Alfonso Valencia Explained

Alfonso Valencia
Academic Advisors:Chris Sander
Known For:BioCreative[1]

Alfonso Valencia is a Spanish biologist, ICREA Professor, current director of the Life Sciences department at Barcelona Supercomputing Center.[2], of Spanish National Bioinformatics Institute (INB-ISCIII), and coordinator of the data pillar of the Spanish Personalised Medicine initiative, IMPaCT. From 2015-2018, he was President of the International Society for Computational Biology.[3]

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.

Education

Valencia studied biology at the Complutense University of Madrid, training in population genetics and biophysics.[4] In 1987 he was a visiting scientist at the American Red Cross Laboratory.[5] He received his PhD in molecular biology in 1988 from the Autonomous University of Madrid.[6] 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.[7]

The 1994 paper "Correlated mutations and residue contacts in proteins",[8] 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.[9]

Research

In 1994 Valencia formed the Protein Design Group at the Spanish National Center for Biotechnology (CNB). He was leader of the Structural and Computational Biology Group at CNIO. 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[10] and Director of the Life Sciences Department of the Barcelona Supercomputing Centre (BSC).[11] [12]

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 [13] 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.

, Valencia has published over 450 peer reviewed papers, which have been cited more than 92.000 times, in scientific journals including Nature,[14] [15] [16] PNAS,[17] Nucleic Acids Research,[18] [19] the Journal of Molecular Biology,[20] [21] [22] Bioinformatics,[23] [24] [25] [26] Genome Biology,[27] [28] [29] [30] PLOS Computational Biology,[31] PLOS Biology,[32] Nature Genetics,[33] [34] Nature Biotechnology,[35] [36] Genome Research,[37] Biochemistry,[38] Current Opinion in Structural Biology,[39] Nature Structural Biology,[40] Trends in Genetics[41] and the Intelligent Systems for Molecular Biology conference.[42]

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. He was a founding member of the International Society for Computational Biology (ISCB) and was honoured as an ISCB Fellow in 2010.[43] Valencia has also served as ISCB Vice President and in 2013 was appointed President-elect. 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).[44]

Valencia participates in several international consortia, such as Genecode / ENCODE,[14] [32] [37] the International Cancer Genome Consortium, the International Rare Diseases Research Consortium (IRDiRC), the International Human Epigenomics Consortium.[36] 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).[4]

