Alfonso Valencia

Alfonso Valencia

Barcelona Supercomputing Center - Centro Nacional de Supercomputación

Life & Medical Sciences

Computational biologist, pioneer scientist applying computer science to solve biological problems, recognized as leader in his field. Focused on the analysis of large collections of genomic data, especially protein interaction networks applied to (epi)Genomics, Cancer Biology and Precision Medicine, his group train the application of Text Mining methodology to biomedical problems. He earned a PhD in Biochemistry and Molecular Biology (UAM) plus a PostDoctoral researcher in Bioinformatics (EMBL Heid). Prof. at ICREA, Scientific Director and Director’s of Life Sciences in BSC-CNS, home of the MareNostrum Supercomputer. Head of the Spanish node of the European Infrastructure for Life-Science Information,ELIXIR. Founding member and President of the ISCB. Elected member of the European Molecular Biology Organization (EMBO). Exec. Editor of "Bioinformatics", OUP of FEBS Letters, Prof. Honoris Causa by the Danish Technical University and advisory board in several Institutions.

Research interests

*Personalized Medicine Initiative: Organize resources for the analysis of large scale genomics and phenotypic data and its translation to clinic.*NLP/text mining: Analyzing large biomedical corpora to detect bioentities relations and specific conditions, e.g. disease specific genes affected in particular contexts.*New approaches to predict protein structures and interactions: exploration of the sequence and structure spaces combined with simulations highly improve prediction methods, useful in applications such as drug design.*Network Biology: Investigation of AI approaches for the analysis of biological networks, ontology constructions and diseases comorbidity.*Evaluation of research and social projects: Analyzing large data sets to assess the impact of specific projects, monitoring, and planning. *Building a sustainable bioinformatic infrastructure: In collaboration with the INB and the EBI, systematically catalog, interoperate and benchmark methods and data resources.

Selected publications

- Reyna, M. et al. 2020, 'Pathway and network analysis of more than 2500 whole cancer genomes', Nature Communications, 11, 1, 729.

- Ostaszewski, M. et al.2020, 'COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.', Scientific Data, 7, 1, 136 - 136.

- Porta-Pardo, Eduard; Valencia, Alfonso; Godzik, Adam 2020, 'Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era', Febs Letters, .

- Ponce-de-Leon, Miguel; Apaolaza, Inigo; Valencia, Alfonso; Planes, Francisco J. 2020, 'On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models', Bioinformatics, 36, 6, 1986 - 1988.

- Cirillo, Davide; Catuara-Solarz, Silvina; Morey, Czuee; Guney, Emre; Subirats, Laia; Mellino, Simona; Gigante, Annalisa; Valencia, Alfonso; Rementeria, Maria Jose; Chadha, Antonella Santuccione; Mavridis, Nikolaos 2020, 'Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare', Npj Digital Medicine, 3, 1, 81.

- Gaudelet, T; Malod-Dognin, N; Sanchez-Valle, J; Pancaldi, V; Valencia, A; Przulj, N 2020, 'Unveiling new disease, pathway, and gene associations via multi-scale neural network', Plos One, 15, 4, e0231059.

- Goldman, M. et al. 2020, 'A user guide for the online exploration and visualization of PCAWG data', Nature Communications, 11, 1, 3400.

- Segales, J. et al. 2020, 'Detection of SARS-CoV-2 in a cat owned by a COVID-19-affected patient in Spain', Proceedings Of The National Academy Of Sciences Of The United States Of America, 117, 40, 24790 - 24793.

- Vergara-Alert, J et al. 2020, 'Pigs are not susceptible to SARS-CoV-2 infection but are a model for viral immunogenicity studies', Transboundary And Emerging Diseases, .