Alfonso Valencia

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Alfonso Valencia
Alfonso Valencia speaking at ISMB/ECCB 2013
Alfonso Valencia speaking at ISMB/ECCB 2013.
Alma mater
Academic advisors Chris Sander[2][3][4]
Known for BioCreative[5][6][7][8]
Notable awards

Alfonso Valencia is a Spanish biologist, the current director of the Spanish National Bioinformatics Institute and the Structural and Computational Biology Group leader at the Spanish National Cancer Research Centre (CNIO).[9] As of 2014, he is also President-elect of the International Society for Computational Biology. His research is focused on the study of protein families and their interaction networks.[1][10][11]


Valencia studied biology at the Complutense University of Madrid, training in population genetics and biophysics.[11] In 1987 he was a Visiting Scientist at the American Red Cross Laboratory.[12] He received his PhD in molecular biology in 1988 from the Autonomous University of Madrid.[10] From 1989 to 1994 he was a Postdoctoral Fellow in the laboratory of Chris Sander at the European Molecular Biology Laboratory (EMBL) in Heidelberg, studying the evolution of protein function using sequence- and structure-based approaches.[12][13]


In 1994 Valencia formed the Protein Design Group at the Spanish National Center for Biotechnology (CNB).[10] He is currently leader of the Structural and Computational Biology Group at CNIO. The research focus of this group is mainly on the understanding of how cancer progresses, using a combination of molecular and evolutionary approaches. The main research goals are to analyse the function and interactions of cancer-related proteins and to develop novel computational methods to analyse, represent and interpret cancer genome information.[14]

As of 2015, Valencia has published over 300 peer reviewed papers,[1][15][16] which have been cited more than 12,000 times,[11] in scientific journals including Nature,[17][18][19] PNAS,[2] Nucleic Acids Research,[20][21] the Journal of Molecular Biology,[22][23][24] Bioinformatics,[25][26][27][28] Genome Biology,[6][7][29][30] PLOS Computational Biology,[31] PLOS Biology,[32] Nature Genetics,[33][34] Nature Biotechnology,[8][35] Genome Research,[36] Biochemistry,[3] Current Opinion in Structural Biology,[37] Nature Structural Biology,[4] Trends in Genetics[38] and the Intelligent Systems for Molecular Biology conference.[39]

Awards and Honours[edit]

Valencia was appointed Research Professor at the CNB in 2005.[10] He was a founding member of the International Society for Computational Biology (ISCB) and was honoured as an ISCB Fellow in 2010.[40] Valencia has also served as ISCB Vice President and in 2013 was appointed President-elect; in 2015, he will replace Burkhard Rost as ISCB President.[11] He is also an elected member of the European Molecular Biology Organization (EMBO).[41]

Valencia participates in several international consortia, such as ENCODE,[17][32][36] the International Cancer Genome Consortium, the International Rare Diseases Research Consortium (IRDiRC), the International Human Epigenomics Consortium[35] and the European Life-sciences Infrastructure for Biological Information (ELIXIR).[11]

He is currently co-executive editor of the journal Bioinformatics and serves on the editorial board of The EMBO Journal and EMBO reports.[10]


