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 their progress and planning of new projects.
*Building a sustainable bioinformatic infrastructure: In collaboration with the Instituto Nacional de Bioinformatica and the European Bioinformatics Infrastructure, systematically catalog, interoperate and benchmark methods and data resources.

Selected publications

– Sanchez-Valle J, Tejero H, Ibanez K, Portero JL, Krallinger M, Al-Shahrour F, Tabares-Seisdedos R, Baudot A & Valencia A 2017, ‘A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer’, Scientific Reports, 7, 4474.

– Krallinger M, Rabal O, Lourenco A, Oyarzabal J & Valencia A 2017, ‘Information Retrieval and Text Mining Technologies for Chemistry’, Chemical Reviews, 117, 12, 7673 – 7761.

– Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D & Valencia A 2017, ‘Automatic identification of informative regions with epigenomic changes associated to hematopoiesis’, Nucleic Acids Research, 45, 16, 9244 – 9259.

Selected research activities

Currrent projects:
- Studying cancer genomics and its variation in different sample. 
-Investigation of the genetic basis of rare diseases and genetic variation, including copy number variants across populations. 
- Investigation of the role, source and impact of phenotypic heterogeneity across and within individuals. 
-Study of disease co-occurrence patterns and their interpretation based on transcriptomes including direct and inverse comorbidity.
- Integration of different types of omics datasets into chromatin states seen in the context of 3D genome structure. 
-Systems biology, logical and agent-based models of tumour cell proliferation applied to drug synergy prediction.
-AI/ML approaches to mapping of biological ontologies.