Pedro Carmona-Saez

Summary

Country: Spain

Publications

  1. ncbi GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists
    Pedro Carmona-Saez
    Biocomputing Unit, National Center of Biotechnology CNB CSIC, C Darwin 3, Campus Universidad Autonoma de Madrid, 28049 Madrid, Spain
    Genome Biol 8:R3. 2007
  2. ncbi bioNMF: a versatile tool for non-negative matrix factorization in biology
    Alberto Pascual-Montano
    Computer Architecture Department, Facultad de Ciencias Fisicas, Universidad Complutense de Madrid, 28040, Spain
    BMC Bioinformatics 7:366. 2006
  3. ncbi Integrated analysis of gene expression by Association Rules Discovery
    Pedro Carmona-Saez
    Biocomputing Unit, National Center for Biotechnology CNB CSIC, Cantoblanco, 28049, Madrid, Spain
    BMC Bioinformatics 7:54. 2006
  4. ncbi Biclustering of gene expression data by Non-smooth Non-negative Matrix Factorization
    Pedro Carmona-Saez
    Biocomputing Unit, National Center of Biotechnology, Campus Universidad Autonoma de Madrid, 28049 Spain
    BMC Bioinformatics 7:78. 2006
  5. ncbi MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures
    Miguel Vazquez
    Software Engineering Department, Facultad de Informatica, Universidad Complutense de Madrid, Madrid, Spain
    Nucleic Acids Res 38:W228-32. 2010
  6. ncbi GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information
    Ruben Nogales-Cadenas
    Computer Architecture Department, Complutense University of Madrid, Madrid, Spain
    Nucleic Acids Res 37:W317-22. 2009
  7. ncbi Discovering semantic features in the literature: a foundation for building functional associations
    Monica Chagoyen
    Biocomputing Unit, Centro Nacional de Biotecnologia CSIC, Madrid, Spain
    BMC Bioinformatics 7:41. 2006
  8. ncbi A literature-based similarity metric for biological processes
    Monica Chagoyen
    Biocomputing Unit, Centro Nacional de Biotecnologia CSIC, Madrid, Spain
    BMC Bioinformatics 7:363. 2006
  9. ncbi ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data
    Federico Abascal
    Biocomputing Unit, National Center of Biotechnology CSIC, Madrid, Spain
    Bioinformatics 24:1208-9. 2008
  10. ncbi SENT: semantic features in text
    Miguel Vazquez
    Software Engineering Department, Complutense University and Biocomputing Unit, National Center for Biotechnology, CNB CSIC, Madrid, Spain
    Nucleic Acids Res 37:W153-9. 2009

Collaborators

Detail Information

Publications12

  1. ncbi GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists
    Pedro Carmona-Saez
    Biocomputing Unit, National Center of Biotechnology CNB CSIC, C Darwin 3, Campus Universidad Autonoma de Madrid, 28049 Madrid, Spain
    Genome Biol 8:R3. 2007
    ..GENECODIS is publicly available at http://genecodis.dacya.ucm.es/...
  2. ncbi bioNMF: a versatile tool for non-negative matrix factorization in biology
    Alberto Pascual-Montano
    Computer Architecture Department, Facultad de Ciencias Fisicas, Universidad Complutense de Madrid, 28040, Spain
    BMC Bioinformatics 7:366. 2006
    ....
  3. ncbi Integrated analysis of gene expression by Association Rules Discovery
    Pedro Carmona-Saez
    Biocomputing Unit, National Center for Biotechnology CNB CSIC, Cantoblanco, 28049, Madrid, Spain
    BMC Bioinformatics 7:54. 2006
    ..However, most of the current approaches to analyze microarray datasets are mainly focused on the analysis of experimental data, and external biological information is incorporated as a posterior process...
  4. ncbi Biclustering of gene expression data by Non-smooth Non-negative Matrix Factorization
    Pedro Carmona-Saez
    Biocomputing Unit, National Center of Biotechnology, Campus Universidad Autonoma de Madrid, 28049 Spain
    BMC Bioinformatics 7:78. 2006
    ..These patterns may provide clues about the main biological processes associated to different physiological states...
  5. ncbi MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures
    Miguel Vazquez
    Software Engineering Department, Facultad de Informatica, Universidad Complutense de Madrid, Madrid, Spain
    Nucleic Acids Res 38:W228-32. 2010
    ..The application is freely available at http://marq.dacya.ucm.es...
  6. ncbi GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information
    Ruben Nogales-Cadenas
    Computer Architecture Department, Complutense University of Madrid, Madrid, Spain
    Nucleic Acids Res 37:W317-22. 2009
    ..In addition, GeneCodis can now be accessed through a public SOAP web services interface, enabling users to perform analysis from their own scripts and workflows. The application is freely available at http://genecodis.dacya.ucm.es...
  7. ncbi Discovering semantic features in the literature: a foundation for building functional associations
    Monica Chagoyen
    Biocomputing Unit, Centro Nacional de Biotecnologia CSIC, Madrid, Spain
    BMC Bioinformatics 7:41. 2006
    ..Therefore, the development of automated text mining tools to assist in such interpretation is one of the main challenges in current bioinformatics research...
  8. ncbi A literature-based similarity metric for biological processes
    Monica Chagoyen
    Biocomputing Unit, Centro Nacional de Biotecnologia CSIC, Madrid, Spain
    BMC Bioinformatics 7:363. 2006
    ..In this line, methods to bridge the gap between the abstract definitions of cellular processes in current schemes and the interlinked nature of biological networks are required...
  9. ncbi ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data
    Federico Abascal
    Biocomputing Unit, National Center of Biotechnology CSIC, Madrid, Spain
    Bioinformatics 24:1208-9. 2008
    ..For a given list of yeast genes ChIPCodis determines which combinations of TFs are significantly over-represented in a series of environmental conditions. Availability: http://chipcodis.dacya.ucm.es..
  10. ncbi SENT: semantic features in text
    Miguel Vazquez
    Software Engineering Department, Complutense University and Biocomputing Unit, National Center for Biotechnology, CNB CSIC, Madrid, Spain
    Nucleic Acids Res 37:W153-9. 2009
    ..This tool provides a user-friendly interface via a web site, and a programmatic access via a SOAP web server. SENT is freely accessible at http://sent.dacya.ucm.es...
  11. ncbi A free radical-generating system induces the cholesterol biosynthesis pathway: a role in Alzheimer's disease
    María Recuero
    Departamento de Biologia Molecular and Centro de Biologia Molecular Severo Ochoa, Cantoblanco, 28049 Madrid, Spain
    Aging Cell 8:128-39. 2009
    ..Gene expression analysis followed by genetic association studies indicates a possible link among oxidative stress, cholesterol metabolism and AD...
  12. ncbi SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays
    Miguel A Anton
    CEIT and TECNUN, University of Navarra, San Sebastian, Spain
    Genome Biol 9:R46. 2008
    ..The results presented here show its robustness and accuracy for real and simulated data...