20 Aug | 2026 Ten quick tips for causal analysis of biomedical omics data. Svinin, G, Loo, RTJ, Kumar, NV, Murthy, VV, Odongo, DU, Díaz-Uriarte, R , Conesa, A, Bontempi, G, Vinga, S, Granata, I, Domingo-Fernández, D, Lecca, P, Kuijjer, ML, Krijthe, JH, Koch, I, Calzone, L, Rombo, SE, Sánchez-Cabo, F, Glaab, E. PLoS Comput Biol - 22 (8) : e1014668 (PMID: 42623411) (doi:10.1371/journal.pcbi.1014668)
21 May | 2025 Evolutionary accumulation modeling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance. Renz, J, Dauda, KA, Aga, ONL, Diaz-Uriarte, R , Löhr, IH, Blomberg, B, Johnston, IG. mBio (PMID: 40396716) (doi:10.1128/mbio.00488-25)
12 Dec | 2024 A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling. Johnston, IG, Diaz-Uriarte, R . Bioinformatics (PMID: 39666947) (doi:10.1093/bioinformatics/btae737)
4 Sep | 2024 HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures. Aga, ONL, Brun, M, Dauda, KA, Diaz-Uriarte, R , Giannakis, K, Johnston, IG. PLoS Comput Biol - 20 (9) : e1012393 (PMID: 39231165) (doi:10.1371/journal.pcbi.1012393)
22 May | 2023 Global epistasis on fitness landscapes. Diaz-Colunga, J , Skwara, A, Gowda, K, Diaz-Uriarte, R , Tikhonov, M, Bajic, D, Sanchez, A. Philos Trans R Soc Lond B Biol Sci - 378 (1877) : 20220053 (PMID: 37004717) (doi:10.1098/rstb.2022.0053)
26 Oct | 2022 EvAM-Tools: tools for evolutionary accumulation and cancer progression models. Diaz-Uriarte, R , Herrera-Nieto, P . Bioinformatics (PMID: 36287062) (doi:10.1093/bioinformatics/btac710)
11 Aug | 2022 Ten quick tips for biomarker discovery and validation analyses using machine learning. Diaz-Uriarte, R , Gómez de Lope, E, Giugno, R, Fröhlich, H, Nazarov, PV, Nepomuceno-Chamorro, IA, Rauschenberger, A, Glaab, E. PLoS Comput Biol - 18 (8) : e1010357 (PMID: 35951526) (doi:10.1371/journal.pcbi.1010357)
23 May | 2022 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". 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. Phys Life Rev - 42 : 19-24 (PMID: 35636230) (doi:10.1016/j.plrev.2022.05.007)
21 Dec | 2021 Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next? Diaz-Colunga, J , Diaz-Uriarte, R . PLoS Comput Biol - 17 (12) : e1009055 (PMID: 34932572) (doi:10.1371/journal.pcbi.1009055)
21 May | 2021 From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics. 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. Phys Life Rev (PMID: 34088608) (doi:10.1016/j.plrev.2021.03.004)
1 Mar | 2021 Simulating Evolution in Asexual Populations with Epistasis. Diaz-Uriarte, R . Methods Mol Biol - 2212 : 121-154 (PMID: 33733354) (doi:10.1007/978-1-0716-0947-7_9)
2 Aug | 2019 Every which way? On predicting tumor evolution using cancer progression models. Diaz-Uriarte, R , Vasallo, C . PLoS Comput. Biol. - 15 (8) : e1007246 (PMID: 31374072) (doi:10.1371/journal.pcbi.1007246)
15 Jul | 2019 Estimating the predictability of cancer evolution. Hosseini, SR, Diaz-Uriarte, R , Markowetz, F, Beerenwinkel, N. Bioinformatics - 35 (14) : i389-i397 (PMID: 31510665) (doi:10.1093/bioinformatics/btz332)
18 Oct | 2017 Cancer Progression Models and Fitness Landscapes: a Many-to-Many Relationship. Diaz-Uriarte, R . Bioinformatics (PMID: 29048486) (doi:10.1093/bioinformatics/btx663)
15 Jun | 2017 OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations. Diaz-Uriarte, R . Bioinformatics - 33 (12) : 1898-1899 (PMID: 28186227) (doi:10.1093/bioinformatics/btx077)
15 May | 2015 Genome wide association study identifies a novel putative mammographic density locus at 1q12-q21. Fernandez-Navarro, P, González-Neira, A, Pita, G, Díaz-Uriarte, R , Tais Moreno, L, Ederra, M, Pedraz-Pingarrón, C, Sánchez-Contador, C, Vázquez-Carrete, JA, Moreo, P, Vidal, C, Salas-Trejo, D, Stone, J, Southey, MC, Hopper, JL, Pérez-Gómez, B, Benitez, J, Pollan, M. Int. J. Cancer - 136 (10) : 2427-2436 (PMID: 25353672) (doi:10.1002/ijc.29299)
