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.
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.
^
abValencia, 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.
PMID2029511.
S2CID43450157.
^
abCasari, 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.
PMID7749921.
S2CID9454891.
^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.
CiteSeerX10.1.1.360.2386.
doi:
10.1006/jmbi.1997.1198.
PMID9281423.
^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.
CiteSeerX10.1.1.139.2639.
doi:
10.1016/S0022-2836(02)00379-0.
PMID12079362.
^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.
PMID10547297.
S2CID16167106.
^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.
PMID22158541.
S2CID205343043.
^
abHarrow, 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.
PMC3431492.
PMID22955987.
^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.
PMID12127457.
^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.
PMID10786287.
^"ISCB Fellows". www.iscb.org. International Society for Computational Biology. Archived from
the original on 2015-03-28.