Publications

(Full list of publications: Google Scholar – PubMed)

* Shared first authors
** Shared corresponding/senior authors

2024

• J. Martorell-Marugán, R. López-Domínguez, JA Villatoro-García, D. Toro-Domínguez, M. Chierici, G. Jurman, P. Carmona-Sáez. Explainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics, bioRxiv 2024
• I. Ellson, J. Martorell-Marugán, P. Carmona-Sáez **, V. Ramos-Mejia**. MiRNA expression as outcome predictor in pediatric AML. Genomic Medicine 2024 IF: 5.3, Q1
• D. Toro-Dominguez, R. López-Domínguez, JA Villatoro-García, C. Marañón, D. Goldman, M. Petri, P. Carmona-Sáez, M. Alarcón-Riquelme. Immune and molecular landscape behind non-response to Mycophenolate Mofetil and Azathioprine in lupus nephritis therapy. ResearchSquare 2024

2023

• J. Martorell-Marugán, M. Chierici, G. Jurman; M.E. Alarcón-Riquelme; P. Carmona-Sáez. Differential diagnosis of Systemic Lupus Erythematosus and Sjögren’s Syndrome using machine learning and multi-omics data. Comput Biol Med., 2023. IF: 6.698, D1
• H. Asenjo, M. Alcazar, M. Espinosa, L. Lopez-Onieva, A. Gallardo, E. Dimitrova, A. Feldmann, T. Pachano, J. Martorell-Marugán, P. Carmona-Saez, A. Sanchez-Pozo, A. Rada-Iglesias, R. Klose, Landeira D. Changes in PRC1 activity during interphase modulate lineage transition in pluripotent cells. Nature Communications. 2023. IF: 17.694, D1
• Villatoro-García JA, López-Domínguez R, Martorell-Marugán J, de Dios Luna J, Lorente JA, Carmona-Sáez P. Exploring the interplay between climate, population immunity and SARS-CoV-2 transmission dynamics in Mediterranean countries Science of the Total Environ. 2021. IF: 9.8, D1
• Domingo-Reinés J, Montes R, Garcia-Moreno A, Gallardo A, Sanchez-Manas JM, Ellson I, Lamolda M, Calabro C, López-Escamez JA, Catalina P, Carmona-Sáez P, Real PJ, Landeira D, Ramos-Mejia V. The pediatric leukemia oncoprotein NUP98-KDM5A induces genomic instability that may facilitate malignant transformation. Cell Death Dis. 2023, IF 9.696 Q1
• J. Martorell-Marugán, M. Chierici, Sara Bandres-Ciga, G. Jurman; P. Carmona-Sáez. Machine Learning Applications in the Study of Parkinson’s Disease: A Systematic Review. Current Bioinformatics, 2023. IF: 4.000, Q1
• Pande Putu Erawijantari, Ece Kartal, José Liñares-Blanco, et al. Microbiome-based risk prediction in incident heart failure: a community challenge. Preprint, medRxiv 2023

