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Gabaldón T, Rainey D, Huynen MA. Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I). J Mol Biol. 2005;348:857-70. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15843018.
Gabaldón T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA. Origin and evolution of the peroxisomal proteome. Biol Direct. 2006;1:8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16556314.
Gabaldón T, Huynen MA. Prediction of protein function and pathways in the genome era. Cell Mol Life Sci. 2004;61:930-44. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15095013.
Gabaldón T, Huynen MA. From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism. PLoS Comput Biol. 2007;3:e219. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17983265.
Gabaldón T, Huynen MA. Shaping the mitochondrial proteome. Biochim Biophys Acta. 2004;1659:212-20. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15576054.
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Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, Oliva B. ModLink+: Improving fold recognition by using protein-protein interactions. Bioinformatics. 2009. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19357100.
Forment J, Gadea J, Huerta L, et al. Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol. 2005;57:375-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15830128.
Fonseca RF, de Carvalho FM, Poletta FA, et al. Family-based genome-wide association study in Patagonia confirms the association of the DMD locus and cleft lip and palate. Eur J Oral Sci. 2015;123(5):381-384. doi:10.1111/eos.12212.
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.
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 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 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.
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.
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.
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.
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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.
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.
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.
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, 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.
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.
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.