J M Carazo

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 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
  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 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
  5. 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
  6. 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
  7. ncbi Organising multi-dimensional biological image information: the BioImage Database
    J M Carazo
    Centro Nacional de Biotecnologia CSIC, Campus Univ Autónoma, E 28049 Madrid, Spain
    Nucleic Acids Res 27:280-3. 1999
  8. ncbi The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel
    M Barcena
    Centro Nacional de Biotecnologia CSIC, Campus Universidad Autonoma de Madrid, 28049 Madrid, Spain
    EMBO J 20:1462-8. 2001
  9. ncbi Automatic particle selection from electron micrographs using machine learning techniques
    C O S Sorzano
    Unidad de Biocomputación, Centro Nacional de Biotecnologia CSIC, Campus Universidad Autónoma s n, 28049 Cantoblanco, Madrid, Spain
    J Struct Biol 167:252-60. 2009
  10. ncbi Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function
    C O S Sorzano
    Unidad de Biocomputación, Centro Nacional de Biotecnologia CSIC, Campus Universidad Autónoma s n, 28049 Cantoblanco, Madrid, Spain
    J Struct Biol 160:249-62. 2007

Collaborators

Detail Information

Publications26

  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 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...
  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 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
    ....
  5. 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...
  6. 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...
  7. ncbi Organising multi-dimensional biological image information: the BioImage Database
    J M Carazo
    Centro Nacional de Biotecnologia CSIC, Campus Univ Autónoma, E 28049 Madrid, Spain
    Nucleic Acids Res 27:280-3. 1999
    ..Two sister home pages of BioImage can be accessed at http://www. bioimage.org and http://www-embl.bioimage.org..
  8. ncbi The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel
    M Barcena
    Centro Nacional de Biotecnologia CSIC, Campus Universidad Autonoma de Madrid, 28049 Madrid, Spain
    EMBO J 20:1462-8. 2001
    ..The central channel of the helicase is almost occluded near the end opposite to DnaC, such that even single-stranded DNA could not pass through. We propose that the DnaB N-terminal domain is located at this face...
  9. ncbi Automatic particle selection from electron micrographs using machine learning techniques
    C O S Sorzano
    Unidad de Biocomputación, Centro Nacional de Biotecnologia CSIC, Campus Universidad Autónoma s n, 28049 Cantoblanco, Madrid, Spain
    J Struct Biol 167:252-60. 2009
    ..This package has been made publicly available in the open-source package Xmipp...
  10. ncbi Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function
    C O S Sorzano
    Unidad de Biocomputación, Centro Nacional de Biotecnologia CSIC, Campus Universidad Autónoma s n, 28049 Cantoblanco, Madrid, Spain
    J Struct Biol 160:249-62. 2007
    ..Our algorithm is capable of estimating the envelope of the CTF which is absolutely needed for the correction of the CTF amplitude changes...
  11. ncbi Mapping and fuzzy classification of macromolecular images using self-organizing neural networks
    A Pascual
    Centro Nacional de Biotecnologia CSIC, Universidad Autonoma, Madrid, Spain
    Ultramicroscopy 84:85-99. 2000
    ..Experimental results prove that this new technique is suitable for working with large, high-dimensional and noisy data sets and, thus, it is proposed to be used as a classification tool in electron microscopy...
  12. ncbi A multiresolution approach to orientation assignment in 3D electron microscopy of single particles
    C O S Sorzano
    Escuela Politecnica Superior, Universidad San Pablo CEU, Campus Urb, Madrid, Spain
    J Struct Biol 146:381-92. 2004
    ..Furthermore, this multiresolution approach is combined with a novel orientation selection strategy. Results obtained from computer simulations as well as experimental data encourage the use of this approach...