2022

• D. Toro-Domínguez, J. Martorell-Marugán, M. Martinez, R. López-Domínguez, E. Carnero, G. Barturen, D. Goldman, M. Petri, P. Carmona-Sáez** M.E. Alarcón-Riquelme** Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression. Brief. Bioinformatics. 2022. IF: 9.5, D1
• Aparicio-Puerta E, Gómez-Martín C, Giannoukakos S, Medina JM, Scheepbouwer C, García-Moreno A, Carmona-Saez P, Fromm B, Pegtel M, Keller A, Marchal JA, Hackenberg M. sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. Nucleic Acids Res. 2022, IF: 14.9, D1
• A. Gallardo, A. Molina, H.G. Asenjo, L. Lopez-Onieva, J. Martorell-Marugán, M. Espinosa-Martinez, C. Griñan-Lison, J.C. Alvarez-Perez, F.E. Cara, S.A. Navarro-Marchal, P. Carmona-Sáez, P.P. Medina, J. A. Marchal, S. Granados-Principal, A. Sánchez-Pozo & D. Landeira. EZH2 endorses cell plasticity to non-small cell lung cancer cells facilitating mesenchymal to epithelial transition and tumour colonization. Oncogene 2022. IF: 8.0, D1
• J.A. Villatoro-García, J. Martorell-Marugán, D. Toro-Domínguez, Y. Román-Montoya, P. Femia, P. Carmona-Sáez. DExMA: An R Package for Performing Gene Expression Meta-Analysis with Missing Genes. Math. 2022. IF: 2.4, D1
• Fernandez-Jimenez et al. A meta-analysis of pre-pregnancy maternal body mass index and placental DNA methylation identifies 27 CpG sites with implications for mother-child health. Communications Biol. 2022, IF: 5.9, Q1
• A. Garcia-Moreno*, R. López-Domínguez*, JA Villatoro-García, A. Ramirez-Mena, E. Aparicio-Puerta, M. Hackenberg, A. Pascual-Montano, P. Carmona-Saez. Functional Enrichment Analysis of Regulatory Elements. Biomededicines 2022. IF: 4.700, Q1
• P. Femia, J. Melchor, P. Carmona-Saez. Mathematical and Computational Methods in Physiology. Front. Physiol. 2022. IF: 4.00, Q2
• Rybakowska P., Van Gassen S., Martorell Marugan J. et al., Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline. STAR Protocols

2021

• T.M. Everson, M. Vives-Usano, E. Seyve, A. Cardenas, M. Lacasaña, JM. Craig, C. Lesseur, ER. Baker, N. Fernandez-Jimenez, B. Heude, P. Perron, B. Gónzalez-Alzaga, J. Halliday, MA. Deyssenroth, MR. Karagas, C. Íñiguez, L. Bouchard, P. Carmona-Sáez et al. Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth. Nature Communications. 2021. IF: 17.694, D1
• Martorell-Marugán J, Villatoro-García JA, García-Moreno A, López-Domínguez R, Requena F, Merelo JJ, Lacasaña M, de Dios Luna J, Díaz-Mochón JJ, Lorente JA, Carmona-Sáez P. DatAC: A visual analytics platform to explore climate and air quality indicators associated with the COVID-19 pandemic in Spain. Science of the Total Environ. 2021. IF: 10.754, D1
• D. Toro-Domínguez*, J.A. Villatoro-García*, J. Martorell-Marugán, Y. Roman, ME Alarcon-Riquelme, P. Carmona-Saez. A survey of gene expression meta-analysis: methods and applications. Brief. Bioinformatics. 2021. IF: 13.994, D1
• G. Barturen, S. Babaei, F. Català-Moll, M. Martínez-Bueno, Z. Makowska, J. Martorell-Marugán, P. Carmona-Sáez, D. Toro-Domníguez, E. Carnero-Montoro, M. Teruel, M. Kerick, M. Acosta-Herrera, et al. Integrative Analysis Reveals a Molecular Stratification of Systemic Autoimmune Diseases. Arthritis Rheumatol. 2021. IF: 15.483, D1
• K. Troulé, H. López-Fernández, S. García-Martín, M. Reboiro-Jato, C. Carretero-Puche, J. Martorell-Marugán, G. Martín-Serrano, P. Carmona-Sáez, D. González-Peña, F. Al-Shahrour, G. Gómez-López. DREIMT: a drug repositioning database and prioritization tool for immunomodulation. Bioinformatics, 2020. IF: 6.931, D1
• Peinado P, Andrades A, Martorell-Marugán J, Haswell JR, Slack FJ, Carmona-Sáez P, Medina PP. The SWI/SNF complex regulates the expression of miR-222, a tumor suppressor microRNA in lung adenocarcinoma. Hum Mol Genet. 2021. Q1
• A. Pozo-Agundo, N. Villaescusa, J. Martorell-Marugán, O. Soriano, S. Leyva, A.B. Jódar-Reyes, L.M. Botella, P. Carmona-Sáez, F.J. Blanco. Identification of Exosomal MicroRNA Signature by Liquid Biopsy in Hereditary Hemorrhagic Telangiectasia Patients. Int J Mol Sci. 2021. Q1
• R. Lopez-Dominguez, D. Toro-Dominguez, J. Martorell-Marugan, A. Garcia-Moreno, C.H Holland, J. Saez-Rodriguez, D. Goldman, M.A Petri, M. E Alarcon-Riquelme, P. Carmona-Saez. Transcription Factor Activity Inference in Systemic Lupus Erythematosus. Life 2021. Q2
• J. Martorell-Marugan, R. Lopez-Dominguez, A. Garcia-Moreno, D. Toro-Dominguez, J. A. Villatoro-Garcia, G. Barturen, A. Martin-Gomez, K. Troule, G. Gomez-Lopez, F. Al-Shahrour, M. Peña-Chilet, J. Dopazo, V. Gonzalez-Rumayor, M.E. Alarcon-Riquelme, P. Carmona-Saez. A comprehensive and centralized database for exploring omics data in Autoimmune Diseases. BMC Bioinformatics 2021. Q2
• A. García-Moreno*, R. López-Domínguez *, A. Ramirez-Mena , A. Pascual-Montano , E. Aparicio-Puerta , M. Hackenberg , P. Carmona-Saez. GeneCodis 4: Expanding the modular enrichment analysis to regulatory elements. bioRxiv 2021 https://doi.org/10.1101/2021.04.15.439962
• Martorell-Marugán J and Carmona-Sáez P. Detecting Differentially Methylated Promoters in Genes Related to Disease Phenotypes Using R. Bio-Protocols 2021

