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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.
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.
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. 2009;155:813-24. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19246752.
Nueda MJosé, Sebastián P, Tarazona S, et al. Functional assessment of time course microarray data. BMC Bioinformatics. 2009;10 Suppl 6:S9. doi:10.1186/1471-2105-10-S6-S9.
Nueda MJ, Conesa A, Westerhuis JA, et al. Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA. Bioinformatics. 2007;23:1792-800. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17519250.
Nueda MJosé, Carbonell J, Medina I, Dopazo J, Conesa A. Serial Expression Analysis: a web tool for the analysis of serial gene expression data. Nucleic Acids Res. 2010;38(Web Server issue):W239-45. doi:10.1093/nar/gkq488.
Nueda MJ, Ferrer A, Conesa A. ARSyN: a method for the identification and removal of systematic noise in multifactorial time course microarray experiments. Biostatistics (Oxford, England). 2011.
Nunez JI, Martin MJ, Piccone ME, et al. Identification of optimal regions for phylogenetic studies on VP1 gene of foot-and-mouth disease virus: analysis of types A and O Argentinean viruses. Vet Res. 2001;32:31-45. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11254175.
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.
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Olanda R, Pérez M, Orduña JM, Tárraga J, Dopazo J. A new parallel pipeline for DNA methylation analysis of long reads datasets. BMC bioinformatics. 2017;18:161. doi:10.1186/s12859-017-1574-3.
Olivares-González L, Velasco S, Gallego I, et al. An SPM-Enriched Marine Oil Supplement Shifted Microglia Polarization toward M2, Ameliorating Retinal Degeneration in Mice. Antioxidants (Basel). 2022;12(1). doi:10.3390/antiox12010098.
Oppert B, Dowd SE, Bouffard P, et al. Transcriptome profiling of the intoxication response of Tenebrio molitor larvae to Bacillus thuringiensis Cry3Aa protoxin. PloS one. 2012;7:e34624. doi:10.1371/journal.pone.0034624.
Orti L, Carbajo RJ, Pieper U, et al. A kernel for open source drug discovery in tropical diseases. PLoS Negl Trop Dis. 2009;3:e418. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19381286.
Orti L, Carbajo RJ, Pieper U, et al. A kernel for the Tropical Disease Initiative. Nat Biotechnol. 2009;27:320-1. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19352362.
Ortiz-Aljaro P, Montes-Cano MAntonio, García-Lozano J-R, et al. Protein and functional isoform levels and genetic variants of the BAFF and APRIL pathway components in systemic lupus erythematosus. Sci Rep. 2022;12(1):11219. doi:10.1038/s41598-022-15549-0.
Ortuno FM, Loucera C, Casimiro-Soriguer CS, et al. Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences. Gigascience. 2021;10(12). doi:10.1093/gigascience/giab078.
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.
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Palacios J, Honrado E, Osorio A, et al. Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers. Breast Cancer Res Treat. 2005;90:5-14. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15770521.
Palomero L, Galván-Femenía I, de Cid R, et al. Immune Cell Associations with Cancer Risk. iScience. 2020;23(7):101296. doi:10.1016/j.isci.2020.101296.
Panjkovich A, Melo F, Marti-Renom MA. Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs. Genome Biol. 2008;9:R68. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18397517.
Pellegrinelli V, Figueroa-Juárez E, Samuelson I, et al. Defective extracellular matrix remodeling in brown adipose tissue is associated with fibro-inflammation and reduced diet-induced thermogenesis. Cell Rep. 2023;42(6):112640. doi:10.1016/j.celrep.2023.112640.
Peña A, Teeling H, Huerta-Cepas J, et al. Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. The ISME journal. 2010.
Peña-Chilet M, Esteban-Medina M, Falco MM, et al. Using mechanistic models for the clinical interpretation of complex genomic variation. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-55454-7.
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.