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PUBLICACIONES

 

 

spacerTrabajos Publicados por Ramón Díaz Uriarte
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  1. Aga, O.N.L.; Brun, M.; Dauda, K.A.; Diaz-Uriarte, R.; Giannakis, K.; Johnston, I.G. "HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures.". PLoS Comput Biol. 20(9): e1012393. (2024). (PMID: 39231165).
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  2. Diaz-Colunga, J.; Skwara, A.; Gowda, K.; Diaz-Uriarte, R.; Tikhonov, M.; Bajic, D.; Sanchez, A. "Global epistasis on fitness landscapes.". Philos Trans R Soc Lond B Biol Sci. 378(1877): 20220053. (2023). (PMID: 37004717).
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  3. Diaz-Uriarte, R.; Herrera-Nieto, P. "EvAM-Tools: tools for evolutionary accumulation and cancer progression models.". Bioinformatics. (): . (2022). (PMID: 36287062).
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  4. Diaz-Uriarte, R.; Gómez de Lope, E.; Giugno, R.; Fröhlich, H.; Nazarov, P.V.; Nepomuceno-Chamorro, I.A.; Rauschenberger, A.; Glaab, E. "Ten quick tips for biomarker discovery and validation analyses using machine learning.". PLoS Comput Biol. 18(8): e1010357. (2022). (PMID: 35951526).
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  5. Manrubia, S.; Cuesta, J.A.; Aguirre, J.; Ahnert, S.E.; Altenberg, L.; Cano, A.V.; Catalán, P.; Diaz-Uriarte, R.; Elena, S.F.; García-Martín, J.A.; Hogeweg, P.; Khatri, B.S.; Krug, J.; Louis, A.A.; Martin, N.S.; Payne, J.L.; Tarnowski, M.J.; Weiß, M. "The long and winding road to understanding organismal construction: Reply to comments on "From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics".". Phys Life Rev. 42(): 19-24. (2022). (PMID: 35636230).
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  6. Diaz-Uriarte, R. "Simulating Evolution in Asexual Populations with Epistasis.". Methods Mol Biol. 2212(): 121-154. (2021). (PMID: 33733354).
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  7. Diaz-Colunga, J.; Diaz-Uriarte, R. "Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?". PLoS Comput Biol. 17(12): e1009055. (2021). (PMID: 34932572).
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  8. Manrubia, S.; Cuesta, J.A.; Aguirre, J.; Ahnert, S.E.; Altenberg, L.; Cano, A.V.; Catalán, P.; Diaz-Uriarte, R.; Elena, S.F.; García-Martín, J.A.; Hogeweg, P.; Khatri, B.S.; Krug, J.; Louis, A.A.; Martin, N.S.; Payne, J.L.; Tarnowski, M.J.; Weiß, M. "From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics.". Phys Life Rev. (): . (2021). (PMID: 34088608).
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  9. Diaz-Uriarte, R.; Vasallo, C. "Every which way? On predicting tumor evolution using cancer progression models.". PLoS Comput. Biol.. 15(8): e1007246. (2019). (PMID: 31374072).
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  10. Hosseini, S.R.; Diaz-Uriarte, R.; Markowetz, F.; Beerenwinkel, N. "Estimating the predictability of cancer evolution.". Bioinformatics. 35(14): i389-i397. (2019). (PMID: 31510665).
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  11. Diaz-Uriarte, R. "Cancer Progression Models and Fitness Landscapes: a Many-to-Many Relationship.". Bioinformatics. (): . (2017). (PMID: 29048486).
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  12. Diaz-Uriarte, R. "OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.". Bioinformatics. 33(12): 1898-1899. (2017). (PMID: 28186227).
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  13. Fernandez-Navarro, P.; González-Neira, A.; Pita, G.; Díaz-Uriarte, R.; Tais Moreno, L.; Ederra, M.; Pedraz-Pingarrón, C.; Sánchez-Contador, C.; Vázquez-Carrete, J.A.; Moreo, P.; Vidal, C.; Salas-Trejo, D.; Stone, J.; Southey, M.C.; Hopper, J.L.; Pérez-Gómez, B.; Benitez, J.; Pollan, M. "Genome wide association study identifies a novel putative mammographic density locus at 1q12-q21.". Int. J. Cancer. 136(10): 2427-2436. (2015). (PMID: 25353672).
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  14. Diaz-Uriarte, R. "Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling.". BMC Bioinformatics. 16(): 41. (2015). (PMID: 25879190).
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  15. Diaz-Uriarte, R. "ADaCGH2: parallelized analysis of (big) CNA data.". Bioinformatics. 30(12): 1759-1761. (2014). (PMID: 24532724).
