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Publications, talks, and courses

Papers, preprints, and technical reports

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.

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., López, 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 Díaz-Uriarte, R. 2007. Flexible and accurate detection of genomic copy-number changes from aCGH. PLoS Computational Biology, 3(6): e122. Preprint + supplementary material. (This is a revised and much improved version of "A flexible statistical method for detecting genomic copy-number changes using Hidden Markov Models with Reversible Jump Markov Chain Monte Carlo. ", COBRA Preprint Series. Article 9.).

Rodríguez, A., Villuendas, R., Yáñez, L., Gómez, M. E., Díaz-Uriarte, 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., 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., Alibés, 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., Díaz-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.

Alibés, A., Yankilevich, P., Cañada, A., and Díaz-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. Díaz-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.

Alibés, A., Morrissey, E. R., Cañada, A., Rueda, O. M., Casado, D., Yankilevich, P., and Díaz-Uriarte, R. 2006. Asterias: a parallelized web-based suite for the analysis of expression and aCGH data. Cancer Informatics, 2 :1-9.

Díaz-Uriarte, R., Alvarez de Andrés, S. 2006. Gene selection and classification of microarray data using random forest. BMC Bioinformatics, 2006, 7:3. (The original tech.report had a somewhat different title "Variable selection from random forests: application to gene expression data"). 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., Díaz-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.

Meléndez, B., Martínez-Delgado, B., Cuadros, M., Fernández, V., Díaz-Uriarte, R., Benítez, 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 Andrés, S., Díaz-Uriarte, R., Osorio, A., Barrosa, A., Paz, M.F., Honrado, E., Rodríguez, R., Urioste, M., Valle, L., Diez, O., Cigudosa, J. C., Dopazo, J., Esteller, M., Benítez, 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

Díaz-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. and an html version.

Díaz-Uriarte, R. 2004. Molecular signatures from gene expression data. Bioinformatics Unit Technical Reports number 004, available here or from arXiv.

Vaquerizas, J., Dopazo, J., & Díaz-Uriarte, R. 2004. DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics, 20: 3656-3658. Older ms.

Meléndez, B., Díaz-Uriarte, R., Martínez-Ramírez, A., Fernández-Piqueras, J., Rivas, C., Dopazo, J., Martínez-Delgado, B., Benítez, 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., Meléndez, B., Cuadros, M., Alvarez, J., Castrillo, J.M., Ruiz de la Parte, A., Mollejo, M., Bellas, C., Diaz-Uriarte, R., Lombardía, L., Al-Shahrour, F., Domínguez, 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., Díaz-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., Díaz-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. pdf.

Díaz-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. pdf.

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. 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, Á., Santoyo, J., Díaz-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. pdf.

Herrero, J., Al-Shahrour, F., Díaz-Uriarte, R., Mateos, Á., 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., Díaz-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., Díaz-Uriarte, R & Dopazo, J. 2003. Gene Expression Data Preprocessing. Bioinformatics, 19: 655-656.

Díaz-Uriarte, R. 2002. Incorrect analysis of crossover trials in animal behaviour research. Animal Behaviour, 63: 815-822. pdf.

Díaz-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.

Díaz-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., & Díaz-Uriarte, R. 1999. Polytomies and independent contrasts: an examination of the bounded degrees of freedom approach. Systematic Biology, 48: 547-558.

Díaz-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., & Díaz-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., & Díaz-Uriarte, R. 1997. Covariation of reproductive traits of lacertid lizards: a comparative study. The American Naturalist, 149: 91-111.

Díaz-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.

Díaz, J. A., Díaz-Uriarte, R., Rodríguez, 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

Díaz-Uriarte, R. 2001. "The analysis of cross-over trials in animal behavior experiments: review and guide to the statistical literature". Samizdat Press.

Díaz-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 Díaz-Uriarte, 1999; chapter 3 as Díaz-Uriarte, 2001 (the math model paper); chapter 4 as Díaz-Uriarte, 2002; and chapter 5 as Díaz-Uriarte, 2001 ---the Samizdat press book).

