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Alfonso Valencia: [Publications] [Author Rank by year] [Co-authors] [Prefers] [Cites] [Cited by]

Publications of Author

  1. Florencio Pazos, Luis Sánchez-Pulido, Juan A. Garcia-Ranca, Miguel A. Andrade, Silvia Atrian, Alfonso Valencia
    Comparative Analysis of Different Methods for the Detection of Specificity Regions in Protein Families. [Citation Graph (0, 0)][DBLP]
    BCEC, 1997, pp:132-145 [Conf]
  2. Florencio Pazos, David Guijas, Manuel J. Gomez, Almudena Trigo, Victor de Lorenzo, Alfonso Valencia
    The Biodegradation Network, a New Scenario for Computational Systems Biology Research. [Citation Graph (0, 0)][DBLP]
    CMSB, 2004, pp:252-256 [Conf]
  3. Christos A. Ouzounis, Alfonso Valencia, Javier Tamames, Peer Bork, Chris Sander
    The Functional Composition of Living Machines as a Design Principle for Artificial Organisms. [Citation Graph (0, 0)][DBLP]
    ECAL, 1995, pp:843-851 [Conf]
  4. Roderic Guigó, Federico Morán, Alfonso Valencia, Josep F. Abril
    ECCB/JBI 2005. [Citation Graph (0, 0)][DBLP]
    ECCB/JBI, 2005, pp:2- [Conf]
  5. Robert Hoffmann, Alfonso Valencia
    Implementing the iHOP concept for navigation of biomedical literature. [Citation Graph (0, 0)][DBLP]
    ECCB/JBI, 2005, pp:258- [Conf]
  6. David de Juan, Mario Mellado, José Miguel Rodríguez-Frade, Patricia Hernanz-Falcón, Antonio Serrano, Antonio del Sol, Alfonso Valencia, Carlos Martínez-A, Ana María Rojas
    A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors. [Citation Graph (0, 0)][DBLP]
    ECCB/JBI, 2005, pp:18- [Conf]
  7. Miguel A. Andrade, Alfonso Valencia
    Automatic Annotation for Biological Sequences by Etraction of Keywords from MEDLINE Abstracts: Development of a Prototype System. [Citation Graph (0, 0)][DBLP]
    ISMB, 1997, pp:25-32 [Conf]
  8. Christian Blaschke, Miguel A. Andrade, Christos A. Ouzounis, Alfonso Valencia
    Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions. [Citation Graph (0, 0)][DBLP]
    ISMB, 1999, pp:60-67 [Conf]
  9. Michael Scharf, Reinhard Schneider, Georg Casari, Peer Bork, Alfonso Valencia, Christos A. Ouzounis, Chris Sander
    GeneQuiz: A Workbench for Sequence Analysis. [Citation Graph (0, 0)][DBLP]
    ISMB, 1994, pp:348-353 [Conf]
  10. José María Fernández, Alfonso Valencia
    XML Databases, are Ready for Bioinformatics? [Citation Graph (0, 0)][DBLP]
    Spanish Bioinformatics Conference, 2004, pp:166-170 [Conf]
  11. Ana María Rojas, Luis Sánchez-Pulido, Agnes Fütterer, Karel H. M. van Wely, Carlos Martínez-A, Alfonso Valencia
    Bioinformatic Analyses of the Dio Family of Proteins. [Citation Graph (0, 0)][DBLP]
    Spanish Bioinformatics Conference, 2004, pp:70-71 [Conf]
  12. Christian Blaschke, Lynette Hirschman, Alfonso Valencia
    Information extraction in molecular biology. [Citation Graph (0, 0)][DBLP]
    Briefings in Bioinformatics, 2002, v:3, n:2, pp:154-165 [Journal]
  13. Federico Abascal, Alfonso Valencia
    Clustering of proximal sequence space for the identification of protein families. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2002, v:18, n:7, pp:908-921 [Journal]
  14. Miguel A. Andrade, N. P. Brown, Christophe Leroy, S. Hörsch, Antoine de Daruvar, C. Reich, A. Franchini, Javier Tamames, Alfonso Valencia, Christos A. Ouzounis, Chris Sander
    Automated genome sequence analysis and annotation. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1999, v:15, n:5, pp:391-412 [Journal]
  15. Miguel A. Andrade, Georg Casari, Antoine de Daruvar, Chris Sander, Reinhard Schneider, Javier Tamames, Alfonso Valencia, Christos A. Ouzounis
    Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. [Citation Graph (0, 0)][DBLP]
    Computer Applications in the Biosciences, 1997, v:13, n:4, pp:481-483 [Journal]
  16. Miguel A. Andrade, Alfonso Valencia
    Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1998, v:14, n:7, pp:600-607 [Journal]
  17. Alex Bateman, Alfonso Valencia
    New Leadership for Bioinformatics. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:12, pp:1821- [Journal]
  18. Alex Bateman, Alfonso Valencia
    An update from the Bioinformatics Editors. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2005, v:21, n:24, pp:4319- [Journal]
  19. Ioannis Iliopoulos, Sophia Tsoka, Miguel A. Andrade, Anton J. Enright, Mark Carroll, Patrick Poullet, Vassilis J. Promponas, Theodore Liakopoulos, Giorgos Palaios, Claude Pasquier, Stavros J. Hamodrakas, Javier Tamames, Asutosh T. Yagnik, Anna Tramontano, Damien Devos, Christian Blaschke, Alfonso Valencia, David Brett, David Martin, Christophe Leroy, Isidore Rigoutsos, Chris Sander, Christos A. Ouzounis
    Evaluation of annotation strategies using an entire genome sequence. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2003, v:19, n:6, pp:717-726 [Journal]
  20. Christian Blaschke, Alexander S. Yeh, Evelyn Camon, Marc Colosimo, Rolf Apweiler, Lynette Hirschman, Alfonso Valencia
    Do you do text? [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2005, v:21, n:23, pp:4199-4200 [Journal]
  21. Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, András Fiser, Florencio Pazos, Alfonso Valencia, Andrej Sali, Burkhard Rost
    EVA: continuous automatic evaluation of protein structure prediction servers. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2001, v:17, n:12, pp:1242-1243 [Journal]
  22. José María Fernández, Alfonso Valencia
    YAdumper: extracting and translating large information volumes from relational databases to structured flat files. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:15, pp:2455-2457 [Journal]
  23. Udo Hahn, Alfonso Valencia
    Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005). [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:6, pp:643-644 [Journal]
  24. Javier Herrero, Alfonso Valencia, Joaquín Dopazo
    A hierarchical unsupervised growing neural network for clustering gene expression patterns. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2001, v:17, n:1, pp:126-136 [Journal]
  25. Victor de Lorenzo, Luis Serrano, Alfonso Valencia
    Synthetic Biology: challenges ahead. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:2, pp:127-128 [Journal]
  26. Christos A. Ouzounis, Alfonso Valencia
    Early bioinformatics: the birth of a discipline - a personal view. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2003, v:19, n:17, pp:2176-2190 [Journal]
