Publications

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Journal Article
Dopazo J, Al-Shahrour F. Expression and microarrays. Methods Mol Biol. 2008;453:245-55. doi:10.1007/978-1-60327-429-6_12.
Bonifaci N, Górski B, Masojć B, et al. Exploring the link between germline and somatic genetic alterations in breast carcinogenesis. PLoS One. 2010;5(11):e14078. doi:10.1371/journal.pone.0014078.
Esteban-Medina M, Peña-Chilet M, Loucera C, Dopazo J. Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models. BMC Bioinformatics. 2019;20(1):370. doi:10.1186/s12859-019-2969-0.
Nobre LS, Al-Shahrour F, Dopazo J, Saraiva LM. Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli. Microbiology (Reading). 2009;155(Pt 3):813-824. doi:10.1099/mic.0.023911-0.
del Pozo MGonzález-, Méndez-Vidal C, Bravo-Gil N, et al. Exome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies. PLoS One. 2014;9(12):e116176. doi:10.1371/journal.pone.0116176.
Luzón-Toro B, Gui H, Ruiz-Ferrer M, et al. Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease. Scientific Reports. 2015;5(1). doi:10.1038/srep16473.
Tort F, García-Silva MTeresa, Ferrer-Cortès X, et al. Exome sequencing identifies a new mutation in SERAC1 in a patient with 3-methylglutaconic aciduria. Mol Genet Metab. 2013;110(1-2):73-7. doi:10.1016/j.ymgme.2013.04.021.
De Baets G, Reumers J, Blanco JDelgado, Dopazo J, Schymkowitz J, Rousseau F. An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins. PLoS computational biology. 2011;7:e1002090. doi:10.1371/journal.pcbi.1002090.
Loucera C, Carmona R, Bostelmann G, et al. Evidence of the association between increased use of direct oral anticoagulants and a reduction in the rate of atrial fibrillation-related stroke and major bleeding at the population level (2012-2019). Med Clin (Barc). 2023. doi:10.1016/j.medcli.2023.10.008.
Hernández P, Huerta-Cepas J, Montaner D, et al. Evidence for systems-level molecular mechanisms of tumorigenesis. BMC Genomics. 2007;8:185. doi:10.1186/1471-2164-8-185.
Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Brief Bioinform. 2011;12(5):442-8. doi:10.1093/bib/bbr022.
Chaves-Blanco L, de Salazar A, Fuentes A, et al. Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice. Epidemiol Infect. 2023;151:e201. doi:10.1017/S095026882300184X.
Huerta-Cepas J, Dopazo J, Gabaldón T. ETE: a python Environment for Tree Exploration. BMC Bioinformatics. 2010;11:24. doi:10.1186/1471-2105-11-24.
Puerto-Camacho P, Diaz-Martin J, Olmedo-Pelayo J, et al. Endoglin and MMP14 Contribute to Ewing Sarcoma Spreading by Modulation of Cell-Matrix Interactions. Int J Mol Sci. 2022;23(15). doi:10.3390/ijms23158657.
Salgado D, Armean IM, Baudis M, et al. The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Res. 2020;9. doi:10.12688/f1000research.24887.1.
Ferreira PG, Muñoz-Aguirre M, Reverter F, et al. The effects of death and post-mortem cold ischemia on human tissue transcriptomes. Nat Commun. 2018;9(1):490. doi:10.1038/s41467-017-02772-x.
Łabaj PP, Dopazo J, Xiao W, Kreil DP. Editorial: Critical assessment of massive data analysis (CAMDA) annual conference 2021. Front Genet. 2023;14:1154398. doi:10.3389/fgene.2023.1154398.
González-Pérez S, Gutiérrez J, Garcia-Garcia F, et al. Early transcriptional defense responses in Arabidopsis cell suspension culture under high-light conditions. Plant Physiol. 2011;156(3):1439-56. doi:10.1104/pp.111.177766.
Vivas Y, Martinez-Garcia C, Izquierdo A, et al. Early peroxisome proliferator-activated receptor gamma regulated genes involved in expansion of pancreatic beta cell mass. BMC Med Genomics. 2011;4:86. doi:10.1186/1755-8794-4-86.
Prieto J, León M, Ponsoda X, et al. Dysfunctional mitochondrial fission impairs cell reprogramming. Cell Cycle. 2016;15(23):3240-3250. doi:10.1080/15384101.2016.1241930.
Niarakis A, Ostaszewski M, Mazein A, et al. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Front Immunol. 2024;14:1282859. doi:10.3389/fimmu.2023.1282859.
Loucera C, Esteban-Medina M, Rian K, Falco MM, Dopazo J, Peña-Chilet M. Drug repurposing for COVID-19 using machine learning and mechanistic models of signal transduction circuits related to SARS-CoV-2 infection. Signal Transduct Target Ther. 2020;5(1):290. doi:10.1038/s41392-020-00417-y.
Bediaga NG, Acha-Sagredo A, Guerra I, et al. DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Res. 2010;12(5):R77. doi:10.1186/bcr2721.
Moura DS, Peña-Chilet M, Varela JAntonio Co, et al. A DNA damage repair gene-associated signature predicts responses of patients with advanced soft-tissue sarcoma to treatment with trabectedin. Mol Oncol. 2021;15(12):3691-3705. doi:10.1002/1878-0261.12996.
Sundaram AYM, Kiron V, Dopazo J, Fernandes JMO. Diversification of the expanded teleost-specific toll-like receptor family in Atlantic cod, Gadus morhua. BMC Evol Biol. 2012;12:256. doi:10.1186/1471-2148-12-256.