Ramon Diaz-Uriarte

Summary

Publications

  1. pmc Asterias: a parallelized web-based suite for the analysis of expression and aCGH data
    Andreu Alibés
    Statistical Computing Team, Structural and Computational Biology Programme, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, Madrid, Spain
    Cancer Inform 3:1-9. 2007
  2. pmc CNVassoc: Association analysis of CNV data using R
    Isaac Subirana
    CIBER Epidemiology and Public Health, Barcelona, Spain
    BMC Med Genomics 4:47. 2011
  3. pmc 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
    Oscar M Rueda
    BMC Bioinformatics 8:394. 2007
  4. pmc SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data
    Ramon Diaz-Uriarte
    Statistical Computing Team, Structural Biology and Biocomputing Programme, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    BMC Bioinformatics 9:30. 2008
  5. pmc GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest
    Ramon Diaz-Uriarte
    Statistical Computing Team, Structural Biology and Biocomputing Programme, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    BMC Bioinformatics 8:328. 2007
  6. pmc ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data
    Ramon Diaz-Uriarte
    Structural Biology and Biocomputing Programme, Spanish National Cancer Center, Madrid, Spain
    PLoS ONE 2:e737. 2007
  7. pmc Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite
    Ramon Diaz-Uriarte
    Statistical Computing Team, Structural and Computational Biology Programme, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    Nucleic Acids Res 35:W75-80. 2007
  8. ncbi request reprint DNMAD: web-based diagnosis and normalization for microarray data
    Juan M Vaquerizas
    Bioinformatics Unit, CNIO, Spanish National Cancer Centre, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
    Bioinformatics 20:3656-8. 2004
  9. pmc GEPAS: A web-based resource for microarray gene expression data analysis
    Javier Herrero
    Bioinformatics Unit, Centro Nacional de Investigaciones Oncologicas, C Melchor Fernandez Almagro 3, 28029, Madrid, Spain
    Nucleic Acids Res 31:3461-7. 2003
  10. pmc IDconverter and IDClight: conversion and annotation of gene and protein IDs
    Andreu Alibés
    Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncologicas, Melchor Fernandez Almagro 3, 28029, Madrid, Spain
    BMC Bioinformatics 8:9. 2007

