Miguel A Andrade

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. pmc NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria
    Miguel A Andrade
    European Molecular Biology Laboratory, Meyerhofstr, 1, 69117 Heidelberg, Germany
    Genome Biol 3:RESEARCH0047. 2002
  2. pmc Systematic association of genes to phenotypes by genome and literature mining
    Jan O Korbel
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Biol 3:e134. 2005
  3. ncbi request reprint A protocol for the update of references to scientific literature in biological databases
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Appl Bioinformatics 2:189-91. 2003
  4. pmc Update on XplorMed: A web server for exploring scientific literature
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Meyerhofstr 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3866-8. 2003
  5. ncbi request reprint Global analysis of bacterial transcription factors to predict cellular target processes
    Tobias Doerks
    EMBL, 69117 Heidelberg, Meyerhofstr 1, Germany
    Trends Genet 20:126-31. 2004
  6. pmc Information extraction from full text scientific articles: where are the keywords?
    Parantu K Shah
    Biocomputing, European Molecular Biology Laboratory, Heidelberg, Germany
    BMC Bioinformatics 4:20. 2003
  7. pmc Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization
    Emmanuel G Reynaud
    Cell Biology and Cell Biophysics Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    BMC Biol 3:21. 2005
  8. ncbi request reprint Exploring MEDLINE abstracts with XplorMed
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Drugs Today (Barc) 38:381-9. 2002
  9. ncbi request reprint Computing fuzzy associations for the analysis of biological literature
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Biotechniques 32:1380-2, 1384-5. 2002
  10. ncbi request reprint Association of genes to genetically inherited diseases using data mining
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Meyerhofstr 1, Heidelberg 69012, Germany
    Nat Genet 31:316-9. 2002

Collaborators

Detail Information

Publications18

  1. pmc NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria
    Miguel A Andrade
    European Molecular Biology Laboratory, Meyerhofstr, 1, 69117 Heidelberg, Germany
    Genome Biol 3:RESEARCH0047. 2002
    ..To find potential targets for drugs active against pathogenic bacteria, we have searched all completely sequenced genomes of pathogenic bacteria for genes relevant for iron transport...
  2. pmc Systematic association of genes to phenotypes by genome and literature mining
    Jan O Korbel
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Biol 3:e134. 2005
    ..Among the clusters, we observe an enrichment of pathogenicity-related associations, suggesting that the approach reveals many novel genes likely to play a role in infectious diseases...
  3. ncbi request reprint A protocol for the update of references to scientific literature in biological databases
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Appl Bioinformatics 2:189-91. 2003
    ..Human experts found the references that the algorithm scored highly were more relevant to the database entry than those scored lowly, suggesting that the algorithm was useful...
  4. pmc Update on XplorMed: A web server for exploring scientific literature
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Meyerhofstr 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3866-8. 2003
    ..Here we describe new features added to XplorMed during the last 2 years (http://www.bork.embl-heidelberg.de/xplormed/)...
  5. ncbi request reprint Global analysis of bacterial transcription factors to predict cellular target processes
    Tobias Doerks
    EMBL, 69117 Heidelberg, Meyerhofstr 1, Germany
    Trends Genet 20:126-31. 2004
    ....
  6. pmc Information extraction from full text scientific articles: where are the keywords?
    Parantu K Shah
    Biocomputing, European Molecular Biology Laboratory, Heidelberg, Germany
    BMC Bioinformatics 4:20. 2003
    ..Several questions arise as to whether the effort of scanning full text articles is worthy, or whether the information that can be extracted from the different sections of an article can be relevant...
  7. pmc Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization
    Emmanuel G Reynaud
    Cell Biology and Cell Biophysics Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    BMC Biol 3:21. 2005
    ..Therefore, they are ideal tools for comparative genomic studies aimed at understanding how aspects of biological complexity such as cellular compartmentalization evolved...
  8. ncbi request reprint Exploring MEDLINE abstracts with XplorMed
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Drugs Today (Barc) 38:381-9. 2002
    ..XplorMed is available http://www.bork. embl-heidelberg.de/xplormed...
  9. ncbi request reprint Computing fuzzy associations for the analysis of biological literature
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Biotechniques 32:1380-2, 1384-5. 2002
    ..Those relations are used to derive ensembles of related words and their associated subsets of abstracts. The algorithm can be used publicly at http:// www.bork.embl-heidelberg.de/xplormed/...
  10. ncbi request reprint Association of genes to genetically inherited diseases using data mining
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Meyerhofstr 1, Heidelberg 69012, Germany
    Nat Genet 31:316-9. 2002
    ..The scoring also indicates that for some diseases, the chance of identifying the underlying gene is higher...
  11. ncbi request reprint Evaluation of annotation strategies using an entire genome sequence
    Ioannis Iliopoulos
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Bioinformatics 19:717-26. 2003
    ..In order to quantify the accuracy and reproducibility of function assignments on a genome-wide scale, we have re-annotated the entire genome sequence of Chlamydia trachomatis (serovar D), in a collaborative manner...
  12. pmc Ranking the whole MEDLINE database according to a large training set using text indexing
    Brian P Suomela
    Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth Rd, Ottawa, Ontario K1H 8L6, Canada
    BMC Bioinformatics 6:75. 2005
    ..This report describes a method that does this ranking using the differences in word content between MEDLINE entries related to a topic and the whole of MEDLINE, in a computational time appropriate for an article search query engine...
  13. pmc G2D: a tool for mining genes associated with disease
    Carolina Perez-Iratxeta
    Ontario Genomics Innovation Centre, Ottawa Health Research Institute, ON K1H 8L6, Ottawa, Canada
    BMC Genet 6:45. 2005
    ..We previously developed an algorithm to prioritize genes on a chromosomal region according to their possible relation to an inherited disease using a combination of data mining on biomedical databases and gene sequence analysis...
  14. ncbi request reprint The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism
    Alexei Savchenko
    Ontario Center for Structural Proteomics, University of Toronto, Canada
    J Biol Chem 280:19213-20. 2005
    ..Our observations, taken together with previous reports, support the conclusion that SBDS and its homologues play a role in RNA metabolism...
  15. pmc ACRATA: a novel electron transfer domain associated to apoptosis and cancer
    Luis Sanchez-Pulido
    Protein Design Group, Centro Nacional de Biotecnologia CNB CSIC, Cantoblanco, Madrid, E 28049, Spain
    BMC Cancer 4:98. 2004
    ..g. STEAP, STAMP1, TSAP6), have been identified in Golgi and cytoplasmic membranes. The exact function of these proteins remains unknown...
  16. ncbi request reprint Worldwide scientific publishing activity
    Carolina Perez-Iratxeta
    Science 297:519. 2002
  17. ncbi request reprint Gene annotation from scientific literature using mappings between keyword systems
    Antonio J Pérez
    University of Malaga, Facultad de Ciencias, Departmento de Genetica, Group of Bioinformatics, Campus Universitario de Teatinos, 29071 Malaga, Spain
    Bioinformatics 20:2084-91. 2004
    ..However, the association of keywords to genes or protein sequences is a difficult process that ultimately implies examination of the literature related to a gene...
  18. pmc The way we write
    Rebecca Netzel
    Institute of Translation and Interpreting, University of Heidelberg, Germany
    EMBO Rep 4:446-51. 2003