applications. Briefings in Bioinformatics. 2021;22(2):1694-1705. DOI: 10.1093/bib/bbaa019
• Everson TM, Vives-Usano M, Seyve E, Cardenas A, Lacasaña M, Craig JM, Lesseur C, Baker ER, Fernandez-Jimenez N, Heude B, Perron P, Gónzalez-Alzaga B, Halliday J, Deyssenroth MA, Karagas MR, Íñiguez C, Bouchard L, Carmona-Sáez P, Loke YJ, Hao K, Belmonte T, Charles MA, Martorell-Marugán J, Muggli E, Chen J, Fernández MF, Tost J, Gómez-Martín A, London SJ, Sunyer J, Marsit CJ, Lepeule J, Hivert MF, Bustamante M. Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth. Nature Communications. 2021;12(1):5095. DOI: 10.1038/s41467-021-24558-y
• Barturen G, Babaei S, Català-Moll F, Martínez-Bueno M, Makowska Z, Martorell-Marugán J, Carmona-Sáez P, Toro-Domínguez D, Carnero-Montoro E, Teruel M, et al. Integrative Analysis Reveals a Molecular Stratification of Systemic Autoimmune Diseases. Arthritis & Rheumatology. 2021;73(6):1073-1085. DOI: 10.1002/art.41610
• Martorell-Marugán J, González-Rumayor V, Carmona-Sáez P. mCSEA: detecting subtle differentially methylated regions. Bioinformatics. 2019;35(18):3257-3262. DOI: 10.1093/bioinformatics/btz096
• Toro-Domínguez D, Martorell-Marugán J, López-Domínguez R, García-Moreno A, González-Rumayor V, Alarcón-Riquelme ME, Carmona-Sáez P. ImaGEO: integrative gene expression meta-analysis from GEO database. Bioinformatics. 2019;35(5):880-882. DOI: 10.1093/bioinformatics/bty721
• Toro-Domínguez D, Martorell-Marugán J, Goldman D, Petri M, Carmona-Sáez P, Alarcón-Riquelme ME. Stratification of Systemic Lupus Erythematosus Patients Into Three Groups of Disease Activity Progression According to Longitudinal Gene Expression. Arthritis & Rheumatology. 2018;70(12):2025-2035. DOI: 10.1002/art.40653
• Carmona-Sáez P, Varela N, Luque MJ, Toro-Domínguez D, Martorell-Marugan J, Alarcón-Riquelme ME, Marañón C. Metagene projection characterizes GEN2.2 and CAL-1 as relevant human plasmacytoid dendritic cell models. Bioinformatics. 2017;33(23):3691-3695. DOI: 10.1093/bioinformatics/btx502
• Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A. GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biology. 2007;8(1):R3. DOI: 10.1186/gb-2007-8-1-r3
• Carmona-Saez P, Pascual-Marqui RD, Tirado F, Carazo JM, Pascual-Montano A. Biclustering of gene expression data by Non-smooth Non-negative Matrix Factorization. BMC Bioinformatics. 2006;7:78. DOI: 10.1186/1471-2105-7-78