12 Feb | 2015 Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling. Diaz-Uriarte, R . BMC Bioinformatics - 16 : 41 (PMID: 25879190) (doi:10.1186/s12859-015-0466-7)
15 Jun | 2014 ADaCGH2: parallelized analysis of (big) CNA data. Diaz-Uriarte, R . Bioinformatics - 30 (12) : 1759-1761 (PMID: 24532724) (doi:10.1093/bioinformatics/btu099)
23 Sep | 2013 An epistatic interaction between the PAX8 and STK17B genes in papillary thyroid cancer susceptibility. 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. PLoS ONE - 8 (9) : e74765 (PMID: 24086368) (doi:10.1371/journal.pone.0074765)
3 Aug | 2012 An optimized predictor panel for colorectal cancer diagnosis based on the combination of tumor-associated antigens obtained from protein and phage microarrays. Barderas, R, Babel, I, Díaz-Uriarte, R , Moreno, V, Suárez, A, Bonilla, F, Villar-Vázquez, R, Capellá, G, Casal, JI. J Proteomics - 75 (15) : 4647-4655 (PMID: 22465712) (doi:10.1016/j.jprot.2012.03.004)
28 Jul | 2011 miRNA expression in diffuse large B-cell lymphoma treated with chemoimmunotherapy. Montes-Moreno, S, Martinez, N, Sanchez-Espiridión, B, Díaz Uriarte, R , Rodriguez, ME, Saez, A, Montalbán, C, Gomez, G, Pisano, DG, García, 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. Blood - 118 (4) : 1034-1040 (PMID: 21633089) (doi:10.1182/blood-2010-11-321554)
24 May | 2011 CNVassoc: Association analysis of CNV data using R. Subirana, I, Diaz-Uriarte, R , Lucas, G, Gonzalez, JR. BMC Med Genomics - 4 : 47 (PMID: 21609482) (doi:10.1186/1755-8794-4-47)
2 Mar | 2011 Identification of MST1/STK4 and SULF1 proteins as autoantibody targets for the diagnosis of colorectal cancer by using phage microarrays. Babel, I, Barderas, R, Diaz-Uriarte, R , Moreno, V, Suarez, A, Fernandez-Aceñero, MJ, Salazar, R, Capellá, G, Casal, JI. Mol. Cell Proteomics - 10 (3) : M110.001784 (PMID: 21228115) (doi:10.1074/mcp.M110.001784)
1 Jul | 2010 waviCGH: a web application for the analysis and visualization of genomic copy number alterations. Carro, A, Rico, D, Rueda, OM, Díaz-Uriarte, R , Pisano, DG. Nucleic Acids Res. - 38 (Web Server issue) : W182-7 (PMID: 20507915) (doi:10.1093/nar/gkq441)
6 Oct | 2009 Identification of tumor-associated autoantigens for the diagnosis of colorectal cancer in serum using high density protein microarrays. Babel, I, Barderas, R, Díaz-Uriarte, R , Martínez-Torrecuadrada, JL, Sánchez-Carbayo, M, Casal, JI. Mol. Cell Proteomics - 8 (10) : 2382-2395 (PMID: 19638618) (doi:10.1074/mcp.M800596-MCP200)
23 Sep | 2009 Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously. Rueda, OM, Diaz-Uriarte, R . BMC Bioinformatics - 10 : 308 (PMID: 19775444) (doi:10.1186/1471-2105-10-308)
1 Aug | 2009 RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions. Rueda, OM, Diaz-Uriarte, R . Bioinformatics - 25 (15) : 1959-1960 (PMID: 19420051) (doi:10.1093/bioinformatics/btp307)
1 Jul | 2009 Pomelo II: finding differentially expressed genes. Morrissey, ER, Diaz-Uriarte, R . Nucleic Acids Res. - 37 (Web Server issue) : W581-6 (PMID: 19435879) (doi:10.1093/nar/gkp366)
10 Apr | 2009 Transcription initiation activity sets replication origin efficiency in mammalian cells. Sequeira-Mendes, J, Díaz-Uriarte, R , Apedaile, A, Huntley, D, Brockdorff, N, Gómez, M. PLoS Genet. - 5 (4) : e1000446 (PMID: 19360092) (doi:10.1371/journal.pgen.1000446)
15 Dec | 2008 E2F2 represses cell cycle regulators to maintain quiescence. Infante, A, Laresgoiti, U, Fernández-Rueda, J, Fullaondo, A, Galán, J, Díaz-Uriarte, R , Malumbres, M, Field, SJ, Zubiaga, AM. Cell Cycle - 7 (24) : 3915-3927 (PMID: 19066456)