  27. Florencio Pazos, O. Olmea, Alfonso Valencia
    A graphical interface for correlated mutations and other protein structure prediction methods. [Citation Graph (0, 0)][DBLP]
    Computer Applications in the Biosciences, 1997, v:13, n:3, pp:319-321 [Journal]
  28. Florencio Pazos, Antonio Rausell, Alfonso Valencia
    Phylogeny-independent detection of functional residues. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:12, pp:1440-1448 [Journal]
  29. Florencio Pazos, Burkhard Rost, Alfonso Valencia
    A platform for integrating threading results with protein family analyses. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1999, v:15, n:12, pp:1062-1063 [Journal]
  30. Burkhard Rost, Barry Honig, Alfonso Valencia
    Bioinformatics in structural genomics - Editorial. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2002, v:18, n:7, pp:897- [Journal]
  31. Javier Tamames, Christos A. Ouzounis, Georg Casari, Chris Sander, Alfonso Valencia
    EUCLID: automatic classification of proteins in functional classes by their database annotations. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1998, v:14, n:6, pp:542-543 [Journal]
  32. Oswaldo Trelles, Miguel A. Andrade, Alfonso Valencia, Emilio L. Zapata, José María Carazo
    Computational space reduction and parallelization of a new clustering approach for large groups of sequences. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1998, v:14, n:5, pp:439-451 [Journal]
  33. Michael L. Tress, Osvaldo Graña, Alfonso Valencia
    SQUARE-determining reliable regions in sequence alignments. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:6, pp:974-975 [Journal]
  34. Alfonso Valencia
    Bioinformatics: Biology by other means. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2002, v:18, n:12, pp:1551-1552 [Journal]
  35. Alfonso Valencia
    Meta, Metan and Cyber Servers. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2003, v:19, n:7, pp:795- [Journal]
  36. Alfonso Valencia, Alex Bateman
    Increasing the Impact of Bioinformatics. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2005, v:21, n:1, pp:1-1 [Journal]
  37. Alfonso Valencia, Alex Bateman
    Software patents in Bioinformatics. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:12, pp:1415- [Journal]
  38. Trey Ideker, Alfonso Valencia
    Bioinformatics in the human interactome project. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:24, pp:2973-2974 [Journal]
  39. Alex Bateman, Alfonso Valencia
    Structural genomics meets computational biology. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:19, pp:2319- [Journal]
  40. Alfonso Valencia, Alex Bateman
    Editorial. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2007, v:23, n:2, pp:133- [Journal]
  41. Luis Sánchez-Pulido, Ana María Rojas, Karel H. M. van Wely, Carlos Martínez-A, Alfonso Valencia
    SPOC: A widely distributed domain associated with cancer, apoptosis and transcription. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2004, v:5, n:, pp:91- [Journal]
  42. Michael L. Tress, Domenico Cozzetto, Anna Tramontano, Alfonso Valencia
    An analysis of the Sargasso Sea resource and the consequences for database composition. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2006, v:7, n:, pp:213- [Journal]
  43. Christian Blaschke, Alfonso Valencia
    The Frame-Based Module of the SUISEKI Information Extraction System. [Citation Graph (0, 0)][DBLP]
    IEEE Intelligent Systems, 2002, v:17, n:2, pp:14-20 [Journal]
  44. Russ B. Altman, Alfonso Valencia, Satoru Miyano, Shoba Ranganathan
    Challenges for Intelligent Systems in Biology. [Citation Graph (0, 0)][DBLP]
    IEEE Intelligent Systems, 2001, v:16, n:6, pp:14-20 [Journal]
  45. Henning Hermjakob, Luisa Montecchi-Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra E. Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso Valencia, Hanah Margalit, John Armstrong, Amos Bairoch, Gianni Cesareni, David James Sherman, Rolf Apweiler
    IntAct: an open source molecular interaction database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2004, v:32, n:Database-Issue, pp:452-455 [Journal]
  46. Ingrid Y. Y. Koh, Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, Narayanan Eswar, Osvaldo Graña, Florencio Pazos, Alfonso Valencia, Andrej Sali, Burkhard Rost
    EVA: evaluation of protein structure prediction servers. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2003, v:31, n:13, pp:3311-3315 [Journal]
  47. Robert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia
    HCAD, closing the gap between breakpoints and genes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:511-513 [Journal]
  48. Florencio Pazos, David Guijas, Alfonso Valencia, Victor de Lorenzo
    MetaRouter: bioinformatics for bioremediation. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:588-592 [Journal]
  49. Osvaldo Graña, Volker A. Eyrich, Florencio Pazos, Burkhard Rost, Alfonso Valencia
    EVAcon: a protein contact prediction evaluation service. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Web-Server-Issue, pp:347-351 [Journal]
  50. Angel Carro, Michael L. Tress, David de Juan, Florencio Pazos, Pedro Lopez-Romero, Antonio del Sol, Alfonso Valencia, Ana María Rojas
    TreeDet: a web server to explore sequence space. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2006, v:34, n:Web-Server-Issue, pp:110-115 [Journal]
  51. José M. G. Izarzugaza, David Juan, Carles Pons, Juan A. G. Ranea, Alfonso Valencia, Florencio Pazos
    TSEMA: interactive prediction of protein pairings between interacting families. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2006, v:34, n:Web-Server-Issue, pp:315-319 [Journal]
  52. Gonzalo Lopez, Alfonso Valencia, Michael L. Tress
    FireDB - a database of functionally important residues from proteins of known structure. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2007, v:35, n:Database-Issue, pp:219-223 [Journal]
  53. Eric W. Brown, William R. Hersh, Alfonso Valencia
    SIGIR 2003 workshop on text analysis and search for bioinformatics. [Citation Graph (0, 0)][DBLP]
    SIGIR Forum, 2004, v:38, n:2, pp:31-36 [Journal]
  54. Manuel Gómez, Ramón Alonso-Allende, Florencio Pazos, Osvaldo Graña, David Juan, Alfonso Valencia
    Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories. [Citation Graph (0, 0)][DBLP]
    T. Comp. Sys. Biology, 2005, v:1, n:, pp:1-13 [Journal]

