Publications
(For citations and related stuff, you can go to my ResearcherID, ORCID ID and Google Scholar links.)
Papers, preprints, and technical reports
Aga, O. N. L., Brun, M., Giannakis, K., Dauda, K. A., Diaz-Uriarte, R., & Johnston, I. (2024). HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures. bioRxiv:10.1101/2024.03.07.583841.
Diaz-Uriarte, R. (2023). A picture guide to cancer progression and monotonic accumulation models: evolutionary assumptions, plausible interpretations, and alternative uses. arXiv:2312.06824.
Fontaneda D, Diaz-Uriarte R. (2023). Adaptive therapy in cancer: the role of restrictions in the accumulation of mutations. bioRxiv:10.1101/2023.05.18.541330.
Diaz-Colunga J, Skwara A, Gowda K, Diaz-Uriarte R, Tikhonov M, Bajic D, & Sanchez A. (2023). Global epistasis on fitness landscapes. Philosophical Transactions of the Royal Society B: Biological Sciences, 378(1877), 20220053.
Diaz-Uriarte R, Herrera-Nieto P. 2022. EvAM-Tools: tools for evolutionary accumulation and cancer progression models. Bioinformatics, 38 (24): 5457--5459..
Diaz-Uriarte R, Gómez de Lope E, Giugno R, Fröhlich H, Nazarov PV, Nepomuceno-Chamorro IA, Rauschenberger, A, Glaab E. 2022. Ten quick tips for biomarker discovery and validation analyses using machine learning. PLoS Computational Biology 18(8): e1010357.
Manrubia S, Cuesta JA, Aguirre J, Ahnert SE, Altenberg L, Cano AV, Catalán P, Diaz-Uriarte R, Elena SF, García-Martín JA, Hogeweg P, Khatri BS, Krug J, Louis AA, Martin NS, Payne JL, Tarnowski MJ, Weiß M. 2022. The long and winding road to understanding organismal construction. Physics of Life Reviews, 42, 19–24. (a reply to comments to Manrubia et al., 2021).
Diaz-Colunga J, Diaz-Uriarte R. 2021. Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next? PLoS Computational Biology, 17(12): e1009055.
Manrubia S, Cuesta JA, Aguirre J, Ahnert SE, Altenberg L, Cano AV, Catalán P, Diaz-Uriarte R, Elena SF, García-Martín JA, Hogeweg P, Khatri BS, Krug J, Louis AA, Martin NS, Payne JL, Tarnowski MJ, Weiß M. 2021. From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics. Physics of Life Reviews, 38: 55-106.
Diaz-Uriarte, R. 2021. Simulating evolution in asexual populations with epistasis. In K.-C. Wong (ed.), Epistasis: Methods and Protocols. Methods in Molecular Biology, 2212, Springer. Chapter 9. (Book's page).
Diaz-Uriarte, R. and Vasallo, C. 2019. Every which way? On predicting tumor evolution using cancer progression models. PLoS Computational Biology 15(8).
Hosseini S-R, Diaz-Uriarte R, Markowetz F, Beerenwinkel N. 2019. Estimating the predictability of cancer evolution. Bioinformatics, 35, i389--i397.
Diaz-Uriarte, R. 2018. Cancer Progression Models And Fitness Landscapes: A Many-To-Many Relationship. Bioinformatics, 34(5): 836--844.
Diaz-Uriarte, R. 2017. OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.Bioinformatics, 33(12): 1898--99 .
Diaz-Uriarte, R. 2015. Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling. BMC Bioinformatics, 16, 41.
Fernandez-Navarro P, Gonzalez-Neira A, Pita G, Diaz-Uriarte R, Tais Moreno L, Ederra M, Pedraz-Pingarron C, Sanchez-Contador C, Vazquez-Carrete JA, Moreo P, Vidal C, Salas-Trejo D, Stone J, Southey MC, Hopper JL, Perez-Gomez B, Benitez J, Pollan M. 2015. Genome wide association study identifies a novel putative mammographic density locus at 1q12-q21. Int J Cancer, 136 (10): 2427--36.
