Alfonso Valencia

































Alfonso Valencia

Alfonso Valencia speaking at ISMB/ECCB 2013
Alfonso Valencia speaking at ISMB/ECCB 2013.

Alma mater


  • Complutense University of Madrid


  • Autonomous University of Madrid (PhD)
Known for
BioCreative[1][2][3][4]
Awards


  • EMBO member


  • ISCB Fellow (2010)
Scientific career
Fields


  • Computational biology

  • Bioinformatics


  • Cancer genomics

  • Text mining


  • Protein evolution[5]
Institutions


  • Spanish National Bioinformatics Institute

  • Spanish National Center for Biotechnology (CNB)

  • European Molecular Biology Laboratory (EMBL)

  • Spanish National Cancer Research Centre

  • Barcelona Supercomputing Center
Academic advisors
Chris Sander[6][7][8]


Alfonso Valencia is a Spanish biologist, ICREA Professor, current director of the Life Sciences department at Barcelona Supercomputing Center.[9] and of Spanish National Bioinformatics Institute (INB-ISCIII). From 2015-2018, he was President of the International Society for Computational Biology.[10] His research is focused on the study of biomedical systems with computational biology and bioinformatics approaches.[5]




Contents






  • 1 Education


  • 2 Research


  • 3 Awards and Honours


  • 4 References





Education


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.[13] 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][14]



Research


In 1994 Valencia formed the Protein Design Group at the Spanish National Center for Biotechnology (CNB).[13] He was leader of the Structural and Computational Biology Group at CNIO.[13] In 2006 he moved to the Spanish National Cancer Research Center (CNIO) as Director of the Structural Biology and Biocomputing programme.


Since 2016 he is ICREA Professor[15] and Director of the Life Sciences Department of the Barcelona Supercomputing Centre (BSC).[16][17]


As computational biologist, the focus of his work is the mechanistic understanding of biological systems, including cancer and other diseases, with a combination of Bioinformatics, Network Biology and Machine Learning approaches. His group has developed systems in the areas of protein structure prediction, protein interactions and protein networks, systems biology, text and data mining, with applications in epigenetic, cancer genomics [18] and disease comorbidity. All these actives converge into the general topic of Personalised Medicine, with particular interest in the interface with Artificial intelligence and High Performance Computing.


As of 2015[update], Valencia has published over 400 peer reviewed papers,[5][19][20] which have been cited more than 40,000 times,[11] in scientific journals including Nature,[21][22][23]PNAS,[6]Nucleic Acids Research,[24][25] the Journal of Molecular Biology,[26][27][28]Bioinformatics,[29][30][31][32]Genome Biology,[2][3][33][34]PLOS Computational Biology,[35]PLOS Biology,[36]Nature Genetics,[37][38]Nature Biotechnology,[4][39]Genome Research,[40]Biochemistry,[7]Current Opinion in Structural Biology,[41]Nature Structural Biology,[8]Trends in Genetics[42] and the Intelligent Systems for Molecular Biology conference.[43]



Awards and Honours


Valencia was appointed Research Professor at the CNB in 2005.[13] He was a founding member of the International Society for Computational Biology (ISCB) and was honoured as an ISCB Fellow in 2010.[44] Valencia has also served as ISCB Vice President and in 2013 was appointed President-elect.[11] From 2015-2018, he was President of the ISCB, succeeding Burkhard Rost. Valencia is Doctor Honoris cause of the Danish DTU and elected member of the European Molecular Biology Organization (EMBO).[45]


Valencia participates in several international consortia, such as Genecode / ENCODE,[21][36][40] the International Cancer Genome Consortium, the International Rare Diseases Research Consortium (IRDiRC), the International Human Epigenomics Consortium.[39] Valencia is Director of the Spanish National Bioinformatics Institute a platform of the ISCIII, the Spanish node of the European Life-sciences Infrastructure for Biological Information (ELIXIR).[11]


He is currently co-executive editor of the journal Bioinformatics, and member of the Editorial boards of eLIFE, FEBS Letters, PeerJ and F1000 Prime.