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  16. Landa, I.; Boullosa, C.; Inglada-Pérez, L.; Sastre-Perona, A.; Pastor, S.; Velázquez, A.; Mancikova, V.; Ruiz-Llorente, S.; Schiavi, F.; Marcos, R.; Malats, N.; Opocher, G.; Diaz-Uriarte, R.; Santisteban, P.; Valencia, A.; Robledo, M. "An epistatic interaction between the PAX8 and STK17B genes in papillary thyroid cancer susceptibility.". PLoS ONE. 8(9): e74765. (2013). (PMID: 24086368).
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  17. Barderas, R.; Babel, I.; Díaz-Uriarte, R.; Moreno, V.; Suárez, A.; Bonilla, F.; Villar-Vázquez, R.; Capellá, G.; Casal, J.I. "An optimized predictor panel for colorectal cancer diagnosis based on the combination of tumor-associated antigens obtained from protein and phage microarrays.". J Proteomics. 75(15): 4647-4655. (2012). (PMID: 22465712).
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  18. Montes-Moreno, S.; Martinez, N.; Sanchez-Espiridión, B.; Díaz Uriarte, R.; Rodriguez, M.E.; Saez, A.; Montalbán, C.; Gomez, G.; Pisano, D.G.; García, J.F.; Conde, E.; Gonzalez-Barca, E.; Lopez, A.; Mollejo, M.; Grande, C.; Martinez, M.A.; Dunphy, C.; Hsi, E.D.; Rocque, G.B.; Chang, J.; Go, R.S.; Visco, C.; Xu-Monette, Z.; Young, K.H.; Piris, M.A. "miRNA expression in diffuse large B-cell lymphoma treated with chemoimmunotherapy.". Blood. 118(4): 1034-1040. (2011). (PMID: 21633089).
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  19. Subirana, I.; Diaz-Uriarte, R.; Lucas, G.; Gonzalez, J.R. "CNVassoc: Association analysis of CNV data using R.". BMC Med Genomics. 4(): 47. (2011). (PMID: 21609482).
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  20. Babel, I.; Barderas, R.; Diaz-Uriarte, R.; Moreno, V.; Suarez, A.; Fernandez-Aceñero, M.J.; Salazar, R.; Capellá, G.; Casal, J.I. "Identification of MST1/STK4 and SULF1 proteins as autoantibody targets for the diagnosis of colorectal cancer by using phage microarrays.". Mol. Cell Proteomics. 10(3): M110.001784. (2011). (PMID: 21228115).
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  21. Carro, A.; Rico, D.; Rueda, O.M.; Díaz-Uriarte, R.; Pisano, D.G. "waviCGH: a web application for the analysis and visualization of genomic copy number alterations.". Nucleic Acids Res.. 38(Web Server issue): W182-7. (2010). (PMID: 20507915).
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  22. Babel, I.; Barderas, R.; Díaz-Uriarte, R.; Martínez-Torrecuadrada, J.L.; Sánchez-Carbayo, M.; Casal, J.I. "Identification of tumor-associated autoantigens for the diagnosis of colorectal cancer in serum using high density protein microarrays.". Mol. Cell Proteomics. 8(10): 2382-2395. (2009). (PMID: 19638618).
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  23. Rueda, O.M.; Diaz-Uriarte, R. "Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously.". BMC Bioinformatics. 10(): 308. (2009). (PMID: 19775444).
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  24. Rueda, O.M.; Diaz-Uriarte, R. "RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions.". Bioinformatics. 25(15): 1959-1960. (2009). (PMID: 19420051).
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  25. Morrissey, E.R.; Diaz-Uriarte, R. "Pomelo II: finding differentially expressed genes.". Nucleic Acids Res.. 37(Web Server issue): W581-6. (2009). (PMID: 19435879).
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  26. Sequeira-Mendes, J.; Díaz-Uriarte, R.; Apedaile, A.; Huntley, D.; Brockdorff, N.; Gómez, M. "Transcription initiation activity sets replication origin efficiency in mammalian cells.". PLoS Genet.. 5(4): e1000446. (2009). (PMID: 19360092).
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  27. Infante, A.; Laresgoiti, U.; Fernández-Rueda, J.; Fullaondo, A.; Galán, J.; Díaz-Uriarte, R.; Malumbres, M.; Field, S.J.; Zubiaga, A.M. "E2F2 represses cell cycle regulators to maintain quiescence.". Cell Cycle. 7(24): 3915-3927. (2008). (PMID: 19066456).