Moneo V, Serelde BG, Blanco-Aparicio C, Diaz-Uriarte R, Aviles P, Santamaria G, Tercero JC, Cuevas C, Carnero A. 2014. Levels of active tyrosine kinase receptor determine the tumor response to Zalypsis. BMC Cancer, 14: 281.
Diaz-Uriarte, R. 2014. ADaCGH2: parallelized analysis of (big) CNA data. Bioinformatics, 30 (12): 1759--61 PubMed link.
Landa I, Boullosa C, Inglada-Perez L, Sastre-Perona A, Pastor S, Velazquez A, Mancikova V, Ruiz-Llorente S, Schiavi F, Marcos R, Malats N, Opocher G, Diaz-Uriarte R, Santisteban P, Valencia A, Robledo M. 2013. An Epistatic Interaction between the PAX8 and STK17B Genes in Papillary Thyroid Cancer Susceptibility. PLoS ONE 8(9):e74765. doi: 10.1371. PubMed link.
Rueda OM, Rueda C, Diaz-Uriarte R. 2013. A Bayesian HMM with random effects and an unknown number of states for DNA copy number analysis. Journal of Statistical Computation and Simulation, 83 (1): 82--96. A previous version, as pdf.
Rueda O.M., Diaz-Uriarte R., Caldas C. 2013. Finding Common Regions of Alteration in Copy Number Data. In: Banerjee D., Shah S. (eds) Array Comparative Genomic Hybridization. Methods in Molecular Biology (Methods and Protocols), vol 973. Humana Press, Totowa, NJ.
Barderas R, Babel I, Diaz-Uriarte R, Moreno V, Suarez A, Bonilla F, Villar-Vazquez R, Capella G, Casal JI. 2012. An optimized predictor panel for colorectal cancer diagnosis based on the combination of tumor-associated antigens obtained from protein and phage microarrays. Journal of Proteomics, 75 (15) 4647--4655. PubMed link.
Subirana I, Diaz-Uriarte R, Lucas G, Gonzalez JR. 2011. CNVassoc: Association analysis of CNV data using R. BMC Medical Genomics, 4: 47.
Montes-Moreno S, Martinez N, Sanchez-Espiridion B, Diaz Uriarte R, Rodriguez ME, Saez A, Montalban C, Gomez G, Pisano DG, Garcia JF, Conde E, Gonzalez-Barca E, Lopez A, Mollejo M, Grande C, Martinez MA, Dunphy C, Hsi ED, Rocque GB, Chang J, Go RS, Visco C, Xu-Monette Z, Young KH, Piris MA. 2011. MicroRNA expression in diffuse large B-cell lymphoma treated with chemoimmunotherapy. Blood, 118(4): 1034--40.
Babel I, Barderas R, Diaz-Uriarte R, Moreno V, Suarez A, Fernandez-Acenero MJ, Salazar R, Capella G, Casal JI. 2011. Identification of MST1/STK4 and SULF1 proteins as autoantibody targets for the diagnosis of colorectal cancer by using phage microarrays. Molecular & Cellular Proteomics.
Fuxjager MJ, Foufopoulos J, Diaz-Uriarte R, Marler CA. 2011. Functionally opposing effects of testosterone on tow different types of parasit: implications for the immunocompetence handicap hypothesis. Functional Ecology, 25: 132--138.
Carro A, Rico D, Rueda OM, Diaz-Uriarte R, Pisano DG. 2010. waviCGH: a web application for the analysis and visualization of genomic copy number alterations. Nucleic Acids Research, 2010, 38(Web Server issue):W182-W187.
Rueda OM, Diaz-Uriarte R. 2010. Finding Recurrent Copy Number Alteration Regions: A Review of Methods. Current Bioinformatics, 5 (1)
Rueda OM, Diaz-Uriarte R. 2009. Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously. BMC Bioinformatics, 10:308. .
Babel I, Barderas R, Diaz-Uriarte R, Martinez-Torrecuadrada JL, Sanchez-Carbayo M, and Casal JI. 2009. Identification of tumour-associated autoantigens for the diagnosis of colorectal cancer in serum using high-density protein microarrays. Molecular & Cellular Proteomics, 8 (10): 2382--95.
