Publications

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Journal Article
del Pozo MGonzález-, Méndez-Vidal C, Santoyo-López J, et al. Deciphering intrafamilial phenotypic variability by exome sequencing in a Bardet-Biedl family. Mol Genet Genomic Med. 2014;2(2):124-33. doi:10.1002/mgg3.50.
del Pozo MGonzález-, Méndez-Vidal C, Santoyo-López J, et al. Deciphering intrafamilial phenotypic variability by exome sequencing in a Bardet–Biedl family. Molecular Genetics & Genomic Medicine. 2014;2:124-133. doi:10.1002/mgg3.50.
Carbonell-Caballero J, López-Quílez A, Conesa D, Dopazo J. Deciphering Genomic Heterogeneity and the Internal Composition of Tumour Activities through a Hierarchical Factorisation Model. Mathematics. 2021;9(21):2833. doi:10.3390/math9212833.
Martinez-Delgado B, Lopez-Martin E, Lara-Herguedas J, et al. De novo small deletion affecting transcription start site of short isoform of AUTS2 gene in a patient with syndromic neurodevelopmental defects. Am J Med Genet A. 2021;185(3):877-883. doi:10.1002/ajmg.a.62017.
Marti-Renom MA, Pieper U, Madhusudhan MS, et al. DBAli tools: mining the protein structure space. Nucleic Acids Res. 2007;35:W393-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17478513.
Marti-Renom MA, Pieper U, Madhusudhan MS, et al. DBAli tools: mining the protein structure space. Nucleic Acids Res. 2007;35(Web Server issue):W393-7. doi:10.1093/nar/gkm236.
Marti-Renom MA, Ilyin VA, Sali A. DBAli: a database of protein structure alignments. Bioinformatics. 2001;17:746-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11524379.
McMahon SA, Miller JL, Lawton JA, et al. The C-type lectin fold as an evolutionary solution for massive sequence variation. Nat Struct Mol Biol. 2005;12:886-92. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16170324.
Conesa A, Weelink G, van den Hondel CA, Punt PJ. C-terminal propeptide of the Caldariomyces fumago chloroperoxidase: an intramolecular chaperone?. FEBS Lett. 2001;503:117-20. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11513866.
Peña-Chilet M, Roldán G, Perez-Florido J, et al. CSVS, a crowdsourcing database of the Spanish population genetic variability. Nucleic Acids Res. 2021;49(D1):D1130-D1137. doi:10.1093/nar/gkaa794.
López-López D, Roldán G, Fernandez-Rueda JL, et al. A crowdsourcing database for the copy-number variation of the Spanish population. Hum Genomics. 2023;17(1):20. doi:10.1186/s40246-023-00466-8.
Fourati S, Talla A, Mahmoudian M, et al. A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-06735-8.
Cubuk C, Loucera C, Peña-Chilet M, Dopazo J. Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer. Int J Mol Sci. 2023;24(8). doi:10.3390/ijms24087450.
Ostaszewski M, Mazein A, Gillespie ME, et al. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Sci Data. 2020;7(1):136. doi:10.1038/s41597-020-0477-8.
Ostaszewski M, Niarakis A, Mazein A, et al. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021;17(10):e10387. doi:10.15252/msb.202110387.
Horcajadas JA, Minguez P, Dopazo J, et al. Controlled ovarian stimulation induces a functional genomic delay of the endometrium with potential clinical implications. J Clin Endocrinol Metab. 2008;93:4500-10. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18697870.
Martinez H, Tárraga J, Medina I, et al. Concurrent and Accurate Short Read Mapping on Multicore Processors. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM. 2015;12:995-1007. doi:10.1109/TCBB.2015.2392077.
Gabaldón T. Computational approaches for the prediction of protein function in the mitochondrion. Am J Physiol Cell Physiol. 2006;291:C1121-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16870830.
F Carmona J, Davalos V, Vidal E, et al. A Comprehensive DNA Methylation Profile of Epithelial-to-Mesenchymal Transition. Cancer research. 2014;74:5608–19. doi:10.1158/0008-5472.CAN-13-3659.
Martorell-Marugán J, López-Domínguez R, García-Moreno A, et al. A comprehensive database for integrated analysis of omics data in autoimmune diseases. BMC Bioinformatics. 2021;22(1):343. doi:10.1186/s12859-021-04268-4.
Su Z, Labaj PP, , et al. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature biotechnology. 2014;32:903–914. doi:10.1038/nbt.2957.
Núñez-Torres R, Pita G, Peña-Chilet M, et al. A Comprehensive Analysis of 21 Actionable Pharmacogenes in the Spanish Population: From Genetic Characterisation to Clinical Impact. Pharmaceutics. 2023;15(4). doi:10.3390/pharmaceutics15041286.
Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA. A composite score for predicting errors in protein structure models. Protein Sci. 2006;15:1653-66. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16751606.
Amadoz A, Hidalgo MR, Cubuk C, Carbonell-Caballero J, Dopazo J. A comparison of mechanistic signaling pathway activity analysis methods. Brief Bioinform. 2019;20(5):1655-1668. doi:10.1093/bib/bby040.
Martin MJ, Herrero J, Mateos A, Dopazo J. Comparing bacterial genomes through conservation profiles. Genome Res. 2003;13:991-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12695324.