Publications

Unidad de Bioinformática y Bioestadística

2020

  1. Plasmatic Membrane Expression of Adhesion Molecules in Human Cardiac Progenitor/Stem Cells Might Explain Their Superior Cell Engraftment after Cell Transplantation. I Ontoria-Oviedo , I Palacios, J Panadero, B Sánchez, F García-García, A López-Cerdán, A Dorronsoro, D Castellano, L Rodríguez-Borlado, A Bernad, and P Sepúlveda. Stem Cells International. 2020 Oct 10, https://doi.org/10.1155/2020/8872009.
  2. CSVS, a crowdsourcing database of the Spanish population genetic variability. Peña-Chilet M, Roldán G, Perez-Florido J, Ortuño FM, Carmona R, Aquino V, Lopez-Lopez D, Loucera C, Fernandez-Rueda JL, Gallego A, García-Garcia F, González-Neira A, Pita G, Núñez-Torres R, Santoyo-López J, Ayuso C, Minguez P, Avila-Fernandez A, Corton M, Moreno-Pelayo MÁ, Morin M, Gallego-Martinez A, Lopez-Escamez JA, Borrego S, Antiñolo G, Amigo J, Salgado-Garrido J, Pasalodos-Sanchez S, Morte B, Carracedo Á, Alonso Á, Dopazo J. Nucleic Acids Res. 2020 Sep 29;. doi: 10.1093/nar/gkaa794. PubMed PMID: 32990755.
  3. Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. Casanova Ferrer F, Pascual M, Hidalgo MR, Malmierca-Merlo P, Guerri C, García-García F. Genes (Basel). 2020 Sep 21;11(9). doi: 10.3390/genes11091106. PubMed PMID: 32967293.
  4. Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.  Yang M, Petralia F, Li Z, Li H, Ma W, Song X, Kim S, Lee H, Yu H, Lee B, Bae S, Heo E, Kaczmarczyk J, Stępniak P, Warchoł M, Yu T, Calinawan AP, Boutros PC, Payne SH, Reva B, Boja E, Rodriguez H, Stolovitzky G, Guan Y, Kang J, Wang P, Fenyö D, Saez-Rodriguez J. Cell Syst. 2020 Aug 26;11(2):186-195.e9. doi: 10.1016/j.cels.2020.06.013. PubMed PMID: 32710834.
  5.  Lack of TLR4 modifies the miRNAs profile and attenuates inflammatory signaling pathways. Ureña-Peralta JR, Pérez-Moraga R, García-García F, Guerri C. PLoS One. 2020;15(8):e0237066. doi: 10.1371/journal.pone.0237066. PubMed PMID: 32780740; PubMed Central PMCID: PMC7418977.
  6. Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis. Fass MI, Rivarola M, Ehrenbolger GF, Maringolo CA, Montecchia JF, Quiroz F, García-García F, Blázquez JD, Hopp HE, Heinz RA, Paniego NB, Lia VV. Sci Rep. 2020 Aug 7;10(1):13347. doi: 10.1038/s41598-020-70315-4. PubMed PMID: 32770047; PubMed Central PMCID: PMC7414910.
  7.  Sex is a strong prognostic factor in stage IV non-small-cell lung cancer patients and should be considered in survival rate estimation. Barquín M, Calvo V, García-García F, Nuñez B, Sánchez-Herrero E, Serna-Blasco R, Auglytė M, Carcereny E, Rodriguez-Abreu D, López Castro R, Guirado M, Camps C, Bosch-Barrera J, Massuti B, Ortega AL, Del Barco E, Gonzalez-Larriba JL, Aguiar D, García-Campelo R, Dómine M, Agraso S, Sala MA, Oramas J, Bernabé R, Blanco R, Parejo C, Cruz A, Menasalvas E, Royuela A, Romero A, Provencio M. Cancer Epidemiol. 2020 Aug;67:101737. doi: 10.1016/j.canep.2020.101737.  PubMed PMID: 32450544.
  8.  Uterine disorders affecting female fertility: what are the molecular functions altered in endometrium?. Devesa-Peiro A, Sebastian-Leon P, Garcia-Garcia F, Arnau V, Aleman A, Pellicer A, Diaz-Gimeno P. Fertil Steril. 2020 Jun;113(6):1261-1274. doi: 10.1016/j.fertnstert.2020.01.025. PubMed PMID: 32482256.
  9.  Rilpivirine attenuates liver fibrosis through selective STAT1-mediated apoptosis in hepatic stellate cells. Martí-Rodrigo A, Alegre F, Moragrega ÁB, García-García F, Martí-Rodrigo P, Fernández-Iglesias A, Gracia-Sancho J, Apostolova N, Esplugues JV, Blas-García A. Gut. 2020 May;69(5):920-932. doi: 10.1136/gutjnl-2019-318372. PubMed PMID: 31530714.