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

Notes and References

  1. Hirschman . L. . Yeh . A. . Blaschke . C. . Valencia . A. . Overview of BioCreAtIvE: Critical assessment of information extraction for biology . 10.1186/1471-2105-6-S1-S1 . BMC Bioinformatics . 6 . S1 . 2005 . Suppl 1 . 15960821 . 1869002 . free .
  2. News: El fichaje de Alfonso Valencia refuerza Barcelona como capital bioinformática. La Vanguardia. 2017-03-07.
  3. Web site: Past Officers and Directors. www.iscb.org. 12 April 2018. en-gb.
  4. Web site: Alfonso Valencia, President-Elect of the ISCB. https://web.archive.org/web/20140110150120/http://www.cnio.es/es/news/docs/Alfonso_Valencia_ISCB_16082013_en.pdf. 2014-01-10. .
  5. Web site: Keynote-Details. ISMB/ECCB 2011. International Society for Computational Biology. 7 January 2014.
  6. Web site: Alfonso Valencia - cnio.es. Centro Nacional de Investigaciones Oncológicas. https://web.archive.org/web/20140720070524/http://www.cnio.es/ing/grupos/plantillas/curriculum.asp?pag=1002. 2014-07-20.
  7. Web site: Alfonso Valencia - EMBRACE. 10 January 2014. https://web.archive.org/web/20140110152455/http://www.embracegrid.info/partners/alfonso-valencia. 2014-01-10. dead.
  8. U Göbel 1, C Sander, R Schneider, A Valencia<, Correlated mutations and residue contacts in proteins, Proteins18(4):309-17. (1994)
  9. Cristina Sáez, El último avance fundamental de la biología se basa en la investigación de un científico español, La Vanguardia, 2 December 2020
  10. Web site: ICREA. www.icrea.cat. en. 2018-10-27.
  11. Web site: Alfonso Valencia is appointed as Director of the Life Sciences Department within BSC BSC-CNS. www.bsc.es. en. 2018-10-27.
  12. News: El fichaje de Alfonso Valencia refuerza Barcelona como capital bioinformática. La Vanguardia. 2018-10-27.
  13. Web site: Structural Computational Biology Group: Overview - cnio.es. Centro Nacional de Investigaciones Oncológicas. 10 January 2014. 27 December 2017. https://web.archive.org/web/20171227082057/http://www.cnio.es/ing/grupos/plantillas/presentacion.asp?grupo=50004294. dead.
  14. ENCODE Project Consortium. Birney E. Stamatoyannopoulos JA . Dutta A. Guigó R. Gingeras TR. Margulies EH. Weng Z. Snyder M. Dermitzakis ET . Ewan Birney . John Stamatoyannopoulos . Anindya Dutta. 10.1038/nature05874 . Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project . Nature . 447 . 7146 . 799–816 . 2007 . 17571346 . 2212820 . 2007Natur.447..799B . etal.
  15. 21642962. 3322590. 2011. Puente. X. S.. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature. 475. 7354. 101–5. 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. Enjuanes. A. 29. 10.1038/nature10113.
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  17. 1323828. 49695. 1992. Bork. P. 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. Sander. C. Valencia. A. 1992PNAS...89.7290B . 10.1073/pnas.89.16.7290 . free.
  18. 10.1093/nar/gkh052. 14681455. 308786. IntAct: An open source molecular interaction database. Nucleic Acids Research. 32. 90001. D452–5. 2004. Hermjakob . H.. Montecchi-Palazzi . L.. Lewington . C.. Mudali . S.. Kerrien . S.. Orchard . S.. Vingron . M.. Roechert . B.. Roepstorff . P.. Valencia . A.. Alfonso Valencia. Margalit . H.. Armstrong . J.. Bairoch . Amos . Amos Bairoch. Cesareni . G.. Sherman . D.. Apweiler . R.. Rolf Apweiler.
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  21. 12079362. 2002. Jensen. L. J.. Prediction of human protein function from post-translational modifications and localization features. Journal of Molecular Biology. 319. 5. 1257–65. 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. 10.1016/S0022-2836(02)00379-0. 10.1.1.139.2639.
  22. 10547297. 1999. Olmea. O. Effective use of sequence correlation and conservation in fold recognition. Journal of Molecular Biology. 293. 5. 1221–39. Rost. B. Valencia. A. 16167106. 10.1006/jmbi.1999.3208.
  23. 11238068. 2001. Herrero. J. A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics. 17. 2. 126–36. Valencia. A. Dopazo. J . 10.1093/bioinformatics/17.2.126. free.
  24. 16204114. 2005. Hoffmann. R. Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics. 21. ii252–8. Valencia. A. Suppl 2. 10.1093/bioinformatics/bti1142. free.
  25. 22399678. 3324521. 2012. Peng. Hanchuan. Bioimage informatics: A new category in Bioinformatics. Bioinformatics. 28. 8. 1057. Bateman. Alex. Alex Bateman. Valencia. Alfonso. Alfonso Valencia. Wren. Jonathan D.. Jonathan Wren (biologist). 10.1093/bioinformatics/bts111.
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  41. 11485799. 2001. Devos. D. Intrinsic errors in genome annotation. Trends in Genetics. 17. 8. 429–31. Valencia. A . 10.1016/s0168-9525(01)02348-4.
  42. 10786287. 1999. Blaschke. C. Automatic extraction of biological information from scientific text: Protein-protein interactions. Proceedings. International Conference on Intelligent Systems for Molecular Biology. 60–7. Andrade. M. A.. Ouzounis. C. Valencia. A.
  43. Web site: ISCB Fellows. www.iscb.org. International Society for Computational Biology. https://web.archive.org/web/20150328182241/http://www.iscb.org/iscb-fellows. 2015-03-28.
  44. Web site: Find an EMBO member. European Molecular Biology Organization. 2015-04-02. 2020-03-21. https://web.archive.org/web/20200321182646/http://www.embo.org/members/find-a-member. dead.

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