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2019

  • 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. In Press
  • 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 Sci Rep. 2019. PMID: 31664045
  • 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 bioRxiv 777458, doi: https://doi.org/10.1101/777458
  • Martorell-Marugan J, Gonzalez-Rumayor V, Carmona-Saez P. mCSEA: Detecting subtle differentially methylated regions.
    Bioinformatics 2019. PMID: 30753302
  • 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. PMID: 30137226
  • 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 21:21. PMID: 30728048
  • 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. PMID: 31333715
  • 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
  • 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.
    Sci Rep. 2019. PMID: 31148571
  • D. Toro-Dominguez, M.E. Alarcon-Riquelme, P. Carmona-Saez. Drug Repurposing from Transcriptome Data: Methods and Applications.
    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;70: 2025–2035. PMID: 29938934
  • 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.
    Sci Rep. 2018;8: 9436. PMID: 29930304
  • Pazos F, Garcia-Moreno A, Oliveros JC. Automatic detection of genomic regions with informative epigenetic patterns.
    BMC Genomics. 2018 Nov 28;19(1):847. PMID: 30486775
  • 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 Feb 1;34(3):524-526. PMID: 28968682

2017

  • 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 Dec 16;18(1):563. PMID: 29246109
  • 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. PMID: 28961902
  • 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. PMID: 28284231

2016

  • 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 Aug;17(12):1327-38. 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 Mar;159(3):728-35. PMID: 26518392

 2015

  • 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
  • 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

2014

  • 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 Dec 3;16(6):489. 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

Previous Years

  • 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 Jul;38(Web Server issue):W228-32. 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 Jun;29(6):1971-80. 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 Jul;37(Web Server issue):W317-22. 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 Jul;37(Web Server issue):W153-9. 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 Apr;8(2):128-39. 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 Jul 1;36(Web Server issue):W523-8. 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 May 1;24(9):1208-9. 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;9(2):R46. doi: 10.1186/gb-2008-9-2-r46. Epub 2008 Feb 29. 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;8(1):R3. 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 Jul 28;7:366. 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 Jul 26;7:363. 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 Sep 1;119(5):1164-75. 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 Feb 17;7:78. 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. 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 Jan 26;7:41. 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,  volume 3646. 2005. DOI: https://doi.org/10.1007/11552253_8

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