References





  1. ^ 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..mw-parser-output cite.citation{font-style:inherit}.mw-parser-output .citation q{quotes:"""""""'""'"}.mw-parser-output .citation .cs1-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/6/65/Lock-green.svg/9px-Lock-green.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .citation .cs1-lock-limited a,.mw-parser-output .citation .cs1-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/d/d6/Lock-gray-alt-2.svg/9px-Lock-gray-alt-2.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .citation .cs1-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/a/aa/Lock-red-alt-2.svg/9px-Lock-red-alt-2.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration{color:#555}.mw-parser-output .cs1-subscription span,.mw-parser-output .cs1-registration span{border-bottom:1px dotted;cursor:help}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/4/4c/Wikisource-logo.svg/12px-Wikisource-logo.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output code.cs1-code{color:inherit;background:inherit;border:inherit;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;font-size:100%}.mw-parser-output .cs1-visible-error{font-size:100%}.mw-parser-output .cs1-maint{display:none;color:#33aa33;margin-left:0.3em}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration,.mw-parser-output .cs1-format{font-size:95%}.mw-parser-output .cs1-kern-left,.mw-parser-output .cs1-kern-wl-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right,.mw-parser-output .cs1-kern-wl-right{padding-right:0.2em}


  2. ^ ab 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.


  3. ^ ab 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.


  4. ^ ab 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.


  5. ^ abc Alfonso Valencia publications indexed by Google Scholar


  6. ^ ab 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.


  7. ^ ab 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.


  8. ^ ab 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.


  9. ^ "El fichaje de Alfonso Valencia refuerza Barcelona como capital bioinformática". La Vanguardia. 2017-03-07.


  10. ^ "Past Officers and Directors". www.iscb.org. Retrieved 12 April 2018.


  11. ^ abcd "Alfonso Valencia, President-Elect of the ISCB" (PDF). Archived from the original (PDF) on 2014-01-10..


  12. ^ ab "Keynote-Details". ISMB/ECCB 2011. International Society for Computational Biology. Retrieved 7 January 2014.


  13. ^ abcd "Alfonso Valencia - cnio.es". Centro Nacional de Investigaciones Oncológicas. Archived from the original on 2014-07-20.


  14. ^ "Alfonso Valencia - EMBRACE". Archived from the original on 2014-01-10. Retrieved 10 January 2014.


  15. ^ "ICREA". www.icrea.cat. Retrieved 2018-10-27.


  16. ^ "Alfonso Valencia is appointed as Director of the Life Sciences Department within BSC | BSC-CNS". www.bsc.es. Retrieved 2018-10-27.


  17. ^ "El fichaje de Alfonso Valencia refuerza Barcelona como capital bioinformática". La Vanguardia. Retrieved 2018-10-27.


  18. ^ "Structural Computational Biology Group: Overview - cnio.es". Centro Nacional de Investigaciones Oncológicas. Retrieved 10 January 2014.


  19. ^ Alfonso Valencia publications from Europe PubMed Central


  20. ^ Alfonso Valencia's publications indexed by the Scopus bibliographic database. (subscription required)


  21. ^ ab 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.CS1 maint: Uses authors parameter (link)


  22. ^ 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.


  23. ^ 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.


  24. ^ 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): D452–5. doi:10.1093/nar/gkh052. PMC 308786. PMID 14681455.


  25. ^ 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.


  26. ^ 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. CiteSeerX 10.1.1.360.2386. doi:10.1006/jmbi.1997.1198. PMID 9281423.


  27. ^ 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. CiteSeerX 10.1.1.139.2639. doi:10.1016/S0022-2836(02)00379-0. PMID 12079362.


  28. ^ 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.


  29. ^ Herrero, J; Valencia, A; Dopazo, J (2001). "A hierarchical unsupervised growing neural network for clustering gene expression patterns". Bioinformatics. 17 (2): 126–36. doi:10.1093/bioinformatics/17.2.126. PMID 11238068.


  30. ^ 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.


  31. ^ 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.


  32. ^ Bateman, Alex; Valencia, Alfonso (2006). "Structural genomics meets computational biology". Bioinformatics. 22 (19): 2319. doi:10.1093/bioinformatics/btl426. PMID 17032684.


  33. ^ 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.


  34. ^ 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.


  35. ^ 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.


  36. ^ ab 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


  37. ^ Hoffmann, R; Valencia, A (2004). "A gene network for navigating the literature". Nature Genetics. 36 (7): 664. doi:10.1038/ng0704-664. PMID 15226743.


  38. ^ 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.


  39. ^ ab 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.


  40. ^ ab 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.


  41. ^ 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.


  42. ^ Devos, D; Valencia, A (2001). "Intrinsic errors in genome annotation". Trends in Genetics. 17 (8): 429–31. doi:10.1016/s0168-9525(01)02348-4. PMID 11485799.


  43. ^ 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.


  44. ^ "ISCB Fellows". www.iscb.org. International Society for Computational Biology. Archived from the original on 2015-03-28.


  45. ^ "Find an EMBO member". European Molecular Biology Organization.







Preceded by
Burkhard Rost
President of the
International Society for Computational Biology
2015 – 2018
 Succeeded by
Thomas Lengauer









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