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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.
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Dopazo H. La clasificación de los organismos. In: Invitación a la Biología. Invitación a la Biología. Buenos Aires: Curtis, Barnes, Schnek & Flores. 2da, Editorial Medica Panamericana; 2006.
Alloza E, Al-Shahrour F, Cigudosa JC, Dopazo J. A large scale survey reveals that chromosomal copy-number alterations significantly affect gene modules involved in cancer initiation and progression. BMC Medical Genomics. 2011;4:37. doi:10.1186/1755-8794-4-37.
Botton A, Galla G, Conesa A, Bachem C, Ramina A, Barcaccia G. Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology. BMC Genomics. 2008;9:347. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18652646.
Yung S, Ledran M, Moreno-Gimeno I, et al. Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells. Hum Mol Genet. 2011;20(24):4932-46. doi:10.1093/hmg/ddr431.
Gabaldón T, Huynen MA. Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. Bioinformatics. 2005;21 Suppl 2:ii144-50. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16204094.
Rossi A, Marti-Renom MA, Sali A. Localization of binding sites in protein structures by optimization of a composite scoring function. Protein Sci. 2006;15:2366-80. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16963645.
Cobo-Vuilleumier N, Lorenzo PI, Rodríguez NGarcía, et al. LRH-1 agonism favours an immune-islet dialogue which protects against diabetes mellitus. Nat Commun. 2018;9(1):1488. doi:10.1038/s41467-018-03943-0.
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Iglesias JManuel, Beloqui I, Garcia-Garcia F, et al. Mammosphere formation in breast carcinoma cell lines depends upon expression of E-cadherin. PLoS One. 2013;8(10):e77281. doi:10.1371/journal.pone.0077281.
Iglesias JManuel, Beloqui I, Garcia-Garcia F, et al. Mammosphere Formation in Breast Carcinoma Cell Lines Depends upon Expression of E-cadherin. PLoS ONE. 2013;8:e77281 -. Available at: http://dx.doi.org/10.1371%2Fjournal.pone.0077281.
Carbonell J, Alloza E, Arce P, et al. A map of human microRNA variation uncovers unexpectedly high levels of variability. Genome medicine. 2012;4:62. doi:10.1186/gm363.
Mapping the human genetic architecture of COVID-19. Nature. 2021;600(7889):472-477. doi:10.1038/s41586-021-03767-x.
Conesa A, Nueda MJ, Ferrer A, Talon M. maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics. 2006;22:1096-102. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16481333.
Sánchez-Tena S, Reyes-Zurita FJ, Díaz-Moralli S, et al. Maslinic Acid-Enriched Diet Decreases Intestinal Tumorigenesis in Apc(Min/+) Mice through Transcriptomic and Metabolomic Reprogramming. PloS one. 2013;8:e59392. doi:10.1371/journal.pone.0059392.
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.
Rian K, Esteban-Medina M, Hidalgo MR, et al. Mechanistic modeling of the SARS-CoV-2 disease map. BioData Min. 2021;14(1):5. doi:10.1186/s13040-021-00234-1.
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.
Cubuk C, Can FE, Peña-Chilet M, Dopazo J. Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments. Cells. 2020;9(7). doi:10.3390/cells9071579.
Brumos J, Colmenero-Flores JM, Conesa A, et al. Membrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstocks. Funct Integr Genomics. 2009. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19190944.
Sola-García A, Cáliz-Molina MÁngeles, Espadas I, et al. Metabolic reprogramming by Acly inhibition using SB-204990 alters glucoregulation and modulates molecular mechanisms associated with aging. Commun Biol. 2023;6(1):250. doi:10.1038/s42003-023-04625-4.
Dopazo J, Zanders E, Dragoni I, Amphlett G, Falciani F. Methods and approaches in the analysis of gene expression data. J Immunol Methods. 2001;250:93-112. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11251224.
Mateos A, Herrero J, Tamames J, Dopazo J. Methods of Microarray Data Analysis IISupervised Neural Networks for Clustering Conditions in DNA Array Data After Reducing Noise by Clustering Gene Expression Profiles. (Lin SM, Johnson KF, eds.). Boston: Kluwer Academic Publishers; 2002:91 - 103. doi:10.1007/b11298210.1007/0-306-47598-7_7.
Rizza S, Conesa A, Juarez J, et al. Microarray analysis of Etrog citron (Citrus medica L.) reveals changes in chloroplast, cell wall, peroxidase and symporter activities in response to viroid infection. Molecular plant pathology. 2012. doi:10.1111/j.1364-3703.2012.00794.x.
Dopazo J. Microarray Data Processing And Analysis. In: Microarray data analysis II. Microarray data analysis II. Kluwer Academic; 2002:43-63.
Shi L, Campbell G, Jones WD, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature biotechnology. 2010;28:827-38. Available at: http://www.nature.com/nbt/journal/v28/n8/full/nbt.1665.html.