Collaborators

Detail Information

Publications20

  1. pmc Asterias: a parallelized web-based suite for the analysis of expression and aCGH data
    Andreu Alibés
    Statistical Computing Team, Structural and Computational Biology Programme, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, Madrid, Spain
    Cancer Inform 3:1-9. 2007
    ..The capability to send results between different applications, access to additional functional information, and parallelized computation make our suite unique and exploit features only available to web-based applications...
  2. pmc CNVassoc: Association analysis of CNV data using R
    Isaac Subirana
    CIBER Epidemiology and Public Health, Barcelona, Spain
    BMC Med Genomics 4:47. 2011
    ..The package includes functions for inferring copy number (CNV genotype calling), but can also accept copy number data generated by other algorithms (e.g. CANARY, CGHcall, IMPUTE)...
  3. pmc 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
    Oscar M Rueda
    BMC Bioinformatics 8:394. 2007
    ..ran the sampler for a severely insufficient number of iterations for a Markov Chain Monte Carlo-based method. Moreover, they did not use the appropriate reference level for the non-altered state...
  4. pmc SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data
    Ramon Diaz-Uriarte
    Statistical Computing Team, Structural Biology and Biocomputing Programme, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    BMC Bioinformatics 9:30. 2008
    ..Most of these methods, however, are not available to biomedical researchers, leading to many re-implementations from scratch of ad-hoc, and suboptimal, approaches with survival data...
  5. pmc GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest
    Ramon Diaz-Uriarte
    Statistical Computing Team, Structural Biology and Biocomputing Programme, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    BMC Bioinformatics 8:328. 2007
    ..Methodologically, such a tool would be of greater use if it incorporates state-of-the-art computational approaches and makes source code available...
  6. pmc ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data
    Ramon Diaz-Uriarte
    Structural Biology and Biocomputing Programme, Spanish National Cancer Center, Madrid, Spain
    PLoS ONE 2:e737. 2007
    ..One of the most common techniques to detect CNAs is array-based comparative genomic hybridization (aCGH). The availability of aCGH platforms and the need for identification of CNAs has resulted in a wealth of methodological studies...
  7. pmc Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite
    Ramon Diaz-Uriarte
    Statistical Computing Team, Structural and Computational Biology Programme, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    Nucleic Acids Res 35:W75-80. 2007
    ..The links and analysis of additional functional information, parallelization of computation and open-source availability of the code make Asterias a unique suite that can exploit features specific to web-based environments...
  8. ncbi request reprint DNMAD: web-based diagnosis and normalization for microarray data
    Juan M Vaquerizas
    Bioinformatics Unit, CNIO, Spanish National Cancer Centre, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
    Bioinformatics 20:3656-8. 2004
    ..This tool offers a user-friendly interface, and is completely integrated within the Gene Expression Pattern Analysis Suite (GEPAS). AVAILABILITY: The tool is accessible on-line at http://dnmad.bioinfo.cnio.es...
  9. pmc GEPAS: A web-based resource for microarray gene expression data analysis
    Javier Herrero
    Bioinformatics Unit, Centro Nacional de Investigaciones Oncologicas, C Melchor Fernandez Almagro 3, 28029, Madrid, Spain
    Nucleic Acids Res 31:3461-7. 2003
    ..On-line tutorials are available from our main web server (http://bioinfo.cnio.es)...
  10. pmc IDconverter and IDClight: conversion and annotation of gene and protein IDs
    Andreu Alibés
    Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncologicas, Melchor Fernandez Almagro 3, 28029, Madrid, Spain
    BMC Bioinformatics 8:9. 2007
    ..When the field of research is one such as microarray experiments, this number may be around 30,000...
  11. ncbi request reprint FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
    Fatima Al-Shahrour
    Bioinformatics Unit, Centro Nacional de Investigaciones Oncologicas CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
    Bioinformatics 20:578-80. 2004
    ....
  12. pmc PaLS: filtering common literature, biological terms and pathway information
    Andreu Alibés
    Statistical Computing Team, Structural and Computational Biology Programme, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    Nucleic Acids Res 36:W364-7. 2008
    ..Those descriptors among these four sources of information that are shared by more members of the list (or lists) are highlighted by PaLS...
  13. pmc Pomelo II: finding differentially expressed genes
    Edward R Morrissey
    Structural and Computational Biology Programme, Spanish National Cancer Center CNIO, Melchor FernA ndez Almagro 3, Madrid, 28029, Spain
    Nucleic Acids Res 37:W581-6. 2009
    ..The possibility of including additional covariates, parallelization of computation, open-source availability of the code and comprehensive testing suite make Pomelo II a unique tool...
  14. pmc Gene selection and classification of microarray data using random forest
    Ramon Diaz-Uriarte
    Bioinformatics Unit, Biotechnology Programme, Spanish National Cancer Centre CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    BMC Bioinformatics 7:3. 2006
    ..Thus, it is important to understand the performance of random forest with microarray data and its possible use for gene selection...
  15. pmc Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously
    Oscar M Rueda
    Structural and Computational Biology Programme, Spanish National Cancer Centre CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
    BMC Bioinformatics 10:308. 2009
    ....
  16. ncbi request reprint Genomic profiling of circulating plasma RNA for the analysis of cancer
    Manuel Collado
    Spanish National Cancer Research Centre CNIO, Madrid, Spain
    Clin Chem 53:1860-3. 2007
    ..The application of genomic profiling techniques to plasma RNA may allow the unbiased selection of cancer markers in the blood, but the informative value of genomic profiling of plasma RNA is currently unknown...
  17. pmc Flexible and accurate detection of genomic copy-number changes from aCGH
    Oscar M Rueda
    Structural and Computational Biology Programme, Spanish National Cancer Centre CNIO, Madrid, Spain
    PLoS Comput Biol 3:e122. 2007
    ..In summary, we provide a rigorous statistical framework for locating genes and chromosomal regions with CNAs with potential applications to cancer and other complex human diseases...
  18. pmc Identification of tumor-associated autoantigens for the diagnosis of colorectal cancer in serum using high density protein microarrays
    Ingrid Babel
    Centro de Investigaciones Biologicas Consejo Superior de Investigaciones Cientificas, Madrid, Spain
    Mol Cell Proteomics 8:2382-95. 2009
    ....
  19. ncbi request reprint Differential gene expression profile in endometrioid and nonendometrioid endometrial carcinoma: STK15 is frequently overexpressed and amplified in nonendometrioid carcinomas
    Gema Moreno-Bueno
    Laboratory of Breast and Gynaecological Cancer, Molecular Pathology Programme, Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
    Cancer Res 63:5697-702. 2003
    ....
  20. pmc RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions
    Oscar M Rueda
    Structural Biology and Biocomputing Programme, Spanish National Cancer Center CNIO, Madrid 28029, Spain
    Bioinformatics 25:1959-60. 2009
    ..Using these probabilites, recurrent regions (over sets of individuals) of copy number alteration can be found...