7 Nov | 2008 Mecp2-null mice provide new neuronal targets for Rett syndrome. Urdinguio, RG, Lopez-Serra, L, Lopez-Nieva, P, Alaminos, M, Diaz-Uriarte, R , Fernandez, AF, Esteller, M. PLoS ONE - 3 (11) : e3669 (PMID: 18989361) (doi:10.1371/journal.pone.0003669)
1 Jul | 2008 PaLS: filtering common literature, biological terms and pathway information. Alibés, A, Cañada, A, Díaz-Uriarte, R . Nucleic Acids Res. - 36 (Web Server issue) : W364-7 (PMID: 18467422) (doi:10.1093/nar/gkn251)
21 Jan | 2008 SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data. Diaz-Uriarte, R . BMC Bioinformatics - 9 : 30 (PMID: 18208605) (doi:10.1186/1471-2105-9-30)
25 Oct | 2007 Genomic profiling of circulating plasma RNA for the analysis of cancer. Collado, M, Garcia, V, Garcia, JM, Alonso, I, Lombardia, L, Diaz-Uriarte, R , Fernández, LA, Zaballos, A, Bonilla, F, Serrano, M. Clin. Chem. - 53 (10) : 1860-1863 (PMID: 17717129) (doi:10.1373/clinchem.2007.089201)
16 Oct | 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. Rueda, OM, Diaz-Uriarte, R . BMC Bioinformatics - 8 : 394 (PMID: 17939873) (doi:10.1186/1471-2105-8-394)
3 Sep | 2007 GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest. Diaz-Uriarte, R . BMC Bioinformatics - 8 : 328 (PMID: 17767709) (doi:10.1186/1471-2105-8-328)
1 Sep | 2007 Molecular heterogeneity in chronic lymphocytic leukemia is dependent on BCR signaling: clinical correlation. Rodríguez, A, Villuendas, R, Yáñez, L, Gómez, ME, Díaz, R , Pollán, M, Hernández, N, de la Cueva, P, Marín, MC, Swat, A, Ruiz, E, Cuadrado, MA, Conde, E, Lombardía, L, Cifuentes, F, Gonzalez, M, García-Marco, JA, Piris, MA, , . Leukemia - 21 (9) : 1984-1991 (PMID: 17611561) (doi:10.1038/sj.leu.2404831)
15 Aug | 2007 ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data. Díaz-Uriarte, R , Rueda, OM. PLoS ONE - 2 (8) : e737 (PMID: 17710137) (doi:10.1371/journal.pone.0000737)
16 Jul | 2007 Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite. Díaz-Uriarte, R , Alibés, A, Morrissey, ER, Cañada, A, Rueda, OM, Neves, ML. Nucleic Acids Res. - 35 (Web Server issue) : W75-80 (PMID: 17488846) (doi:10.1093/nar/gkm229)
1 Jun | 2007 Flexible and accurate detection of genomic copy-number changes from aCGH. Rueda, OM, Díaz-Uriarte, R . PLoS Comput. Biol. - 3 (6) : e122 (PMID: 17590078) (doi:10.1371/journal.pcbi.0030122)
13 Apr | 2007 Levels of p27(kip1) determine Aplidin sensitivity. Moneo, V, Serelde, BG, Leal, JF, Blanco-Aparicio, C, Diaz-Uriarte, R , Aracil, M, Tercero, JC, Jimeno, J, Carnero, A. Mol. Cancer Ther. - 6 (4) : 1310-1316 (PMID: 17431109) (doi:10.1158/1535-7163.MCT-06-0729)
3 Feb | 2007 Asterias: a parallelized web-based suite for the analysis of expression and aCGH data. Alibés, A, Morrissey, ER, Cañada, A, Rueda, OM, Casado, D, Yankilevich, P, Díaz-Uriarte, R . Cancer Inform - 3 : 1-9 (PMID: 19455230)
10 Jan | 2007 IDconverter and IDClight: conversion and annotation of gene and protein IDs. Alibés, A, Yankilevich, P, Cañada, A, Díaz-Uriarte, R . BMC Bioinformatics - 8 : 9 (PMID: 17214880) (doi:10.1186/1471-2105-8-9)
6 Jan | 2006 Gene selection and classification of microarray data using random forest. Díaz-Uriarte, R , Alvarez de Andrés, S. BMC Bioinformatics - 7 : 3 (PMID: 16398926) (doi:10.1186/1471-2105-7-3)
1 Jul | 2005 Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. Al-Shahrour, F, Díaz-Uriarte, R , Dopazo, J. Bioinformatics - 21 (13) : 2988-2993 (PMID: 15840702) (doi:10.1093/bioinformatics/bti457)