Rueda OM, Diaz-Uriarte R. 2009. RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions. Bioinformatics 2009 25(15):1959-1960
Morrissey E, Diaz-Uriarte R. 2009. Pomelo II: finding differentially expressed genes. Nucl. Acids. Res, doi: 10.1093/nar/gkp366.
Sequeira-Mendes J, Diaz-Uriarte R, Apedaile A, Huntley D, Brockdorff N, Gomez M. 2009. Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells. PLoS Genetics, 5(4): e1000446. doi:10.1371/journal.pgen.1000446.
Urdinguio RG, Lopez-Serra L, Lopez-Nieva P, Alaminos M, Diaz-Uriarte R, et al. 2008. Mecp2-Null Mice Provide New Neuronal Targets for Rett Syndrome. PLoS ONE 3(11): e3669 doi:10.1371/journal.pone.0003669
Alibes, A., Cañada, A., Diaz-Uriarte, R. 2008. PaLS: filtering common literature, biological terms and pathway information. Nucl. Acids Res. 2008 36: W364-W367.
Diaz-Uriarte, R. 2008. SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data. BMC Bioinformatics, 2008, 9:30.
Infante A, Laresgoiti U, Fernandez-Rueda J, Fullaondo A, Galan J, Diaz-Uriarte R, Malumbres M, Field SJ, Zubiaga AM. 2008. E2F2 represses cell cycle regulators to maintain quiescence. Cell Cycle, 7: 3915-3927.
Rueda, O.M. and Diaz-Uriarte, R. 2007. 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, 2007, 8:394.
Collado, M., Garcia, V., Garcia, J.M., Alonso, I., Lombardia, L., Diaz-Uriarte, R., Lopez, L. A., Zaballos, A., Bonilla, F., and Serrano, M. 2007. Genomic Profiling of Circulating Plasma RNA for the Analysis of Cancer. Clin Chem, 53: 1860-1863
Diaz-Uriarte, R. 2007. GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest. BMC Bioinformatics, 8: 328
Diaz-Uriarte, R. and Rueda, O. M. 2007. ADaCGH: a parallelized web-based application and R package for the analysis of aCGH data. PLoS ONE, 2 (8): e737.
Rueda, O. M., and Diaz-Uriarte, R. 2007. Flexible and accurate detection of genomic copy-number changes from aCGH. PLoS Computational Biology, 3(6): e122.
Rodriguez, A., Villuendas, R., Yañez, L., Gomez, M. E., Diaz-Uriarte, R., Pollan, M., Hernandez, N., de la Cueva, P., Marin, M. C., Swat, A., Ruiz, E., Cuadrado, M. A., Conde, E., Lombardia, L., Cifuentes, F., Gonzalez, M., Garcia-Marco J. A., and Piris, M. A. 2007. Molecular heterogeneity in chronic lymphocytic leukemia is dependent on BCR signaling: clinical correlation. Leukemia, 21, 1984 -1991.
Diaz-Uriarte, R., Alibes, A., Morrissey, E. R., Cañada, A., Rueda, O.M., Neves, M. L. 2007. Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite. Nucleic Acids Research,2007, 35, No. suppl_2 W75-W80.
Moneo, V., Serelde, B. G., Leal, J.F.M., Blanco-Aparicio, C., Diaz-Uriarte, R., Aracil, M., Tercero, J.C., Jimeno, J., and Carnero, A. 2007. Levels of p27kip1 determine Aplidin sensitivity. Molecular Cancer Therapeutics, 6, 1310-1316.
Alibes, A., Yankilevich, P., Cañada, A., and Diaz-Uriarte, R. 2007. IDconverter and IDClight: Conversion and annotation of gene and protein IDs. BMC Bioinformatics 2007, 8:9.
Castilla, A. M., A. A. Dhondt, R. Diaz-Uriarte, and D. Westmoreland. 2007. Predation in ground nesting birds: an experimental study using natural egg-color variation. Avian Conservation and Ecology - Écologie et conservation des oiseaux 2(1): 2.