2020

• H. Gómez, A. Gallardo, L. López-Onieva, I. Tejada, J. Martorell-Marugán, P. Carmona-Sáez, D. Landeira Polycomb regulation is coupled to cell cycle transition in pluripotent stem cells. Science Advances. 2020 D1
• B. López-Longarela, E. E. Morrison, J.D. Tranter, L. Chahman-Vos, J. Léonard, J. Gautier, S. Laurent, A. Lartigau, E. Boitier, L. Sautier, P. Carmona-Saez, J. Martorell-Marugan, R.J. Mellanby, S. Pernagallo, H. Ilyine, D.M. Rissin, D.C. Duffy, J.W. Dear, J.J. Díaz-Mochón. Direct detection of circulating microRNA-122 using dynamic chemical labelling with single molecule detection overcomes stability and isomiR challenges for biomarker qualification. Analytical Chem. 2020. D1
• C. Peris-Torres, M.C. Plaza-Calonge, R. López-Domínguez, S. Domínguez-García, A. Barrientos-Durán, P. Carmona-Sáez and Juan Carlos Rodríguez-Manzaneque. Extracellular Protease ADAMTS1 Is Required at Early Stages of Human Uveal Melanoma Development by Inducing Stemness and Endothelial-Like Features on Tumor Cells. Cancers, 2020. Q1
• L. Lopez-Caraballo, J. Martorell-Marugan, P. Carmona-Saez, E. Gonzalez-Muñoz. iPS-Derived Early Oligodendrocyte Progenitor Cells from SPMS Patients Reveal Deficient In Vitro Cell Migration Stimulation. Cells, 2020. Q1
• L. Lopez-Caraballo, J. Martorell-Marugan, P. Carmona-Saez, E. Gonzalez-Muñoz. Analysis of menstrual blood stromal cells reveals SOX15 triggers oocyte-based human cell reprogramming. iScience, 2020. Q1
• AB Carrillo‐Gálvez, S. Gálvez‐Peisl, JE González‐Correa, M. de Haro‐Carrillo, V. Ayllón, P. Carmona‐Sáez, V. Ramos‐Mejía, P. Galindo‐Moreno, F. E. Cara, S. Granados‐Principal, P. Muñoz, F. Martin, P. Anderson. GARP is a key molecule for mesenchymal stromal cell reponses to TGF-β and fundamental to control mitochondrial ROS levels. Stem Cells Transl Med. 10.1002, 2020. Q1
• A. Gallardo, A. Molina, H.G. Asenjo, J. Martorell-Marugán, R. Montes, V. Ramos-Mejia, A. Sanchez-Pozo, P. Carmona-Sáez, L. Lopez-Onieva, D. Landeira The molecular clock protein Bmal1 regulates cell differentiation in mouse embryonic stem cells. Life Scie. Alliance 3, 2020. Q1
• A. García-Moreno, P. Carmona-Sáez. Computational Methods and Software Tools for Functional Analysis of miRNA Data. Biomolecules. 2020. Q2