  1. ^ a b c Alfonso Valencia's publications indexed by Google Scholar, a service provided by Google
  2. ^ a b Bork, P; Sander, C; Valencia, A (1992). "An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins". Proceedings of the National Academy of Sciences of the United States of America 89 (16): 7290–4. Bibcode:1992PNAS...89.7290B. doi:10.1073/pnas.89.16.7290. PMC 49695. PMID 1323828. 
  3. ^ a b Valencia, A.; Chardin, P.; Wittinghofer, A.; Sander, C. (1991). "The ras protein family: Evolutionary tree and role of conserved amino acids". Biochemistry 30 (19): 4637–4648. doi:10.1021/bi00233a001. 
  4. ^ a b Casari, G; Sander, C; Valencia, A (1995). "A method to predict functional residues in proteins". Nature Structural Biology 2 (2): 171–8. doi:10.1038/nsb0295-171. PMID 7749921. 
  5. ^ Hirschman, L.; Yeh, A.; Blaschke, C.; Valencia, A. (2005). "Overview of BioCreAtIvE: Critical assessment of information extraction for biology". BMC Bioinformatics 6: S1. doi:10.1186/1471-2105-6-S1-S1. PMC 1869002. PMID 15960821. 
  6. ^ a b Krallinger, M; Morgan, A; Smith, L; Leitner, F; Tanabe, L; Wilbur, J; Hirschman, L; Valencia, A (2008). "Evaluation of text-mining systems for biology: Overview of the Second Bio Creative community challenge". Genome Biology. 9 Suppl 2: S1. doi:10.1186/gb-2008-9-s2-s1. PMC 2559980. PMID 18834487. 
  7. ^ a b Krallinger, M; Leitner, F; Rodriguez-Penagos, C; Valencia, A (2008). "Overview of the protein-protein interaction annotation extraction task of Bio Creative II". Genome Biology. 9 Suppl 2: S4. doi:10.1186/gb-2008-9-s2-s4. PMC 2559988. PMID 18834495. 
  8. ^ a b Leitner, F; Chatr-Aryamontri, A; Mardis, S. A.; Ceol, A; Krallinger, M; Licata, L; Hirschman, L; Cesareni, G; Valencia, A (2010). "The FEBS Letters/Bio Creative II.5 experiment: Making biological information accessible". Nature Biotechnology 28 (9): 897–9. doi:10.1038/nbt0910-897. PMID 20829821. 
  9. ^ "Structural Computational Biology Group: Personnel -". Centro Nacional de Investigaciones Oncológicas. Retrieved 7 January 2014. 
  10. ^ a b c d e "Alfonso Valencia -". Centro Nacional de Investigaciones Oncológicas. Archived from the original on 2014-07-20. 
  11. ^ a b c d e "Alfonso Valencia, President-Elect of the ISCB" (PDF). Archived from the original (PDF) on 2014-01-10. 
  12. ^ a b "Keynote-Details". ISMB/ECCB 2011. International Society for Computational Biology. Retrieved 7 January 2014. 
  13. ^ "Alfonso Valencia - EMBRACE". Retrieved 10 January 2014. 
  14. ^ "Structural Computational Biology Group: Overview -". Centro Nacional de Investigaciones Oncológicas. Retrieved 10 January 2014. 
  15. ^ Alfonso Valencia publications from Europe PubMed Central
  16. ^ Alfonso Valencia's publications indexed by the Scopus bibliographic database, a service provided by Elsevier. (subscription required)
  17. ^ a b ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346. 
  18. ^ Puente, X. S.; Pinyol, M; Quesada, V; Conde, L; Ordóñez, G. R.; Villamor, N; Escaramis, G; Jares, P; Beà, S; González-Díaz, M; Bassaganyas, L; Baumann, T; Juan, M; López-Guerra, M; Colomer, D; Tubío, J. M.; López, C; Navarro, A; Tornador, C; Aymerich, M; Rozman, M; Hernández, J. M.; Puente, D. A.; Freije, J. M.; Velasco, G; Gutiérrez-Fernández, A; Costa, D; Carrió, A; Guijarro, S; et al. (2011). "Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia". Nature 475 (7354): 101–5. doi:10.1038/nature10113. PMC 3322590. PMID 21642962. 
