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Papers and reprints Other publications Talks and presentations Courses about the R statistical computing system)

Publications, talks, and courses

Papers, preprints, and technical reports

Rueda OM, Rueda C, Diaz-Uriarte R. 2011. A Bayesian HMM with random effects and an unknown number of states for DNA copy number analysis. Journal of Statistical Computation and Simulation, in press. A previous version, as pdf.

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, in press.

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, in press.

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). Download the pdf. (A former version appeared as a preprint in COBRA Preprint Series, Article 42.).

Rueda OM, Diaz-Uriarte R. 2009. Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously. BMC Bioinformatics, 10:308. (This is the final, publised version of the former " Detection of Recurrent Copy Number Alterations in the Genome: a Probabilistic Approach2, available from COBRA Preprint Series, Article 43.).

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, in press.

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. 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.). This paper, and some other papers in this page, are part of Oscar Rueda's PhD thesis ("Statistical methods for the analysis of copy number alterations in the genome"). You can download his thesis here

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 - Ã‰cologie 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. (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., 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. and anhtml version.

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

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

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.pdf.

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. pdf.

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.pdf.

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". Samizdat Press.

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.

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.

Presentacion (pdf) del Master Biofisica, UAM, Madrid, 6-11-2008 to 13-11-2008.
Curso de doctorado Genomica Funcional: tecnicas de analisis 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 EspaÃ±ola de Biometria, 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 about biclustering. (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 Patologia Molecular. An updated version with similar focus is the talk I gave on July 2004 as part of the Master en Oncologia Molecular, at CNIO, and the Bioinformatics Master, and I presented a similar talk in Barcelona, at the Institute of Biomedical Research (Parque Cientifico de Barcelona).
Molecular signatures talk at the 2003 CNIO retreat. A similar talk was given at the October 2003ESF Workshop at CNIO. A similar (but much shorter) talk was given at theWye 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.

Teaching

Some of my presentations for classes. 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.

pdf para las clases de la asignatura Bioinformatica, del grado de Bioquimica de la UAM.
Class notes for course BM-13 (Bioinformatica Avanzada y Biologia de Sistemas, Programa Oficial de Posgrado en Bioquimica, Biologia Molecular, Biomedicina y Biotecnologia. UAM), for 2010-2011: Expression arrays: differential expression, classification and aCGH: segmentation, integration of expression data, etc.
Presentacion (pdf) para las clases del Master Biofisica, UAM, Madrid, 6-11-2008 to 13-11-2008.

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 estadistico R (Courses about the R statistical computing system) ---most of the material is in Spanish

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 astar.gz or WinZip format.

Voy a dar unos cursos sobre el uso y programación del sistema estadistico R. El primero a traves de la Red Tematica del CSIC de Bioinformatica. Otros en el CNIO (pagina accesible solo desde el CNIO).

Los objetivos y el temario estan disponibles aqui.
I taught another R course in Santander, at the Oceanographical Institute, in 2006. Here are the slides.
And another two, at Azti-Tecnalia, on July and October 2008. Here are the slides.
Class notes for a former (2009) crash R course, part of BM-1. These notes are based on the original ones by S. Ellner and B. Bolker. The Rnw file (Sweave) (plus the bib, png, sty, etc, etc) that generate the pdf, R code, etc, are available here; this should work in any reasonable LaTeX installation, at least under Linux/Unix (use the script "make.course.sh").
The pdf for a long course on R and statistics taught at the Master en Bioinformatica y Biologia Computacional, 2010-2011.(And no, we did not cover all of the material).
Together with Juan Ramon Gonzalez, at the CREAL, Barcelona, I have taught a couple of courses on advanced R programming during 2010 (one in May and one in December). Here is the pdf for the part I taught, Debugging and parallelization.

Ramon Diaz-Uriarte

Last modified: February 2011