  55. Protein Interactions Extracted from Genomes and Papers. [Citation Graph (, )][DBLP]


  56. Text mining in genomics and systems biology. [Citation Graph (, )][DBLP]


  57. Editorial. [Citation Graph (, )][DBLP]


  58. iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology. [Citation Graph (, )][DBLP]


  59. SOA-Based Integration of Text Mining Services. [Citation Graph (, )][DBLP]


  60. Classification of protein families and detection of the determinant residues with an improved self-organizing map. [Citation Graph (, )][DBLP]


  61. Progress and challenges in predicting protein-protein interaction sites. [Citation Graph (, )][DBLP]


  62. Determination and validation of principal gene products. [Citation Graph (, )][DBLP]


  63. TopoGSA: network topological gene set analysis. [Citation Graph (, )][DBLP]


  64. Defining functional distances over Gene Ontology. [Citation Graph (, )][DBLP]


  65. Enhancing the prediction of protein pairings between interacting families using orthology information. [Citation Graph (, )][DBLP]


  66. Overview of BioCreAtIvE: critical assessment of information extraction for biology. [Citation Graph (, )][DBLP]


  67. Evaluation of BioCreAtIvE assessment of task 2. [Citation Graph (, )][DBLP]


  68. A sentence sliding window approach to extract protein annotations from biomedical articles. [Citation Graph (, )][DBLP]


  69. Automated Alphabet Reduction for Protein Datasets. [Citation Graph (, )][DBLP]


  70. An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D. [Citation Graph (, )][DBLP]


  71. Extraction of human kinase mutations from literature, databases and genotyping studies. [Citation Graph (, )][DBLP]


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