  19. ^ International Cancer Genome Consortium; Hudson, T. J.; Anderson, W; Artez, A; Barker, A. D.; Bell, C; Bernabé, R. R.; Bhan, M. K.; Calvo, F; Eerola, I; Gerhard, D. S.; Guttmacher, A; Guyer, M; Hemsley, F. M.; Jennings, J. L.; Kerr, D; Klatt, P; Kolar, P; Kusada, J; Lane, D. P.; Laplace, F; Youyong, L; Nettekoven, G; Ozenberger, B; Peterson, J; Rao, T. S.; Remacle, J; Schafer, A. J.; Shibata, T; et al. (2010). "International network of cancer genome projects". Nature 464 (7291): 993–8. Bibcode:2010Natur.464..993T. doi:10.1038/nature08987. PMC 2902243. PMID 20393554. 
  20. ^ Hermjakob, H.; Montecchi‐Palazzi, L.; Lewington, C.; Mudali, S.; Kerrien, S.; Orchard, S.; Vingron, M.; Roechert, B.; Roepstorff, P.; Valencia, A.; Margalit, H.; Armstrong, J.; Bairoch, Amos; Cesareni, G.; Sherman, D.; Apweiler, R. (2004). "IntAct: An open source molecular interaction database". Nucleic Acids Research 32 (90001): 452D. doi:10.1093/nar/gkh052. PMC 308786. PMID 14681455. 
  21. ^ Van Ham, R. C.; Kamerbeek, J; Palacios, C; Rausell, C; Abascal, F; Bastolla, U; Fernández, J. M.; Jiménez, L; Postigo, M; Silva, F. J.; Tamames, J; Viguera, E; Latorre, A; Valencia, A; Morán, F; Moya, A (2003). "Reductive genome evolution in Buchnera aphidicola". Proceedings of the National Academy of Sciences 100 (2): 581–6. Bibcode:2003PNAS..100..581V. doi:10.1073/pnas.0235981100. PMC 141039. PMID 12522265. 
  22. ^ Pazos, F; Helmer-Citterich, M; Ausiello, G; Valencia, A (1997). "Correlated mutations contain information about protein-protein interaction". Journal of Molecular Biology 271 (4): 511–23. doi:10.1006/jmbi.1997.1198. PMID 9281423. 
  23. ^ Jensen, L. J.; Gupta, R; Blom, N; Devos, D; Tamames, J; Kesmir, C; Nielsen, H; Staerfeldt, H. H.; Rapacki, K; Workman, C; Andersen, C. A.; Knudsen, S; Krogh, A; Valencia, A; Brunak, S (2002). "Prediction of human protein function from post-translational modifications and localization features". Journal of Molecular Biology 319 (5): 1257–65. doi:10.1016/S0022-2836(02)00379-0. PMID 12079362. 
  24. ^ Olmea, O; Rost, B; Valencia, A (1999). "Effective use of sequence correlation and conservation in fold recognition". Journal of Molecular Biology 293 (5): 1221–39. doi:10.1006/jmbi.1999.3208. PMID 10547297. 
  25. ^ Herrero, J; Valencia, A; Dopazo, J (2001). "A hierarchical unsupervised growing neural network for clustering gene expression patterns". Bioinformatics (Oxford, England) 17 (2): 126–36. doi:10.1093/bioinformatics/17.2.126. PMID 11238068. 
  26. ^ Hoffmann, R; Valencia, A (2005). "Implementing the iHOP concept for navigation of biomedical literature". Bioinformatics. 21 Suppl 2: ii252–8. doi:10.1093/bioinformatics/bti1142. PMID 16204114. 
  27. ^ Peng, Hanchuan; Bateman, Alex; Valencia, Alfonso; Wren, Jonathan D. (2012). "Bioimage informatics: A new category in Bioinformatics". Bioinformatics 28 (8): 1057. doi:10.1093/bioinformatics/bts111. PMC 3324521. PMID 22399678. 
  28. ^ Bateman, Alex; Valencia, Alfonso (2006). "Structural genomics meets computational biology". Bioinformatics 22 (19): 2319. doi:10.1093/bioinformatics/btl426. PMID 17032684. 
  29. ^ Juncker, A. S.; Jensen, L. J.; Pierleoni, A; Bernsel, A; Tress, M. L.; Bork, P; von Heijne, G; Valencia, A; Ouzounis, C. A.; Casadio, R; Brunak, S (2009). "Sequence-based feature prediction and annotation of proteins". Genome Biology 10 (2): 206. doi:10.1186/gb-2009-10-2-206. PMC 2688272. PMID 19226438. 