2019

• Martorell-Marugán J, González-Rumayor V, Carmona-Saez P. mCSEA: detecting subtle differentially methylated regions. Bioinformatics. 2019. D1
• Toro-Domínguez D, Martorell-Marugán J, López-Dominguez R, García-Moreno A, González-Rumayor V, Alarcón-Riquelme ME, Carmona-Saez P. ImaGEO: Integrative Gene Expression Meta-Analysis from GEO database. Bioinformatics. 2019. D1
• D. Toro-Domínguez, R. Domínguez-Lopez, A. García Moreno, J.A. Villatoro-García, J. Martorell-Marugán, D. Goldman, M. Petri, D. Wojdyla, B.A. Pons-Estel, D. Isenberg, G. Morales-Montes de Oca, M.I.Trejo-Zambrano, B. García González, D. Gómez-Martín, J. Romero-Díaz, P. Carmona-Sáez ** and M. E. Alarcón-Riquelme ** Differential Treatments and Risk for Severe Nephritis Based on a Longitudinal Systemic Lupus Erythematosus Stratification. Scientific Rep. 2019. Q1
• A. Rodríguez-Martínez, D. de Miguel-Pérez, F. Gabriel Ortega, JL García-Puche, I. Robles-Fernández, J. Exposito, J. Martorell-Marugan, P. Carmona-Sáez, MC Garrido-Navas, C. Rolfo, H. Ilyine, JA Lorente, M Legueren and MJ Serrano. Exosomal miRNA profile as complementary tool in the diagnostic and prediction of treatment response in localized breast cancer under neoadjuvant chemotherapy. Breast Cancer Research, 2019. Q1
• B. Ramos-Molina, L. Sánchez-Alcoholado, A. Cabrera-Mulero, R. López-Domínguez, P. Carmona-Sáez, E. García-Fuentes, I. Moreno-Indias, FJ Tinahones. Gut Microbiota Composition is Associated with the Global DNA Methylation Pattern in Obesity. Frontiers in Genetics 2019. Q2
• F. Requena, HG. Asenjo, G. Barturen, J. Martorell-Marugán, P. Carmona-Sáez, D. Landeira. NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule. Scientific Rep. 2019. Q1
• J. Martorell-Marugán, S. Tabik, Y. Benhammou, C. del Val, I. Zwir, F. Herrera, P. Carmona-Sáez. Deep Learning in Omics Data Analysis and Precision Medicine. Chapter in Computational Biology. Codon Publications; 2019 Nov 21.
• D. Toro-Dominguez, M.E. Alarcon-Riquelme, P. Carmona-Saez. Drug Repurposing from Transcriptome Data: Methods and Applications. Chapter in In Silico Drug Design. Repurposing Techniques and Methodologies. DOI: B978-0-12-816125-8.00011-0

2018

• 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 Rheumatol. 2018. D1
• Alvarez-Cubero MJ, Santiago O, Martínez-Labarga C, Martínez-García B, Marrero-Díaz R, Rubio-Roldan A, Pérez-Gutiérrez AM, Carmona-Saez P, Lorente JA, Martinez-Gonzalez LJ. Methodology for Y Chromosome Capture: A complete genome sequence of Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads. Scientific Rep. 2018. Q1

