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D
Dopazo J. Functional profiling methods in cancer. In: Grützmann R, Pilarsky C, eds. Methods in molecular biology (Clifton, N.J.).Vol 576. Methods in molecular biology (Clifton, N.J.).; 2010:363-74.
Dopazo J, Mendoza A, Herrero J, et al. Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate. Microb Drug Resist. 2001;7:99-125. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11442348.
Durban J, Juárez P, Angulo Y, et al. Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing. BMC genomics. 2011;12:259.
E
Eduati F, Mangravite LM, Wang T, et al. Prediction of human population responses to toxic compounds by a collaborative competition. Nature biotechnology. 2015. doi:10.1038/nbt.3299.
Elena SF, Dopazo J, de la Pena M, Flores R, Diener TO, Moya A. Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment. J Mol Evol. 2001;53:155-9. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11479686.
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.
Espadaler J, Eswar N, Querol E, et al. Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics. 2008;9:249. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18505562.
Espadaler J, Aragues R, Eswar N, et al. Detecting remotely related proteins by their interactions and sequence similarity. Proc Natl Acad Sci U S A. 2005;102:7151-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15883372.
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.
Esteban-Medina M, Roque VManuel de, Herráiz-Gil S, Peña-Chilet M, Dopazo J, Loucera C. drexml: A command line tool and Python package for drug repurposing. Comput Struct Biotechnol J. 2024;23:1129-1143. doi:10.1016/j.csbj.2024.02.027.
Esteban-Medina M, Loucera C, Rian K, et al. The mechanistic functional landscape of retinitis pigmentosa: a machine learning-driven approach to therapeutic target discovery. J Transl Med. 2024;22(1):139. doi:10.1186/s12967-024-04911-7.
Eswar N, John B, Mirkovic N, et al. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res. 2003;31:3375-80. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824331.
Eswar N, Webb B, Marti-Renom MA, et al. Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics. 2006;Chapter 5:Unit 5 6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18428767.
Ewing AD, Houlahan KE, Hu Y, et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. participants ICGC-TCGADREAMSoma, Xi L, Dewal N, et al., eds. Nature methods. 2015. doi:10.1038/nmeth.3407.
Eyrich VA, Marti-Renom MA, Przybylski D, et al. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics. 2001;17:1242-3. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11751240.
F
Falco MM, Bleda M, Carbonell-Caballero J, Dopazo J. The pan-cancer pathological regulatory landscape. Scientific reports. 2016;6:39709. doi:10.1038/srep39709.
Falco MM, Bleda M, Carbonell-Caballero J, Dopazo J. The pan-cancer pathological regulatory landscape. Scientific Reports. 2016;6(1). doi:10.1038/srep39709.
Falco MM, Peña-Chilet M, Loucera C, Hidalgo MR, Dopazo J. Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscapeAbstract. NAR Cancer. 2020;2(2). doi:10.1093/narcan/zcaa011.
Fernández RM, Bleda M, Luzón-Toro B, et al. Pathways systematically associated to Hirschsprung's disease. Orphanet J Rare Dis. 2013;8:187. doi:10.1186/1750-1172-8-187.
Fernandez P, Soria M, Blesa D, et al. Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray. PloS one. 2012;7:e45899. doi:10.1371/journal.pone.0045899.
Fernández RM, Bleda M, Luzón-Toro B, et al. Pathways systematically associated to Hirschsprung’s disease. Orphanet journal of rare diseases. 2013;8:187. doi:10.1186/1750-1172-8-187.
Fernández RMa, Bleda M, Núñez-Torres R, et al. Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung's disease. Orphanet J Rare Dis. 2012;7:103. doi:10.1186/1750-1172-7-103.
Fernández RMa, Bleda M, Núñez-Torres R, et al. Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung’s disease. Orphanet journal of rare diseases. 2012;7:103. doi:10.1186/1750-1172-7-103.
Fernández-Palacios P, Galán-Sánchez F, Casimiro-Soriguer CS, et al. Genotypic characterization and antimicrobial susceptibility of human isolates in Southern Spain. Microbiol Spectr. 2024;12(10):e0102824. doi:10.1128/spectrum.01028-24.
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.