  30. ^ Baudot, A; Gómez-López, G; Valencia, A (2009). "Translational disease interpretation with molecular networks". Genome Biology 10 (6): 221. doi:10.1186/gb-2009-10-6-221. PMC 2718486. PMID 19591646. 
  31. ^ Vazquez, M; de la Torre, V; Valencia, A (2012). "Chapter 14: Cancer genome analysis". PLoS Computational Biology 8 (12): e1002824. Bibcode:2012PLSCB...8E2824V. doi:10.1371/journal.pcbi.1002824. PMC 3531315. PMID 23300415. 
  32. ^ a b ENCODE Project Consortium (2011). Becker PB, ed. "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)". PLOS Biology 9 (4): e1001046. doi:10.1371/journal.pbio.1001046. PMC 3079585. PMID 21526222.  open access publication - free to read
  33. ^ Hoffmann, R; Valencia, A (2004). "A gene network for navigating the literature". Nature Genetics 36 (7): 664. doi:10.1038/ng0704-664. PMID 15226743. 
  34. ^ Quesada, V; Conde, L; Villamor, N; Ordóñez, G. R.; Jares, P; Bassaganyas, L; Ramsay, A. J.; Beà, S; Pinyol, M; Martínez-Trillos, A; López-Guerra, M; Colomer, D; Navarro, A; Baumann, T; Aymerich, M; Rozman, M; Delgado, J; Giné, E; Hernández, J. M.; González-Díaz, M; Puente, D. A.; Velasco, G; Freije, J. M.; Tubío, J. M.; Royo, R; Gelpí, J. L.; Orozco, M; Pisano, D. G.; Zamora, J; et al. (2011). "Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia". Nature Genetics 44 (1): 47–52. doi:10.1038/ng.1032. PMID 22158541. 
  35. ^ a b Adams, D; Altucci, L; Antonarakis, S. E.; Ballesteros, J; Beck, S; Bird, A; Bock, C; Boehm, B; Campo, E; Caricasole, A; Dahl, F; Dermitzakis, E. T.; Enver, T; Esteller, M; Estivill, X; Ferguson-Smith, A; Fitzgibbon, J; Flicek, P; Giehl, C; Graf, T; Grosveld, F; Guigo, R; Gut, I; Helin, K; Jarvius, J; Küppers, R; Lehrach, H; Lengauer, T; Lernmark, Åke; et al. (2012). "BLUEPRINT to decode the epigenetic signature written in blood". Nature Biotechnology 30 (3): 224–6. doi:10.1038/nbt.2153. PMID 22398613. 
  36. ^ a b Harrow, J; Frankish, A; Gonzalez, J. M.; Tapanari, E; Diekhans, M; Kokocinski, F; Aken, B. L.; Barrell, D; Zadissa, A; Searle, S; Barnes, I; Bignell, A; Boychenko, V; Hunt, T; Kay, M; Mukherjee, G; Rajan, J; Despacio-Reyes, G; Saunders, G; Steward, C; Harte, R; Lin, M; Howald, C; Tanzer, A; Derrien, T; Chrast, J; Walters, N; Balasubramanian, S; Pei, B; et al. (2012). "GENCODE: The reference human genome annotation for the ENCODE Project". Genome Research 22 (9): 1760–74. doi:10.1101/gr.135350.111. PMC 3431492. PMID 22955987. 
  37. ^ Valencia, A; Pazos, F (2002). "Computational methods for the prediction of protein interactions". Current Opinion in Structural Biology 12 (3): 368–73. doi:10.1016/s0959-440x(02)00333-0. PMID 12127457. 
  38. ^ Devos, D; Valencia, A (2001). "Intrinsic errors in genome annotation". Trends in genetics : TIG 17 (8): 429–31. doi:10.1016/s0168-9525(01)02348-4. PMID 11485799. 
  39. ^ Blaschke, C; Andrade, M. A.; Ouzounis, C; Valencia, A (1999). "Automatic extraction of biological information from scientific text: Protein-protein interactions". Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology: 60–7. PMID 10786287. 
  40. ^ "ISCB Fellows". International Society for Computational Biology. Archived from the original on 2015-03-28. 
  41. ^ "Find an EMBO member". European Molecular Biology Organization.