Alibes, A., Morrissey, E. R., Cañada, A., Rueda, O. M., Casado, D., Yankilevich, P., and Diaz-Uriarte, R. 2006. Asterias: a parallelized web-based suite for the analysis of expression and aCGH data. Cancer Informatics, 2 :1-9.
Diaz-Uriarte, R., Alvarez de Andres, S. 2006. Gene selection and classification of microarray data using random forest. BMC Bioinformatics, 2006, 7:3. Supplementary material page
Vaquerizas, J., Conde, L., Yankilevich, P., Cabezon, A., Minguez, P., Diaz-Uriarte, R., Al-Shahrour, F., Herrero, J., Dopazo, J. 2005. GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Research, i33 (Web Server issue): W616-W620.
Al-Shahrour, F., Diaz-Uriarte, R., Dopazo, J. 2005. Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. Bioinformatics, 2005;21: 2988-2993.Abstract.
Melendez, B., Martinez-Delgado, B., Cuadros, M., Fernandez, V., Diaz-Uriarte, R., Benitez, J. 2005. Identification of amplified and highly expressed genes in amplicons of the T-cell line huT78 detected by cDNA microarray CGH. Molecular Cancer 2005, 4:5. Full paper
Alvarez de Andres, S., Diaz-Uriarte, R., Osorio, A., Barrosa, A., Paz, M.F., Honrado, E., Rodriguez, R., Urioste, M., Valle, L., Diez, O., Cigudosa, J. C., Dopazo, J., Esteller, M., Benitez, J. 2005. A predictor based on the somatic chnages of the BRCA1/2 breast cancer tumors identifies the non-BRCA1/2 tumors with BRCA1 promoter hypermethylation. Clinical Cancer Research, 11: 1146--1153.Full paper
Diaz-Uriarte, R. 2004. Supervised methods with genomic data: a review and cautionary view. Pp. 193-214 in "Data analysis and visualisation in genomics and proteomics", edited by by F. Azuaje, and J.Dopazo, John Wiley & Sons, New York. Original ms.
Diaz-Uriarte, R. 2004. Molecular signatures from gene expression data. Bioinformatics Unit Technical Reports number 004, available from arXiv.
Vaquerizas, J., Dopazo, J., & Diaz-Uriarte, R. 2004. DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics, 20: 3656-3658.
Melendez, B., Diaz-Uriarte, R., Martinez-Ramirez, A., Fernandez-Piqueras, J., Rivas, C., Dopazo, J., Martinez-Delgado, B., Benitez, J. 2004. Gene expression analysis on chromosomal regions of gain or loss in genetic material detected by comparative genomic hybridization. Genes Chromosomes and Cancer, 41: 353-365.Abstract.
Martinez-Delgado, B., Melendez, B., Cuadros, M., Alvarez, J., Castrillo, J.M., Ruiz de la Parte, A., Mollejo, M., Bellas, C., Diaz-Uriarte, R., Lombardia, L., Al-Shahrour, F., Dominguez, O., Cascon, A., Robledo, M., Rivas, C., Benitez, J. 2004. Expression Profi ing of T-Cel Lymphomas Differentiates Periphera and Lymphoblastic Lymphomas and Defines Surviva Related Genes. Clinical Cancer Research, 10: 4971-4982.
Herrero, J., Vaquerizas, J., Al-Shahrour, F., Conde, L., Mateos, A., Santoyo, J., Diaz-Uriarte, R. & Dopazo, J. 2004. New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Research, 32 (Web Server issue), W485--W491.
Al-Shahrour, F., Diaz-Uriarte, R. & Dopazo, J. 2004. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20, 578--580.
Diaz-Uriarte, R, Al-Shahrour, F., & Dopazo, J. 2003. Use of GO terms to understand the biological significance of microarray differential gene expression data. in K. F. Johnson and S. M. Lin (eds.), Methods of microarray data analysis: Papers from CAMDA 2002. Kluwer Academic. pp. 233-247.
Moreno-Bueno, G., Sanchez-Estevez, C., Cassia, R., Rodriguez-Perales, S., Diaz-Uriarte, R., Dominguez, O., Hardisson, D., Andujar, M., Prat, J., Matias-Guiu, X., Cigudosa, J.C., & Palacios, J. 2003. Differential Gene Expression Profile in Endometrioid and Nonendometrioid Endometrial Carcinoma: STK15 Is Frequently Overexpressed and Amplified in Nonendometrioid Carcinomas. Cancer Research 63, 5697--5702.
