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

- Bellido et al. 2018, 'Association Between Germline Mutations in &ITBRF1&IT, a Subunit of the RNA Polymerase III Transcription Complex, and Hereditary Colorectal Cancer', Gastroenterology, 154, 1, 181.

- Rodriguez JM, Rodriguez-Rivas J, Di Domenico T, Vazquez J, Valencia A & Tress ML 2018, 'APPRIS 2017: principal isoforms for multiple gene sets', Nucleic Acids Research, 46, D1, D213 - D217.

- Ecker S, Pancaldi V, Valencia A, Beck S & Paul DS 2018, 'Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity', Bioessays, 40, 2, 1700148.

- Grassi L et al. 2018, 'Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils', Cell Reports24, 10, 2784-2794.

- Mur P et al. 2018, 'Germline mutations in the spindle assembly checkpoint genes BUB1 and BUB3 are infrequent in familial colorectal cancer and polyposis', Molecular Cancer, 17:23.