Alfonso Valencia

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Alfonso Valencia
ISMBECCB13-012.jpg
Alfonso Valencia speaking at ISMB/ECCB 2013.
Alma mater
Known for BioCreative [1] [2] [3] [4]
Awards
Scientific career
Fields
Institutions
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] of Spanish National Bioinformatics Institute (INB-ISCIII), and coordinator of the data pillar of the Spanish Personalised Medicine initiative, IMPaCT. From 2015 to 2018, he was President of the International Society for Computational Biology. [10]

Contents

His research interest is the development of Computational Biology methods and their application to biomedical problems. Some of the computational methods he developed are considered pioneering work in areas such as biological text mining, protein coevolution, disease networks and more recently modelling cellular systems (digital twins). He participates in some of the key cancer related international consortia. In terms of community services, he is one of the initial promoters of the ELIXIR infrastructure, founder of the Spanish and International Bioinformatics networks and former president of ISCB, the international professional association of Bioinformaticians. He is Executive Editor of the main journal in the field (Bioinformatics OUP).

His research is focused on the study of biomedical systems with computational biology and bioinformatics approaches. [5]

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]

The 1994 paper "Correlated mutations and residue contacts in proteins", [15] of which Valencia was senior author, established the idea that correlated mutations at corresponding locations in the DNA sequences in different organisms could indicate that those locations corresponded to amino-acid residues that were physically close to each other in the final protein, informing the prediction of contact maps. This previously unconsidered source of side information for protein structure prediction became used with increasing effectiveness in the 2010s, leading ultimately to the success of DeepMind's AlphaFold 2 algorithm in 2020. [16]

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 [17] and Director of the Life Sciences Department of the Barcelona Supercomputing Centre (BSC). [18] [19]

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 [20] 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 2024, Valencia has published over 450 peer reviewed papers, [5] [21] [22] which have been cited more than 92.000 times, [11] in scientific journals including Nature , [23] [24] [25] PNAS , [6] Nucleic Acids Research , [26] [27] the Journal of Molecular Biology , [28] [29] [30] Bioinformatics , [31] [32] [33] [34] Genome Biology , [2] [3] [35] [36] PLOS Computational Biology , [37] PLOS Biology , [38] Nature Genetics , [39] [40] Nature Biotechnology , [4] [41] Genome Research , [42] Biochemistry , [7] Current Opinion in Structural Biology , [43] Nature Structural Biology , [8] Trends in Genetics [44] and the Intelligent Systems for Molecular Biology conference. [45]

Awards and honours

Valencia has been nominated Corresponding Member of the Academy of Medicine of Zaragoza, Spain, in 2024. He was also 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. [46] Valencia has also served as ISCB Vice President and in 2013 was appointed President-elect. [11] From 2015 to 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). [47]

Valencia participates in several international consortia, such as Genecode / ENCODE, [23] [38] [42] the International Cancer Genome Consortium, the International Rare Diseases Research Consortium (IRDiRC), the International Human Epigenomics Consortium. [41] 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.

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References

  1. ↑ Hirschman, L.; Yeh, A.; Blaschke, C.; Valencia, A. (2005). "Overview of BioCreAtIvE: Critical assessment of information extraction for biology". BMC Bioinformatics. 6 (Suppl 1): S1. doi: 10.1186/1471-2105-6-S1-S1 . PMC   1869002 . PMID   15960821.
  2. 1 2 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. 1 2 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. 1 2 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. S2CID   5648695.
  5. 1 2 3 Alfonso Valencia publications indexed by Google Scholar
  6. 1 2 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. 1 2 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. PMID   2029511. S2CID   43450157.
  8. 1 2 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. S2CID   9454891.
  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. 1 2 3 4 "Alfonso Valencia, President-Elect of the ISCB" (PDF). Archived from the original (PDF) on 2014-01-10..
  12. 1 2 "Keynote-Details". ISMB/ECCB 2011. International Society for Computational Biology. Retrieved 7 January 2014.
  13. 1 2 3 4 "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. ↑ U Göbel 1, C Sander, R Schneider, A Valencia<, Correlated mutations and residue contacts in proteins, Proteins18(4):309-17. (1994) doi : 10.1002/prot.340180402
  16. ↑ Cristina Sáez, El último avance fundamental de la biología se basa en la investigación de un científico español, La Vanguardia , 2 December 2020
  17. ↑ "ICREA". www.icrea.cat. Retrieved 2018-10-27.
  18. ↑ "Alfonso Valencia is appointed as Director of the Life Sciences Department within BSC | BSC-CNS". www.bsc.es. Retrieved 2018-10-27.
  19. ↑ "El fichaje de Alfonso Valencia refuerza Barcelona como capital bioinformática". La Vanguardia. Retrieved 2018-10-27.
  20. ↑ "Structural Computational Biology Group: Overview - cnio.es". Centro Nacional de Investigaciones Oncológicas. Archived from the original on 27 December 2017. Retrieved 10 January 2014.
  21. ↑ Alfonso Valencia publications from Europe PubMed Central
  22. ↑ Alfonso Valencia's publications indexed by the Scopus bibliographic database. (subscription required)
  23. 1 2 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.
  24. ↑ 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.
  25. ↑ 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.
  26. ↑ 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.
  27. ↑ 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.
  28. ↑ 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.
  29. ↑ 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.
  30. ↑ 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. S2CID   16167106.
  31. ↑ 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.
  32. ↑ 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.
  33. ↑ 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.
  34. ↑ Bateman, Alex; Valencia, Alfonso (2006). "Structural genomics meets computational biology". Bioinformatics. 22 (19): 2319. doi: 10.1093/bioinformatics/btl426 . PMID   17032684.
  35. ↑ 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.
  36. ↑ 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.
  37. ↑ 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.
  38. 1 2 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 logo PLoS transparent.svg
  39. ↑ Hoffmann, R; Valencia, A (2004). "A gene network for navigating the literature". Nature Genetics. 36 (7): 664. doi: 10.1038/ng0704-664 . PMID   15226743.
  40. ↑ 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. S2CID   205343043.
  41. 1 2 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. hdl: 11858/00-001M-0000-000E-E88D-5 . PMID   22398613. S2CID   5116136.
  42. 1 2 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.
  43. ↑ 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.
  44. ↑ 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.
  45. ↑ 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: 60–7. PMID   10786287.
  46. ↑ "ISCB Fellows". www.iscb.org. International Society for Computational Biology. Archived from the original on 2015-03-28.
  47. ↑ "Find an EMBO member". European Molecular Biology Organization. Archived from the original on 2020-03-21. Retrieved 2015-04-02.
Preceded by President of the
International Society for Computational Biology
2015 – 2018		Succeeded by
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