  10.  Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies. Bogliolo M, Pujol R, Aza-Carmona M, Muñoz-Subirana N, Rodriguez-Santiago B, Casado JA, Rio P, Bauser C, Reina-Castillón J, Lopez-Sanchez M, Gonzalez-Quereda L, Gallano P, Catalá A, Ruiz-Llobet A, Badell I, Diaz-Heredia C, Hladun R, Senent L, Argiles B, Bergua Burgues JM, Bañez F, Arrizabalaga B, López Almaraz R, Lopez M, Figuera Á, Molinés A, Pérez de Soto I, Hernando I, Muñoz JA, Del Rosario Marin M, Balmaña J, Stjepanovic N, Carrasco E, Cuesta I, Cosuelo JM, Regueiro A, Moraleda Jimenez J, Galera-Miñarro AM, Rosiñol L, Carrió A, Beléndez-Bieler C, Escudero Soto A, Cela E, de la Mata G, Fernández-Delgado R, Garcia-Pardos MC, Sáez-Villaverde R, Barragaño M, Portugal R, Lendinez F, Hernadez I, Vagace JM, Tapia M, Nieto J, Garcia M, Gonzalez M, Vicho C, Galvez E, Valiente A, Antelo ML, Ancliff P, Garcia F, Dopazo J, Sevilla J, Paprotka T, Pérez-Jurado LA, Bueren J, Surralles J. J Med Genet. 2020 Apr;57(4):258-268. doi: 10.1136/jmedgenet-2019-106249. PubMed PMID: 31586946.
  11.  Association of a single nucleotide polymorphism in the ubxn6 gene with long-term non-progression phenotype in HIV-positive individuals. Díez-Fuertes F, De La Torre-Tarazona HE, Calonge E, Pernas M, Bermejo M, García-Pérez J, Álvarez A, Capa L, García-García F, Saumoy M, Riera M, Boland-Auge A, López-Galíndez C, Lathrop M, Dopazo J, Sakuntabhai A, Alcamí J. Clin Microbiol Infect. 2020 Jan;26(1):107-114. doi: 10.1016/j.cmi.2019.05.015. PubMed PMID: 31158522.
  12. Transcriptomic Analysis Reveals a Differential Gene Expression Profile Between Two Sunflower Inbred Lines with Different Ability to Tolerate Water Stress. M Escalante, A Vigliocco, Sebastián Moschen, P Fernández, R Heinz, F Garcia-Garcia, J A Di Rienzo, A Andrade, S Alemano. Plant Mol Biol Rep 38, 222–237 (2020). https://doi.org/10.1007/s11105-020-01192-4.
  13. Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscape. MM Falco, M Peña-Chilet, C Loucera, MR Hidalgo, J Dopazo. NAR Cancer, Volume 2, Issue 2, June 2020, zcaa011, https://doi.org/10.1093/narcan/zcaa011.
  14. Medical imaging data structure extended to multiple modalities and anatomical regions. J. M. Saborit-Torres, J. J. Saenz-Gamboa, J. À. Montell, J. M. Salinas, J. A. Gómez, I. Stefan, M. Caparrós, F. García-García, J. Domenech, J. V. Manjón, G. Rojas, A. Pertusa, A. Bustos, G. González, J. Galant, M. de la Iglesia-Vayá. arXiv:2010.00434.
  15. BIMCV COVID-19+: a large annotated dataset of RX and CT images from COVID-19 patients. M de la Iglesia Vayá, JM Saborit, J Angel Montell, A Pertusa, A Bustos, M Cazorla, J Galant, X Barber, D Orozco-Beltrán, F García-García, M Caparrós, G González, JM Salinas. arXiv: 2006.01174.
  16. De-identifying Spanish medical texts – Named Entity Recognition applied to radiology reports. I Perez-Diez, R Perez-Moraga, A Lopez-Cerdan, M Caparros Redondo, JM Salinas-Serrano, M de la Iglesia-Vaya. medRxiv 2020.04.09.20058958; doi: https://doi.org/10.1101/2020.04.09.20058958.
  17. Mechanistic modeling of the SARS-CoV-2 disease map. K Rian, M Esteban-Medina, MR Hidalgo, C Çubuk, MM Falco, C Loucera, D Gunyel, M Ostaszewski, M Peña-Chilet, J Dopazo. bioRxiv 2020.04.12.025577; doi: https://doi.org/10.1101/2020.04.12.025577.
  18. Sex differences in the progression from NAFL to NASH: a functional meta-analysis of transcriptomic studies. JF Català-Senent, MR Hidalgo, M Berenguer, G Parthasarathy, H Malhi, P Malmierca-Merlo, M de la Iglesia-Vayá, F Garcia-Garcia. medRxiv 2020.06.03.20118570; doi: https://doi.org/10.1101/2020.06.03.20118570.
  19. Functional signatures in non-small-cell lung cancer: a systematic review and meta-analysis of sex-based differences in transcriptomic studies. I Pérez-Díez, MR Hidalgo, P Malmierca-Merlo, R Farràs, M de la Iglesia-Vayá, M Provencio, A Romero, F García-García. medRxiv 2020.08.24.20180026; doi: https://doi.org/10.1101/2020.08.24.20180026.