  13. ncbi Designing and executing scientific workflows with a programmable integrator
    M Chagoyen
    Biocomputing Unit, Centro Nacional de Biotecnologia, Madrid 28049, Spain
    Bioinformatics 20:2092-100. 2004
    ..In most cases there is no standard solution for workflow design and execution and tailored scripting mechanisms are implemented in a case by case basis...
  14. ncbi XMIPP: a new generation of an open-source image processing package for electron microscopy
    C O S Sorzano
    Unidad de Biocomputación, Centro Nacional de Biotecnologia CSIC, Campus Universidad Autónoma s n, 28049 Cantoblanco, Madrid, Spain
    J Struct Biol 148:194-204. 2004
    ..Moreover, by focusing on those developments that distinguish Xmipp from other packages available, we illustrate its added value to the electron microscopy community...
  15. ncbi pH-controlled quaternary states of hexameric DnaB helicase
    L E Donate
    Campus de Cantoblanco, Centro Nacional de Biotecnologia CSIC, Madrid, 28049, Spain
    J Mol Biol 303:383-93. 2000
    ..Structural consequences of this quaternary polymorphism, as well as its functional implications for helicase activity, are discussed...
  16. ncbi Integrating electron microscopy information into existing Distributed Annotation Systems
    J R Macias
    Unidad de Biocomputación, Centro Nacional de Biotecnologia CSIC, Campus de Cantoblanco UAM, C Darwin 3, 28049 Madrid, Spain
    J Struct Biol 158:205-13. 2007
    ....
  17. ncbi Two-step interferometry by a regularized optical flow algorithm
    J Vargas
    Biocomputing Unit, Centro Nacional de Biotecnologia CSIC, Madrid, Spain
    Opt Lett 36:3485-7. 2011
    ..The proposed technique has been applied to simulated and experimental interferograms obtaining satisfactory results. A complete MATLAB software package is provided in [http://goo.gl/Snnz7]...
  18. ncbi Nonsmooth nonnegative matrix factorization (nsNMF)
    Alberto Pascual-Montano
    Computer Architecture and System Engineering Department, Facultad de Ciencias Fisicas, Universidad Complutense, Madrid, Spain
    IEEE Trans Pattern Anal Mach Intell 28:403-15. 2006
    ....
  19. ncbi Normalizing projection images: a study of image normalizing procedures for single particle three-dimensional electron microscopy
    C O S Sorzano
    Biocomputing Unit, National Center of Biotechnology (CSIC, , 28049 Cantoblanco, Madrid, Spain
    Ultramicroscopy 101:129-38. 2004
    ..We finally show that the use of the different normalization methods affects the reconstruction quality, providing guidance on the choice of normalization procedures...
  20. ncbi Transfer function restoration in 3D electron microscopy via iterative data refinement
    C O S Sorzano
    , Universidad San Pablo-CEU, , s/n, 28668 Boadilla del Monte, Madrid, Spain
    Phys Med Biol 49:509-22. 2004
    ..In this work we make use of the iterative data refinement (IDR) technique to ameliorate the effect of the CTF. It is demonstrated that the approach can be successfully applied to noisy data...
  21. ncbi A novel neural network technique for analysis and classification of EM single-particle images
    A Pascual-Montano
    , , Madrid, 28049, Spain
    J Struct Biol 133:233-45. 2001
    ....
  22. ncbi The effect of overabundant projection directions on 3D reconstruction algorithms
    C O Sorzano
    , , Madrid, 28049, Spain
    J Struct Biol 133:108-18. 2001
    ....
  23. ncbi Three-dimensional reconstructions from cryoelectron microscopy images reveal an intimate complex between helicase DnaB and its loading partner DnaC
    C San Martin
    Centro Nacional de Biotecnologia, Universidad Autonoma de Madrid, Cantoblanco, 28049, Madrid, Spain
    Structure 6:501-9. 1998
    ..It was hoped that the structures would provide insight into the mechanisms of helicase activity...
  24. ncbi A structural model for the Escherichia coli DnaB helicase based on electron microscopy data
    M C San Martin
    Centro Nacional de Biotecnología C S I C, Universidad Autonoma de Madrid, Cantoblanco, Spain
    J Struct Biol 114:167-76. 1995
    ..There is a channel through the particle that appears fully open on both sides. Based on these results, a structural model for the oligomer is presented, and functional implications are considered...