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** Shared Corresponding authors

2021

  1. 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. Sci. Total Environ. 2021 IF 6.551, D1
  2. 2020

  3. 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. Bioinfor. 2020. IF 9.101, D1
  4. 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. IF: 13.116, D1
  5. 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. IF 6.350, D1
  6. 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: 5.610  D1
  7. 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. IF: 6.162, Q1
  8. 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. IF: 4.366, Q1
  9. 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. IF: 4.447, Q1
  10. 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. IF: 5.962, Q1
  11. 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 IF: 2.622, Q2
  12. A. García-Moreno,  P. Carmona-Sáez. Computational Methods and Software Tools for Functional Analysis of miRNA Data. Biomolecules. 2020. IF 4.082, Q2
  13. 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. medRxiv 2020.02.21.20021618; doi: https://doi.org/10.1101/2020.02.21.20021618
  14. 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. bioRxiv 2020  doi: https://doi.org/10.1101/2020.06.10.144972
  15. 2019

  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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, YJ. Loke, K. Hao, et al. Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth. bioRxiv 663567; doi: https://doi.org/10.1101/663567
  22. 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.
  23. 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
  24. 2018

  25. 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
  26. 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
  27. Nueda MJ, Martorell-Marugan J, Martí C, Tarazona S, Conesa A. Identification and visualization of differential isoform expression in RNA-seq time series. Bioinformatics. 2018, D1
  28. 2017

  29. 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 Dec 1;33(23):3691-3695, D1
  30. 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 16;18(1):563, Q1
  31. 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 Mar 11;19(1):54, Q1
  32. 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 11(13):1172-1185. Q1
  33. 2016

  34. 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, 17(12):1327-38. PMID: 27464309
  35. 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 Mar;159(3):728-35. PMID: 26518392
  36. 2015

  37. 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 Aug 7;47:e176. PMID: 26251261
  38. 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. PMID: 26049584
  39. 2014

  40. 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 3;16(6):489. PMID: 25466291
  41.  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
  42. Previous Years

  43. 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
  44. 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 Jul;38(Web Server issue):W228-32. PMID: 20513648
  45. 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 Jun;29(6):1971-80. PMID: 19528454
  46. 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 Jul;37(Web Server issue):W317-22. PMID: 19465387
  47. 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
  48. 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 (Web Server issue):W153-9. PMID: 19458159
  49. 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 Apr;8(2):128-39. PMID: 19239419
  50. 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 Jul 1;36(Web Server issue):W523-8. PMID: 18515346
  51. 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 May 1;24(9):1208-9. PMID: 18339638
  52. 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;9(2):R46. PMID: 18312629
  53. 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;8(1):R3. PMID: 17204154
  54. 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 Jul 28;7:366. PMID: 16875499
  55. Chagoyen M, Carmona-Saez P, Gil C, Carazo JM, Pascual-Montano A. A literature-based similarity metric for biological processes. BMC Bioinformatics. 2006 Jul 26;7:363. PMID: 16872502
  56. 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 Sep 1;119(5):1164-75. PMID: 16557594
  57. 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 Feb 17;7:78. PMID: 16503973
  58. 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. PMID: 16464256
  59. 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 Jan 26;7:41. PMID: 16438716
  60. 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,  volume 3646. 2005. DOI: https://doi.org/10.1007/11552253_8