Al-Shahrour, F., Herrero, J., Mateos, A., Santoyo, J., Diaz-Uriarte, R. & Dopazo, J. 2003. Using Gene Ontology on genome-scale studies to find significant associations of biologically relevant terms to group of genes. Neural Networks for Signal Processing XIII. IEEE Press.
Herrero, J., Al-Shahrour, F., Diaz-Uriarte, R., Mateos, A., Vaquerizas, J.M., Santoyo, J. & Dopazo, J. 2003. GEPAS, a web-based resource for microarray gene expression data analysis. Nucleic Acids Research 31(13), 3461--3467.
Herrero, J., Diaz-Uriarte, R & Dopazo, J. 2003. An approach to inferring transcriptional regulation among genes from large-scale expression data. Functional and Comparative Genomics, 4: 148-154.
Herrero, J., Diaz-Uriarte, R & Dopazo, J. 2003. Gene Expression Data Preprocessing. Bioinformatics, 19: 655-656.
Diaz-Uriarte, R. 2002. Incorrect analysis of crossover trials in animal behaviour research. Animal Behaviour, 63: 815-822. PDF.
Diaz-Uriarte, R. 2001. Territorial intrusion risk and antipredator behaviour: a mathematical model. Proceedings of the Royal Society of London, Series B, 268: 1165-1173. PDF. Appendices in PDF.
Diaz-Uriarte, R. 1999. Anti-predator behaviour changes following an aggressive encounter in the lizard Tropidurus hispidus. Proceedings of the Royal Society of London, Series B, 266: 2457-2464.PDF.
Garland, T. Jr., & Diaz-Uriarte, R. 1999. Polytomies and independent contrasts: an examination of the bounded degrees of freedom approach. Systematic Biology, 48: 547-558.
Diaz-Uriarte, R., & Garland, T. Jr. 1998. Effects of branch length errors on the performance of phylogenetically independent contrasts. Systematic Biology, 47: 654-672.
Garland, T. Jr., Martin, K. L. M., & Diaz-Uriarte, R. 1997. Reconstructing ancestral trait values using squared-change parsimony: plasma osmolarity at the origin of amniotes. Pp. 425-501 in: S. S. Sumida & K. L. M. Martin (eds.), Amniote origins: completing the transition to land, Academic Press, San Diego.
Bauwens, D., & Diaz-Uriarte, R. 1997. Covariation of life-hiostory traits in lacertid lizards: a comparative study. The American Naturalist, 149: 91-111.
Diaz-Uriarte, R, & Garland T. Jr. 1996. Testing hypotheses of correlated evolution using phylogenetically independent contrasts: sensitivity to deviations from Brownian motion. Systematic Biology, 45: 27-47.
Diaz, J. A., Diaz-Uriarte, R., Rodriguez, A. 1996. Influence of behavioral thermoregulation on the use of vertical surfaces by Iberian wall lizards, Podarcis hispanica. Journal of Herpetology, 30: 548-552.
Other publications
Diaz-Uriarte, R. 2001. "The analysis of cross-over trials in animal behavior experiments: review and guide to the statistical literature". This used to be at Samizdat Press, though that site does not seem to be available now.
Diaz-Uriarte, R. 2000. Effects of aggressive interactions on antipredator behavior: empirical and theoretical aspects. PhD Thesis. PDF or the slightly better looking original Postscript (the pdf was obtained via ps2pdf and some fonts can look ugly on the screen). (Note that all of the thesis except chapter 2 has already been published; chapter 1 as Diaz-Uriarte, 1999; chapter 3 as Diaz-Uriarte, 2001 (the math model paper); chapter 4 as Diaz-Uriarte, 2002; and chapter 5 as Diaz-Uriarte, 2001 ---the Samizdat press book).
Diaz-Uriarte, R., and Diez, I. 1985. Las Aves Urbanas. Ediciones Penthalon.
Last modified: May 2023