Díaz-Uriarte, R., and Díez, I. 1985. Las Aves Urbanas. Ediciones Penthalon.

Talks and presentations

Please note: all this talks have a copyright holder (myself). Unless otherwise stated, they are all under a Creative Commons license. So feel free to use them, etc. But, please, give credit where credit is due.

Curso de doctorado Genómica Funcional: técnicas de análisis masivos de datos, Madrid, 17-01-2008.
Developing web-based and parallelized biostatistics/bioinformatics applications: ADaCGH as a case example. I gave this talk at the Statistical Computing 2007, Schloss (Germany) workshop, and a very similar one at the Statistics for Biomolecular Data Integration and Modeling, 2007, Ascona (Switzerland) and the ERCIM WG on Computing and Statistics kick-off meeting, 2007, Geneva (Switzerland).
Analysis of aCGH data: statistical models and computational challenges, a talk at the Computational Biology Group Meeting from CNIO
Introduction to biostatistics: differentially expressed genes and classification/prediction of disease status/prognosis from microarray data, a class given at the Molecular Oncology Master, 2007, CNIO, Madrid, Spain.
Asterias: an example of using R in a web-based bioinformatics suite of tools, a mini-talk given at useR 2006.
An applied statistician in microarray and genomics worlds: Review and reflections , invited talk at the X Conferencia Española de Biometría, Oviedo, Spain, 26-05-2005.
Variable selection from random forests: application to gene expression data., talk at the 5th Annual Spanish Bioinformatics Conference, Barcelona, Spain, December 2004.
Plaid models et al (beware, a 7.7 MB download!), given on January 2004 at the System's Biology seminar at CNIO. (Includes discussion of Plaid, COSA ---Clustering on subsets of attributes---, xMotif, SAMBA, Cheng and Church, PRM, and a few others).
Searching for prognostic factors: review and admonitions given on November 2003 at CNIO as part of the II Ciclo Curso Patología Molecular. An updated version with similar focus is the talk I gave on July 2004 as part of the Master en Oncología Molecular, at CNIO, and the Bioinformatics Master, and I presented a similar talk in Barcelona, at the Institute of Biomedical Research (Parque Científico de Barcelona).
Molecular signatures talk at the 2003 CNIO retreat. A similar talk was given at the October 2003 ESF Workshop at CNIO. A similar (but much shorter) talk was given at the Wye workshop on statistical analysis of gene expression data (if that link does not work, try this older one).
Use of GO Terms to Understand the Biological Significance of Microarray Differential Gene Expression Data, with J. Dopazo, a presentation given in November 2002 at CAMDA 02.

Courses

I've taught some courses for CNIO and a some masters programs (Bioinformatics, Computational Biology, Oncology) and other instructional programs. The most relevant presentations are above.

Cursos sobre el sistema estadístico R (Courses about the R statistical computing system)

The following is a course taught in Spanish. The slides themselves are in Spanish, but the comments to the code and other files are in English. You can download them as tar.gz or WinZip format.

Voy a dar unos cursos sobre el uso y programación del sistema estadístico R. El primero a traves de la Red Temática del CSIC de Bioinformática. Otros en el CNIO (página accesible sólo desde el CNIO).

Los objetivos y el temario están disponibles aquí.

Puedes descargar el material para el curso, incluyendo la presentación (en pdf), la presentación para ser impresa (en formato "4 slides por página", y sin efectos dinámicos ---fichero curso-R.4.pdf), ficheros de configuración para XEmacs, y algo de código en R. Dos formatos, tar.gz y WinZip. Es muy conveniente que imprimas la presentación (el fichero curso-R.4.pdf) antes de venir al curso. Además, es muy recomendable que eches un vistazo a la presentación para estar seguro de que el curso es lo que esperas que sea.

I taught another R course in Santander, at the Oceanographical Institute, in 2006. Here are the slides.

Ramón Díaz-Uriarte

Last modified: March 2008