Alfonso Valencia

Jose Manuel Rodriguez, Paolo Maietta, Iakes Ezkurdia, Alessandro Pietrelli, Jan-Jaap Wesselink, Gonzalo López, Alfonso Valencia, Michael L. Tress: APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Research 41(Database-Issue): 110-117 (2013)

Milana Frenkel-Morgenstern, Alessandro Gorohovski, Vincent Lacroix, Mark F. Rogers, Kristina Ibanez, Cesar Boullosa, Eduardo Andrés León, Asa Ben-Hur, Alfonso Valencia: ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Research 41(Database-Issue): 142-151 (2013)

Thilo Muth, Juan A. García-Martín, Antonio Rausell, David de Juan, Alfonso Valencia, Florencio Pazos: JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinformatics 28(4): 584-586 (2012)

Hanchuan Peng, Alex Bateman, Alfonso Valencia, Jonathan D. Wren: Bioimage informatics: a new category in Bioinformatics. Bioinformatics 28(8): 1057 (2012)

Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp: Mirroring co-evolving trees in the light of their topologies. Bioinformatics 28(9): 1202-1208 (2012)

Milana Frenkel-Morgenstern, Alfonso Valencia: Novel domain combinations in proteins encoded by chimeric transcripts. Bioinformatics 28(12): 67-74 (2012)

David Salgado, Martin Krallinger, Marc Depaule, Elodie Drula, Ashish V. Tendulkar, Florian Leitner, Alfonso Valencia, Christophe Marcelle: MyMiner: a web application for computer-assisted biocuration and text annotation. Bioinformatics 28(17): 2285-2287 (2012)

Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Reinhard Schneider, Alfonso Valencia: EnrichNet: network-based gene set enrichment analysis. Bioinformatics 28(18): 451-457 (2012)

Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans: Machine Reading of Biomedical Texts about Alzheimer's Disease. CLEF (Online Working Notes/Labs/Workshop) 2012

José M. G. Izarzugaza, Miguel Vazquez, Angela del Pozo, Alfonso Valencia: wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases. AIMM 2012

Vivekanand Samant, Arvind Hulgeri, Alfonso Valencia, Ashish V. Tendulkar: Accurate Demarcation of Protein Domain Linkers based on Structural Analysis of Linker Probable Region. CoRR abs/1211.5520 (2012)

Olli-P. Kallioniemi, Lodewyk F. A. Wessels, Alfonso Valencia: On the organization of bioinformatics core services in biology-based research institutes. Bioinformatics 27(10): 1345 (2011)

Dorota Herman, David Ochoa, David de Juan, Daniel Lopez, Alfonso Valencia, Florencio Pazos: Selection of organisms for the co-evolution-based study of protein interactions. BMC Bioinformatics 12: 363 (2011)

José M. G. Izarzugaza, Lisa E. M. Hopcroft, Anja Baresic, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia: Characterization of pathogenic germline mutations in human Protein Kinases. BMC Bioinformatics 12(S-4): S1 (2011)

Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu: Overview of the BioCreative III Workshop. BMC Bioinformatics 12(S-8): S1 (2011)

Gonzalo López, Paolo Maietta, Jose Manuel Rodriguez, Alfonso Valencia, Michael L. Tress: firestar - advances in the prediction of functionally important residues. Nucleic Acids Research 39(Web-Server-Issue): 235-241 (2011)

Miguel P. Rocha, Juan M. Corchado Rodríguez, Florentino Fdez-Riverola, Alfonso Valencia (Eds.): 5th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2011, April 6-8, 2011, Salamanca, Spain. Advances in Intelligent and Soft Computing 93, Springer 2011, isbn 978-3-642-19913-4

Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp: Mirroring co-evolving trees in the light of their topologies. CoRR abs/1110.5704 (2011)

Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Alfonso Valencia: TopoGSA: network topological gene set analysis. Bioinformatics 26(9): 1271-1272 (2010)

Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Alfonso Valencia: Extending pathways and processes using molecular interaction networks to analyse cancer genome data. BMC Bioinformatics 11: 597 (2010)

Martin Krallinger, Ashish V. Tendulkar, Florian Leitner, Andrew Chatr-aryamontri, Alfonso Valencia: The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions. BMC Bioinformatics 11(S-5): O1 (2010)