2019

  1.  Using mechanistic models for the clinical interpretation of complex genomic variation. Peña-Chilet M, Esteban-Medina M, Falco MM, Rian K, Hidalgo MR, Loucera C, Dopazo J. Sci Rep. 2019 Dec 12;9(1):18937. doi: 10.1038/s41598-019-55454-7. PubMed PMID: 31831811; PubMed Central PMCID: PMC6908734.
  2. Differences in gene expression profiling and biomarkers between histological colorectal carcinoma subsets from the serrated pathway. García-Solano J, Turpin-Sevilla MDC, García-García F, Carbonell-Muñoz R, Torres-Moreno D, Conesa A, Conesa-Zamora P. Histopathology. 2019 Oct;75(4):496-507. doi: 10.1111/his.13889. PubMed PMID: 31025430.
  3.  A comparison of mechanistic signaling pathway activity analysis methods. Amadoz A, Hidalgo MR, Çubuk C, Carbonell-Caballero J, Dopazo J. Brief Bioinform. 2019 Sep 27;20(5):1655-1668. doi: 10.1093/bib/bby040. Review. PubMed PMID: 29868818; PubMed Central PMCID: PMC6917216.
  4.  Fibroblast activation and abnormal extracellular matrix remodelling as common hallmarks in three cancer-prone genodermatoses. Chacón-Solano E, León C, Díaz F, García-García F, García M, Escámez MJ, Guerrero-Aspizua S, Conti CJ, Mencía Á, Martínez-Santamaría L, Llames S, Pévida M, Carbonell-Caballero J, Puig-Butillé JA, Maseda R, Puig S, de Lucas R, Baselga E, Larcher F, Dopazo J, Del Río M. Br J Dermatol. 2019 Sep;181(3):512-522. doi: 10.1111/bjd.17698. PubMed PMID: 30693469; PubMed Central PMCID: PMC6850467.
  5. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Nat Commun. 2019 Jun 17;10(1):2674. doi: 10.1038/s41467-019-09799-2. PubMed PMID: 31209238; PubMed Central PMCID: PMC6572829.
  6. Characterization of molecular mechanisms underlying the axonal Charcot-Marie-Tooth neuropathy caused by MORC2 mutations.  Sancho P, Bartesaghi L, Miossec O, García-García F, Ramírez-Jiménez L, Siddell A, Åkesson E, Hedlund E, Laššuthová P, Pascual-Pascual SI, Sevilla T, Kennerson M, Lupo V, Chrast R, Espinós C. Hum Mol Genet. 2019 May 15;28(10):1629-1644. doi: 10.1093/hmg/ddz006. PubMed PMID: 30624633.
  7.  Differential expression of circulating miRNAs as a novel tool to assess BAG3-associated familial dilated cardiomyopathy. Zaragoza C, Saura M, Hernández I, Ramirez-Carracedo R, García-García F, Zamorano JL, Mangas A, Toro R. Biosci Rep. 2019 Mar 29;39(3). doi: 10.1042/BSR20180934. Print 2019 Mar 29. PubMed PMID: 30792263; PubMed Central PMCID: PMC6418398.
  8. Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models. Çubuk C, Hidalgo MR, Amadoz A, Rian K, Salavert F, Pujana MA, Mateo F, Herranz C, Carbonell-Caballero J, Dopazo J. NPJ Syst Biol Appl. 2019;5:7. doi: 10.1038/s41540-019-0087-2. PubMed PMID: 30854222; PubMed Central PMCID: PMC6397295.