2017

• 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. D1
• Martorell-Marugan J, Toro-Dominguez D, Alarcon-Riquelme ME, Carmona-Saez P. MetaGenyo: a web tool for meta-analysis of genetic association studies. BMC Bioinformatics. 2017. Q1
• Toro-Domínguez D, Carmona-Sáez P**, Alarcón-Riquelme ME**. Support for phosphoinositol 3 kinase and mTOR inhibitors as treatment for lupus using in-silico drug-repurposing analysis.Arthritis Res Ther. 2017. Q1
• Herrera-Merchan A, Cuadros M, Rodriguez MI, Rodriguez S, Torres R,Estecio M, Coira IF, Loidi C, Saiz M, Carmona-Saez P, et al. The value of lncRNA FENDRR and FOXF1 as a prognostic factor for survival of lung adenocarcinoma. Oncotarget. 2017. Q1

Previous Years

• Díaz-Villamarín X, Dávila-Fajardo CL, Martínez-González LJ, Carmona-Sáez P, Sánchez-Ramos J, Álvarez Cubero MJ, Salmerón-Febres LM, Cabeza Barrera J, Fernández-Quesada F. Genetic polymorphisms influence on the response to clopidogrel in peripheral artery disease patients following percutaneous transluminal angioplasty. Pharmacogenomics. 2016. Q3 PMID: 27464309
• Melero JT, Ortega FG, Gonzalez AM, Carmona-Saez P, Garcia Puche JL, Sugarbaker PH, Delgado M, Lorente JA, Serrano MJ. Prognostic factor analysis of circulating tumor cells in peripheral blood of patients with peritoneal carcinomatosis of colon cancer origin treated with cytoreductive surgery plus an intraoperative hyperthermic intraperitoneal chemotherapy procedure (CRS + HIPEC). Surgery 2016 .D1. PMID: 26518392
• Alvarez-Cubero MJ, Martinez-Gonzalez LJ, Saiz M, Carmona-Saez P, Alvarez JC, Pascual-Geler M, Lorente JA, Cozar JM. Prognostic role of genetic biomarkers in clinical progression of prostate cancer.Exp Mol Med. 2015. Q1 PMID: 26251261
• Gómez Peña C, Dávila-Fajardo CL, Martínez-González LJ, Carmona-Sáez P, Soto Pino MJ, Sánchez Ramos J, Moreno Escobar E, Blancas I, Fernández JJ, Fernández D, Correa C, Cabeza Barrera J. Influence of the HER2 Ile655Val polymorphism on trastuzumab-induced cardiotoxicity in HER2-positive breast cancer patients: a meta-analysis. Pharmacogenet Genomics. 2015. Q2 PMID: 26049584
• Toro-Domínguez D, Carmona-Sáez P**, Alarcón-Riquelme ME**. Shared signatures between rheumatoid arthritis, systemic lupus erythematosus and Sjögren’s syndrome uncovered through gene expression meta-analysis. Arthritis Res Ther. 2014. Q2 PMID: 25466291
• Anton MA, Gorostiaga D, Guruceaga E, Segura V, Carmona-Saez P, Pascual-Montano A, Pio R, Montuenga LM, Rubio A.SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays.Book Chapter. Bioinformatics: The Impact of Accurate Quantification on Proteomic and Genetic Analysis and Research. ISBN 9781771880190
• C. Borgelt, X. Yang, R. Nogales-Cadenas, P. Carmona-Saez, A. Pascual-Montano. Finding closed frequent item sets by intersecting transactions. 2011. Proceedings of the 14th International Conference on Extending Database Technology, 367-37. DOI: 10.1145/1951365.1951410
• Vazquez M, Nogales-Cadenas R, Arroyo J, Botías P, García R, Carazo JM, Tirado F, Pascual-Montano A, Carmona-Saez P. MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. Nucleic Acids Res. 2010. D1 PMID: 20513648