Florian Leitner, Scott A. Mardis, Martin Krallinger, Gianni Cesareni, Lynette Hirschman, Alfonso Valencia: An Overview of BioCreative II.5. IEEE/ACM Trans. Comput. Biology Bioinform. 7(3): 385-399 (2010)

José M. Fernández, Robert Hoffmann, Alfonso Valencia: iHOP Web Services Family. JBI 2010: 102-107

José M. Fernández, Alfonso Valencia: Bioinformatic Software Developments in Spain. JBI 2010: 108-120

Iakes Ezkurdia, Lisa Bartoli, Piero Fariselli, Rita Casadio, Alfonso Valencia, Michael L. Tress: Progress and challenges in predicting protein-protein interaction sites. Briefings in Bioinformatics 10(3): 233-246 (2009)

Jaume Bacardit, Michael Stout, Jonathan D. Hirst, Alfonso Valencia, Robert Elliott Smith, Natalio Krasnogor: Automated Alphabet Reduction for Protein Datasets. BMC Bioinformatics 10 (2009)

Martin Krallinger, José M. G. Izarzugaza, Carlos Rodríguez Penagos, Alfonso Valencia: Extraction of human kinase mutations from literature, databases and genotyping studies. BMC Bioinformatics 10(S-8): 1 (2009)

José M. G. Izarzugaza, Anja Baresic, Lisa E. M. McMillan, Corin Yeats, Andrew B. Clegg, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia: An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D. BMC Bioinformatics 10(S-8): 5 (2009)

Guillermo Carbajosa, Almudena Trigo, Alfonso Valencia, Ildefonso Cases: Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Research 37(Database-Issue): 598-602 (2009)

Eduardo Andrés León, Iakes Ezkurdia, Beatriz García, Alfonso Valencia, David de Juan: EcID. A database for the inference of functional interactions in E. coli. Nucleic Acids Research 37(Database-Issue): 629-635 (2009)

Martin Krallinger, Carlos Rodríguez Penagos, Ashish V. Tendulkar, Alfonso Valencia: PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucleic Acids Research 37(Web-Server-Issue): 160-165 (2009)

Johannes Starlinger, Florian Leitner, Alfonso Valencia, Ulf Leser: SOA-Based Integration of Text Mining Services. SERVICES I 2009: 99-106

Michael L. Tress, Jan-Jaap Wesselink, Adam Frankish, Gonzalo López, Nick Goldman, Ari Löytynoja, Tim Massingham, Fabio Pardi, Simon Whelan, Jennifer Harrow, Alfonso Valencia: Determination and validation of principal gene products. Bioinformatics 24(1): 11-17 (2008)

José M. G. Izarzugaza, David de Juan, Carles Pons, Florencio Pazos, Alfonso Valencia: Enhancing the prediction of protein pairings between interacting families using orthology information. BMC Bioinformatics 9 (2008)

Angela del Pozo, Florencio Pazos, Alfonso Valencia: Defining functional distances over Gene Ontology. BMC Bioinformatics 9 (2008)

Alfonso Valencia: Protein Interactions Extracted from Genomes and Papers. APBC 2008: 7

Zhang-Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu: iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology. BIBM 2008: 467-472

Alfonso Valencia: Text mining in genomics and systems biology. DTMBIO 2008: 3-4

Alfonso Valencia, Ildefonso Cases: Editorial. ISMB 2008

Alfonso Valencia, Alex Bateman: Editorial. Bioinformatics 23(2): 133 (2007)

Gonzalo López, Alfonso Valencia, Michael L. Tress: FireDB - a database of functionally important residues from proteins of known structure. Nucleic Acids Research 35(Database-Issue): 219-223 (2007)

Ildefonso Cases, David G. Pisano, Eduardo Andrés León, Angel Carro, José María Fernández, Gonzalo Gómez-López, Jose Manuel Rodriguez, Jaime F. Vera, Alfonso Valencia, Ana María Rojas: CARGO: a web portal to integrate customized biological information. Nucleic Acids Research 35(Web-Server-Issue): 16-20 (2007)

José M. Fernández, Robert Hoffmann, Alfonso Valencia: iHOP web services. Nucleic Acids Research 35(Web-Server-Issue): 21-26 (2007)