1 Jul | 2005 GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Vaquerizas, JM, Conde, L, Yankilevich, P, Cabezón, A, Minguez, P, Díaz-Uriarte, R , Al-Shahrour, F, Herrero, J, Dopazo, J. Nucleic Acids Res. - 33 (Web Server issue) : W616-20 (PMID: 15980548) (doi:10.1093/nar/gki500)
1 Feb | 2005 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. Alvarez, S, Diaz-Uriarte, R , Osorio, A, Barroso, A, Melchor, L, Paz, MF, Honrado, E, Rodríguez, R, Urioste, M, Valle, L, Díez, O, Cigudosa, JC, Dopazo, J, Esteller, M, Benitez, J. Clin. Cancer Res. - 11 (3) : 1146-1153 (PMID: 15709182)
18 Jan | 2005 Identification of amplified and highly expressed genes in amplicons of the T-cell line huT78 detected by cDNA microarray CGH. Meléndez, B, Martínez-Delgado, B, Cuadros, M, Fernández, V, Díaz-Uriarte, R , Benítez, J. Mol. Cancer - 4 (1) : 5 (PMID: 15656903) (doi:10.1186/1476-4598-4-5)
12 Dec | 2004 DNMAD: web-based diagnosis and normalization for microarray data. Vaquerizas, JM, Dopazo, J, Díaz-Uriarte, R . Bioinformatics - 20 (18) : 3656-3658 (PMID: 15247094) (doi:10.1093/bioinformatics/bth401)
1 Dec | 2004 Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization. Meléndez, B, Díaz-Uriarte, R , Cuadros, M, Martínez-Ramírez, A, Fernández-Piqueras, J, Dopazo, A, Cigudosa, JC, Rivas, C, Dopazo, J, Martínez-Delgado, B, Benítez, J. Genes Chromosomes Cancer - 41 (4) : 353-365 (PMID: 15382261) (doi:10.1002/gcc.20105)
1 Aug | 2004 Expression profiling of T-cell lymphomas differentiates peripheral and lymphoblastic lymphomas and defines survival related genes. Martinez-Delgado, B, Meléndez, B, Cuadros, M, Alvarez, J, Castrillo, JM, 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. Clin Cancer Res - 10 (15) : 4971-4982 (PMID: 15297397) (doi:10.1158/1078-0432.CCR-04-0269)
1 Jul | 2004 New challenges in gene expression data analysis and the extended GEPAS. Herrero, J, Vaquerizas, JM, Al-Shahrour, F, Conde, L, Mateos, A, Díaz-Uriarte, JS , Dopazo, J. Nucleic Acids Res - 32 (Web Server issue) : W485-91 (PMID: 15215434) (doi:10.1093/nar/gkh421)
1 Mar | 2004 FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Al-Shahrour, F, Díaz-Uriarte, R , Dopazo, J. Bioinformatics - 20 (4) : 578-580 (PMID: 14990455) (doi:10.1093/bioinformatics/btg455)
1 Dec | 2003 An approach to inferring transcriptional regulation among genes from large-scale expression data. Herrero, J, Díaz-Uriarte, R , Dopazo, J. Comp. Funct. Genomics - 4 (1) : 148-154 (PMID: 18629097) (doi:10.1002/cfg.237)
15 Sep | 2003 Differential gene expression profile in endometrioid and nonendometrioid endometrial carcinoma: STK15 is frequently overexpressed and amplified in nonendometrioid carcinomas. 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, JC, Palacios, J. Cancer Res. - 63 (18) : 5697-5702 (PMID: 14522886)
1 Jul | 2003 GEPAS: A web-based resource for microarray gene expression data analysis. Herrero, J, Al-Shahrour, F, Díaz-Uriarte, R , Mateos, A, Vaquerizas, JM, Santoyo, J, Dopazo, J. Nucleic Acids Res. - 31 (13) : 3461-3467 (PMID: 12824345)
22 Mar | 2003 Gene expression data preprocessing. Herrero, J, Díaz-Uriarte, R , Dopazo, J. Bioinformatics - 19 (5) : 655-656 (PMID: 12651726)
7 Jun | 2001 Territorial intrusion risk and antipredator behaviour: a mathematical model. Díaz-Uriarte, R . Proc Biol Sci - 268 (1472) : 1165-1173 (PMID: 11375105) (doi:10.1098/rspb.2001.1637)
1 Sep | 1999 Polytomies and phylogenetically independent contrasts: examination of the bounded degrees of freedom approach. Garland, T, Díaz-Uriarte, R . Syst. Biol. - 48 (3) : 547-558 (PMID: 12066293)
1 Dec | 1998 Effects of branch length errors on the performance of phylogenetically independent contrasts. Díaz-Uriarte, R , Garland, T. Syst. Biol. - 47 (4) : 654-672 (PMID: 12066309)