• Kökény S, Papp J, Weber G, Vaszkó T, Carmona-Saez P, Oláh E. Ribavirin acts via multiple pathways in inhibition of leukemic cell proliferation. Anticancer Res. 2009. Q4 PMID: 19528454
• Nogales-Cadenas R*, Carmona-Saez P*, Vazquez M, Vicente C, Yang X, Tirado F, Carazo JM, Pascual-Montano A. GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. Nucleic Acids Res. 2009. D1 PMID: 19465387
• M. Vázquez, R. Nogales, P. Carmona-Saez, A. Pascual, J. Pavón. Rbbt: a framework for fast bioinformatics development with ruby. Book Chapter: Advances in Bioinformatics, Springer. 2010, 201-208. DOI: https://doi.org/10.1007/978-3-642-13214-8_26
• Vazquez M, Carmona-Saez P, Nogales-Cadenas R, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A. SENT: semantic features in text. Nucleic Acids Res. 2009. D1 PMID: 19458159
• Recuero M, Vicente MC, Martínez-García A, Ramos MC, Carmona-Saez P, Sastre I, Aldudo J, Vilella E, Frank A, Bullido MJ, Valdivieso F. A free radical-generating system induces the cholesterol biosynthesis pathway: a role in Alzheimer’s disease. Aging Cell. 2009. D1 PMID: 19239419
• Mejía-Roa E, Carmona-Saez P, Nogales R, Vicente C, Vázquez M, Yang XY, García C, Tirado F, Pascual-Montano A. bioNMF: a web-based tool for nonnegative matrix factorization in biology. Nucleic Acids Res. 2008. Q1 PMID: 18515346
• Abascal F, Carmona-Saez P, Carazo JM, Pascual-Montano A.ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data. Bioinformatics. 2008. D1 PMID: 18339638
• Anton MA, Gorostiaga D, Guruceaga E, Segura V, Carmona-Saez P, Pascual-Montano A, Pio R, Montuenga LM, Rubio A.SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays. Genome Biol. 2008. D1 PMID: 18312629
• 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 Biol. 2007. D1 PMID: 17204154
• Pascual-Montano A, Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Marqui RD. bioNMF: a versatile tool for non-negative matrix factorization in biology. BMC Bioinformatics. 2006. Q1 PMID: 16875499
• Chagoyen M, Carmona-Saez P, Gil C, Carazo JM, Pascual-Montano A. A literature-based similarity metric for biological processes. BMC Bioinformatics. 2006 . Q1 PMID: 16872502
• Hernández-Vargas H, Ballestar E, Carmona-Saez P, von Kobbe C, Bañón-Rodríguez I, Esteller M, Moreno-Bueno G, Palacios J. Transcriptional profiling of MCF7 breast cancer cells in response to 5-Fluorouracil: relationship with cell cycle changes and apoptosis, and identification of novel targets of p53.Int J Cancer. 2006. Q1 PMID: 16557594
• 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 Q1 PMID: 16503973
• Carmona-Saez P, Chagoyen M, Rodriguez A, Trelles O, Carazo JM, Pascual-Montano A.Integrated analysis of gene expression by Association Rules Discovery. BMC Bioinformatics. 2006 Feb 7;7:54. Q1 PMID: 16464256
• Chagoyen M, Carmona-Saez P, Shatkay H, Carazo JM, Pascual-Montano A. Discovering semantic features in the literature: a foundation for building functional associations. BMC Bioinformatics. 2006. Q1 PMID: 16438716
• A. Fazel Famili, Z. Liu, P. Carmona-Saez, A. Mullick. Knowledge Discovery in the Identification of Differentially Expressed Genes in Tumoricidal Macrophage. Lecture Notes in Computer Science, 2005. Q4 DOI: https://doi.org/10.1007/11552253_8