Gonzalo López, Alfonso Valencia, Michael L. Tress: firestar - prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Research 35(Web-Server-Issue): 573-577 (2007)

Victor de Lorenzo, Luis Serrano, Alfonso Valencia: Synthetic Biology: challenges ahead. Bioinformatics 22(2): 127-128 (2006)

Udo Hahn, Alfonso Valencia: Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005). Bioinformatics 22(6): 643-644 (2006)

Alfonso Valencia, Alex Bateman: Software patents in Bioinformatics. Bioinformatics 22(12): 1415 (2006)

Florencio Pazos, Antonio Rausell, Alfonso Valencia: Phylogeny-independent detection of functional residues. Bioinformatics 22(12): 1440-1448 (2006)

Alex Bateman, Alfonso Valencia: Structural genomics meets computational biology. Bioinformatics 22(19): 2319 (2006)

Trey Ideker, Alfonso Valencia: Bioinformatics in the human interactome project. Bioinformatics 22(24): 2973-2974 (2006)

Michael L. Tress, Domenico Cozzetto, Anna Tramontano, Alfonso Valencia: An analysis of the Sargasso Sea resource and the consequences for database composition. BMC Bioinformatics 7: 213 (2006)

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. Nucleic Acids Research 34(Web-Server-Issue): 110-115 (2006)

José M. G. Izarzugaza, David de Juan, Carles Pons, Juan A. G. Ranea, Alfonso Valencia, Florencio Pazos: TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Research 34(Web-Server-Issue): 315-319 (2006)

Alfonso Valencia, Alex Bateman: Increasing the Impact of Bioinformatics. Bioinformatics 21(1): 1-1 (2005)

Christian Blaschke, Alexander S. Yeh, Evelyn Camon, Marc E. Colosimo, Rolf Apweiler, Lynette Hirschman, Alfonso Valencia: Do you do text? Bioinformatics 21(23): 4199-4200 (2005)

Alex Bateman, Alfonso Valencia: An update from the Bioinformatics Editors. Bioinformatics 21(24): 4319 (2005)

Christian Blaschke, Eduardo Andrés León, Martin Krallinger, Alfonso Valencia: Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics 6(S-1) (2005)

Lynette Hirschman, Alexander S. Yeh, Christian Blaschke, Alfonso Valencia: Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics 6(S-1) (2005)

Martin Krallinger, Maria Padron, Alfonso Valencia: A sentence sliding window approach to extract protein annotations from biomedical articles. BMC Bioinformatics 6(S-1) (2005)

Robert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia: HCAD, closing the gap between breakpoints and genes. Nucleic Acids Research 33(Database-Issue): 511-513 (2005)

Florencio Pazos, David Guijas, Alfonso Valencia, Victor de Lorenzo: MetaRouter: bioinformatics for bioremediation. Nucleic Acids Research 33(Database-Issue): 588-592 (2005)

Osvaldo Graña, Volker A. Eyrich, Florencio Pazos, Burkhard Rost, Alfonso Valencia: EVAcon: a protein contact prediction evaluation service. Nucleic Acids Research 33(Web-Server-Issue): 347-351 (2005)

Manuel Gómez, Ramón Alonso-Allende, Florencio Pazos, Osvaldo Graña, David de Juan, Alfonso Valencia: Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories. T. Comp. Sys. Biology 1: 1-13 (2005)

Roderic Guigó, Federico Morán, Alfonso Valencia, Josep F. Abril: ECCB/JBI 2005. ECCB/JBI 2005: 2

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. ECCB/JBI 2005: 18

Robert Hoffmann, Alfonso Valencia: Implementing the iHOP concept for navigation of biomedical literature. ECCB/JBI 2005: 258

Michael L. Tress, Osvaldo Graña, Alfonso Valencia: SQUARE-determining reliable regions in sequence alignments. Bioinformatics 20(6): 974-975 (2004)

Alex Bateman, Alfonso Valencia: New Leadership for Bioinformatics. Bioinformatics 20(12): 1821 (2004)

José María Fernández, Alfonso Valencia: YAdumper: extracting and translating large information volumes from relational databases to structured flat files. Bioinformatics 20(15): 2455-2457 (2004)

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. BMC Bioinformatics 5: 91 (2004)

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. Nucleic Acids Research 32(Database-Issue): 452-455 (2004)