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  28. Urdinguio, R.G.; Lopez-Serra, L.; Lopez-Nieva, P.; Alaminos, M.; Diaz-Uriarte, R.; Fernandez, A.F.; Esteller, M. "Mecp2-null mice provide new neuronal targets for Rett syndrome.". PLoS ONE. 3(11): e3669. (2008). (PMID: 18989361).
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  29. Alibés, A.; Cañada, A.; Díaz-Uriarte, R. "PaLS: filtering common literature, biological terms and pathway information.". Nucleic Acids Res.. 36(Web Server issue): W364-7. (2008). (PMID: 18467422).
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  30. Diaz-Uriarte, R. "SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data.". BMC Bioinformatics. 9(): 30. (2008). (PMID: 18208605).
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  31. Rueda, O.M.; Diaz-Uriarte, R. "A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.". BMC Bioinformatics. 8(): 394. (2007). (PMID: 17939873).
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  32. Collado, M.; Garcia, V.; Garcia, J.M.; Alonso, I.; Lombardia, L.; Diaz-Uriarte, R.; Fernández, L.A.; Zaballos, A.; Bonilla, F.; Serrano, M. "Genomic profiling of circulating plasma RNA for the analysis of cancer.". Clin. Chem.. 53(10): 1860-1863. (2007). (PMID: 17717129).
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  33. Diaz-Uriarte, R. "GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest.". BMC Bioinformatics. 8(): 328. (2007). (PMID: 17767709).
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  34. Rodríguez, A.; Villuendas, R.; Yáñez, L.; Gómez, M.E.; Díaz, R.; Pollán, M.; Hernández, N.; de la Cueva, P.; Marín, M.C.; Swat, A.; Ruiz, E.; Cuadrado, M.A.; Conde, E.; Lombardía, L.; Cifuentes, F.; Gonzalez, M.; García-Marco, J.A.; Piris, M.A.; , . "Molecular heterogeneity in chronic lymphocytic leukemia is dependent on BCR signaling: clinical correlation.". Leukemia. 21(9): 1984-1991. (2007). (PMID: 17611561).
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  35. Díaz-Uriarte, R.; Rueda, O.M. "ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.". PLoS ONE. 2(8): e737. (2007). (PMID: 17710137).
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  36. Díaz-Uriarte, R.; Alibés, A.; Morrissey, E.R.; Cañada, A.; Rueda, O.M.; Neves, M.L. "Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite.". Nucleic Acids Res.. 35(Web Server issue): W75-80. (2007). (PMID: 17488846).
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  37. Rueda, O.M.; Díaz-Uriarte, R. "Flexible and accurate detection of genomic copy-number changes from aCGH.". PLoS Comput. Biol.. 3(6): e122. (2007). (PMID: 17590078).
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  38. Moneo, V.; Serelde, B.G.; Leal, J.F.; Blanco-Aparicio, C.; Diaz-Uriarte, R.; Aracil, M.; Tercero, J.C.; Jimeno, J.; Carnero, A. "Levels of p27(kip1) determine Aplidin sensitivity.". Mol. Cancer Ther.. 6(4): 1310-1316. (2007). (PMID: 17431109).
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  39. Alibés, A.; Morrissey, E.R.; Cañada, A.; Rueda, O.M.; Casado, D.; Yankilevich, P.; Díaz-Uriarte, R. "Asterias: a parallelized web-based suite for the analysis of expression and aCGH data.". Cancer Inform. 3(): 1-9. (2007). (PMID: 19455230).
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  40. Alibés, A.; Yankilevich, P.; Cañada, A.; Díaz-Uriarte, R. "IDconverter and IDClight: conversion and annotation of gene and protein IDs.". BMC Bioinformatics. 8(): 9. (2007). (PMID: 17214880).
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  41. Díaz-Uriarte, R.; Alvarez de Andrés, S. "Gene selection and classification of microarray data using random forest.". BMC Bioinformatics. 7(): 3. (2006). (PMID: 16398926).
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  42. Al-Shahrour, F.; Díaz-Uriarte, R.; Dopazo, J. "Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.". Bioinformatics. 21(13): 2988-2993. (2005). (PMID: 15840702).
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  43. Vaquerizas, J.M.; Conde, L.; Yankilevich, P.; Cabezón, A.; Minguez, P.; Díaz-Uriarte, R.; Al-Shahrour, F.; Herrero, J.; Dopazo, J. "GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.". Nucleic Acids Res.. 33(Web Server issue): W616-20. (2005). (PMID: 15980548).