2018

  1.  Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape. Cubuk C, Hidalgo MR, Amadoz A, Pujana MA, Mateo F, Herranz C, Carbonell-Caballero J, Dopazo J. Cancer Res. 2018 Nov 1;78(21):6059-6072. doi: 10.1158/0008-5472.CAN-17-2705. PubMed PMID: 30135189.
  2. Deep sequencing and miRNA profiles in alcohol-induced neuroinflammation and the TLR4 response in mice cerebral cortex. Ureña-Peralta JR, Alfonso-Loeches S, Cuesta-Diaz CM, García-García F, Guerri C. Sci Rep. 2018 Oct 29;8(1):15913. doi: 10.1038/s41598-018-34277-y. PubMed PMID: 30374194; PubMed Central PMCID: PMC6206094.
  3.  Extracellular Vesicles Secreted by Hypoxic AC10 Cardiomyocytes Modulate Fibroblast Cell Motility. Ontoria-Oviedo I, Dorronsoro A, Sánchez R, Ciria M, Gómez-Ferrer M, Buigues M, Grueso E, Tejedor S, García-García F, González-King H, Garcia NA, Peiró-Molina E, Sepúlveda P. Front Cardiovasc Med. 2018;5:152. doi: 10.3389/fcvm.2018.00152. PubMed PMID: 30410918; PubMed Central PMCID: PMC6209632.
  4. A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection.  Fourati S, Talla A, Mahmoudian M, Burkhart JG, Klén R, Henao R, Yu T, Aydın Z, Yeung KY, Ahsen ME, Almugbel R, Jahandideh S, Liang X, Nordling TEM, Shiga M, Stanescu A, Vogel R, Pandey G, Chiu C, McClain MT, Woods CW, Ginsburg GS, Elo LL, Tsalik EL, Mangravite LM, Sieberts SK. Nat Commun. 2018 Oct 24;9(1):4418. doi: 10.1038/s41467-018-06735-8. PubMed PMID: 30356117; PubMed Central PMCID: PMC6200745.
  5.  Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome. Hidalgo MR, Amadoz A, Çubuk C, Carbonell-Caballero J, Dopazo J. Biol Direct. 2018 Aug 22;13(1):16. doi: 10.1186/s13062-018-0219-4. PubMed PMID: 30134948; PubMed Central PMCID: PMC6106876.
  6.  The effects of death and post-mortem cold ischemia on human tissue transcriptomes. Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, Curado J, Aguet F, Oliveira C, Dopazo J, Sammeth M, Ardlie KG, Guigó R. Nat Commun. 2018 Feb 13;9(1):490. doi: 10.1038/s41467-017-02772-x. PubMed PMID: 29440659; PubMed Central PMCID: PMC5811508.
  7.  Prognostic value of quantitative ctDNA levels in non small cell lung cancer patients. Provencio M, Torrente M, Calvo V, Pérez-Callejo D, Gutiérrez L, Franco F, Pérez-Barrios C, Barquín M, Royuela A, García-García F, Bueno C, Garcia-Grande A, Camps C, Massuti B, Sotomayor E, Romero A. Oncotarget. 2018 Jan 2;9(1):488-494. doi: 10.18632/oncotarget.22470. PubMed PMID: 29416630; PubMed Central PMCID: PMC5787483.

 All contributions in PubMed