Eric W. Brown, William R. Hersh, Alfonso Valencia: SIGIR 2003 workshop on text analysis and search for bioinformatics. SIGIR Forum 38(2): 31-36 (2004)

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. CMSB 2004: 252-256

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. Spanish Bioinformatics Conference 2004: 70-71

José María Fernández, Alfonso Valencia: XML Databases, are Ready for Bioinformatics? Spanish Bioinformatics Conference 2004: 166-170

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. Bioinformatics 19(6): 717-726 (2003)

Alfonso Valencia: Meta, Metan and Cyber Servers. Bioinformatics 19(7): 795 (2003)

Christos A. Ouzounis, Alfonso Valencia: Early bioinformatics: the birth of a discipline - a personal view. Bioinformatics 19(17): 2176-2190 (2003)

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. Nucleic Acids Research 31(13): 3311-3315 (2003)

Christian Blaschke, Lynette Hirschman, Alfonso Valencia: Information extraction in molecular biology. Briefings in Bioinformatics 3(2): 154-165 (2002)

Burkhard Rost, Barry Honig, Alfonso Valencia: Bioinformatics in structural genomics - Editorial. Bioinformatics 18(7): 897 (2002)

Federico Abascal, Alfonso Valencia: Clustering of proximal sequence space for the identification of protein families. Bioinformatics 18(7): 908-921 (2002)

Alfonso Valencia: Bioinformatics: Biology by other means. Bioinformatics 18(12): 1551-1552 (2002)

Christian Blaschke, Alfonso Valencia: The Frame-Based Module of the SUISEKI Information Extraction System. IEEE Intelligent Systems 17(2): 14-20 (2002)

Javier Herrero, Alfonso Valencia, Joaquín Dopazo: A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 17(1): 126-136 (2001)

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. Bioinformatics 17(12): 1242-1243 (2001)

Russ B. Altman, Alfonso Valencia, Satoru Miyano, Shoba Ranganathan: Challenges for Intelligent Systems in Biology. IEEE Intelligent Systems 16(6): 14-20 (2001)

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. Bioinformatics 15(5): 391-412 (1999)

Florencio Pazos, Burkhard Rost, Alfonso Valencia: A platform for integrating threading results with protein family analyses. Bioinformatics 15(12): 1062-1063 (1999)

Christian Blaschke, Miguel A. Andrade, Christos A. Ouzounis, Alfonso Valencia: Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions. ISMB 1999: 60-67

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. Bioinformatics 14(5): 439-451 (1998)

Javier Tamames, Christos A. Ouzounis, Georg Casari, Chris Sander, Alfonso Valencia: EUCLID: automatic classification of proteins in functional classes by their database annotations. Bioinformatics 14(6): 542-543 (1998)

Miguel A. Andrade, Alfonso Valencia: Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. Bioinformatics 14(7): 600-607 (1998)

Miguel A. Andrade, Georg Casari, Chris Sander, Alfonso Valencia: Classification of protein families and detection of the determinant residues with an improved self-organizing map. Biological Cybernetics 76(6): 441-450 (1997)

Florencio Pazos, O. Olmea, Alfonso Valencia: A graphical interface for correlated mutations and other protein structure prediction methods. Computer Applications in the Biosciences 13(3): 319-321 (1997)

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. Computer Applications in the Biosciences 13(4): 481-483 (1997)

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. BCEC 1997: 132-145

Miguel A. Andrade, Alfonso Valencia: Automatic Annotation for Biological Sequences by Etraction of Keywords from MEDLINE Abstracts: Development of a Prototype System. ISMB 1997: 25-32

Terry Gaasterland, Peter D. Karp, Kevin Karplus, Christos A. Ouzounis, Chris Sander, Alfonso Valencia (Eds.): Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece, June 21-26, 1997. AAAI 1997, isbn 1-57735-022-7

Christos A. Ouzounis, Alfonso Valencia, Javier Tamames, Peer Bork, Chris Sander: The Functional Composition of Living Machines as a Design Principle for Artificial Organisms. ECAL 1995: 843-851

Michael Scharf, Reinhard Schneider, Georg Casari, Peer Bork, Alfonso Valencia, Christos A. Ouzounis, Chris Sander: GeneQuiz: A Workbench for Sequence Analysis. ISMB 1994: 348-353