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  44. Alvarez, S.; Diaz-Uriarte, R.; Osorio, A.; Barroso, A.; Melchor, L.; Paz, M.F.; Honrado, E.; Rodríguez, R.; Urioste, M.; Valle, L.; Díez, O.; Cigudosa, J.C.; Dopazo, J.; Esteller, M.; Benitez, J. "A predictor based on the somatic genomic changes of the BRCA1/BRCA2 breast cancer tumors identifies the non-BRCA1/BRCA2 tumors with BRCA1 promoter hypermethylation.". Clin. Cancer Res.. 11(3): 1146-1153. (2005). (PMID: 15709182).
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  45. Meléndez, B.; Martínez-Delgado, B.; Cuadros, M.; Fernández, V.; Díaz-Uriarte, R.; Benítez, J. "Identification of amplified and highly expressed genes in amplicons of the T-cell line huT78 detected by cDNA microarray CGH.". Mol. Cancer. 4(1): 5. (2005). (PMID: 15656903).
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  46. Vaquerizas, J.M.; Dopazo, J.; Díaz-Uriarte, R. "DNMAD: web-based diagnosis and normalization for microarray data.". Bioinformatics. 20(18): 3656-3658. (2004). (PMID: 15247094).
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  47. Meléndez, B.; Díaz-Uriarte, R.; Cuadros, M.; Martínez-Ramírez, A.; Fernández-Piqueras, J.; Dopazo, A.; Cigudosa, J.C.; Rivas, C.; Dopazo, J.; Martínez-Delgado, B.; Benítez, J. "Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization.". Genes Chromosomes Cancer. 41(4): 353-365. (2004). (PMID: 15382261).
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  48. Martinez-Delgado, B.; Meléndez, B.; Cuadros, M.; Alvarez, J.; Castrillo, J.M.; Ruiz De La Parte, A.; Mollejo, M.; Bellas, C.; Diaz, R.; Lombardía, L.; Al-Shahrour, F.; Domínguez, O.; Cascon, A.; Robledo, M.; Rivas, C.; Benitez, J. "Expression profiling of T-cell lymphomas differentiates peripheral and lymphoblastic lymphomas and defines survival related genes.". Clin Cancer Res. 10(15): 4971-4982. (2004). (PMID: 15297397).
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  49. Herrero, J.; Vaquerizas, J.M.; Al-Shahrour, F.; Conde, L.; Mateos, A.; Díaz-Uriarte, J.S.; Dopazo, J. "New challenges in gene expression data analysis and the extended GEPAS.". Nucleic Acids Res. 32(Web Server issue): W485-91. (2004). (PMID: 15215434).
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  50. Al-Shahrour, F.; Díaz-Uriarte, R.; Dopazo, J. "FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.". Bioinformatics. 20(4): 578-580. (2004). (PMID: 14990455).
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  51. Herrero, J.; Díaz-Uriarte, R.; Dopazo, J. "An approach to inferring transcriptional regulation among genes from large-scale expression data.". Comp. Funct. Genomics. 4(1): 148-154. (2003). (PMID: 18629097).
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  52. Moreno-Bueno, G.; Sánchez-Estévez, C.; Cassia, R.; Rodríguez-Perales, S.; Díaz-Uriarte, R.; Domínguez, O.; Hardisson, D.; Andujar, M.; Prat, J.; Matias-Guiu, X.; Cigudosa, J.C.; Palacios, J. "Differential gene expression profile in endometrioid and nonendometrioid endometrial carcinoma: STK15 is frequently overexpressed and amplified in nonendometrioid carcinomas.". Cancer Res.. 63(18): 5697-5702. (2003). (PMID: 14522886).
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  53. Herrero, J.; Al-Shahrour, F.; Díaz-Uriarte, R.; Mateos, A.; Vaquerizas, J.M.; Santoyo, J.; Dopazo, J. "GEPAS: A web-based resource for microarray gene expression data analysis.". Nucleic Acids Res.. 31(13): 3461-3467. (2003). (PMID: 12824345).
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  54. Herrero, J.; Díaz-Uriarte, R.; Dopazo, J. "Gene expression data preprocessing.". Bioinformatics. 19(5): 655-656. (2003). (PMID: 12651726).
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  55. Díaz-Uriarte, R. "Territorial intrusion risk and antipredator behaviour: a mathematical model.". Proc Biol Sci. 268(1472): 1165-1173. (2001). (PMID: 11375105).
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  56. Garland, T.; Díaz-Uriarte, R. "Polytomies and phylogenetically independent contrasts: examination of the bounded degrees of freedom approach.". Syst. Biol.. 48(3): 547-558. (1999). (PMID: 12066293).
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  57. Díaz-Uriarte, R.; Garland, T. "Effects of branch length errors on the performance of phylogenetically independent contrasts.". Syst. Biol.. 47(4): 654-672. (1998). (PMID: 12066309).
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