Alfonso Valencia Herrera

Alfonso Valencia Herrera

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 Natural Language technology to the biomedical domain. 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. Head of the Spanish node of the European Infrastructure for Life-Science Information, ELIXIR. Founding member and former President of the ISCB. Elected member of the European Molecular Biology Organization (EMBO). Executive Editor of "Bioinformatics" OUP, Section Editor of Mol Oncol. Editor FEBS Letters, Prof. Honoris Causa by the Danish Technical University.

Research interests

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 what is now the ELIXIR infrastructure, founder of the Spanish Bioinformatics network and founder member and former president of ISCB the professional association of Bioinformaticians and the Executive Editor of the main journal in the field (Bioinformatics OUP).

Selected publications

- Ponce-de-Leon M, Montagud A, Noël V, Meert A, Pradas G, Barillot E, Calzone L & Valencia A 2023, 'PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks', npj Systems Biology and Applications, 9 (54).

- Sánchez-Valle J & Valencia A 2023, 'Molecular bases of comorbidities: present and future perspectives', Trends In Genetics, 39, 10, 773 - 786.

- Rovirosa L, Tomás-Daza L, Urmeneta B, Valencia A & Javierre BM 2023, 'An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations', Jove-journal Of Visualized Experiments, 194, 10.3791/65316.

- Tomás-Daza L, Rovirosa L, López-Martí P, et al. 2023, 'Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution'. Nature communications 14, 268.


- Armaos A, Serra F, Núñez-Carpintero I, Seo JH, Baca SC, Gustincich S, Valencia A, Freedman ML, Cirillo D, Giambartolomei C & Tartaglia GG 2023, 'The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer', Nature communications, 14 - 1 - - .

Selected research activities

of two
1) Network-based method for biological data integration in precision medicine. Iker Núñez
2) Evaluating protein folding predictions and functional annotations: A comprehensive analysis of recent advancements in the protein structural field. Victoria Isabel Ruiz Serra
Conferences & talks:
-July 10th. Keynote, "Network-Based Approaches to Two Different Disease Scenarios" NetBioMed.   
-July 24th. Keynote, "Network-based Perspectives on Two Diverse Disease Scenarios: Rare Diseases and COVID-19 Spread in Spain" ISMB/ECCB 2023
-June 14th. Invited section talk  " The cancer data management and analysis infrastructure proposed by EOSC4CANCER" EACR2023
-April 19th.
Invited talk.  "Personalized Medicine and Virtual Digital Twins in Accelerating Times". EATRIS-Plus Summer School in Personalised Medicine. INFARMED