Francisco Javier de la Cruz Montserrat

Francisco Javier de la Cruz Montserrat

Vall d'Hebron Institut de Recerca

Life & Medical Sciences

My career revolves around the application of in silico tools to address biological questions. My Ph.D. focused on the study of protein structure principles underlying function, work that I pursued at the National Institutes of Health (1993–1997) and University College London (1997–2000). After joining ICREA, this topic continued to dominate my activities (Parc Científic de Barcelona, 2001–2009; IBMB-CSIC, 2009–2012). However, my interests have gradually shifted toward the study of translational problems in biomedicine. In particular, in 2012 I joined the Vall d'Hebron Institute of Research (VHIR) to enhance the applicability of our work on the pathogenicity of genetic variants, bringing it closer to healthcare stakeholders. This research earned our group consistently top-ranking positions across three consecutive editions of the prestigious CAGI contest (CAGI 5, 6, and 7), establishing us as an international reference in the field.

Research interests

Our main research aims at understanding the molecular basis of hereditary disease, integrating two complementary aspects: the molecular impact of causative variants and how genetic background regulates the propagation of this impact. At a technical level, to reach our objective, we integrate the results of the most advanced genomic experiments (single-cell, Hi-C, etc.) using advanced AI tools. To enhance the biomedical reach of our research, we work in collaboration with clinical groups from different hospitals. As a result of these efforts, we have recently made significant advances in understanding the functional effect of BRCA1/2 protein variants underlying hereditary breast and ovarian cancers. Finally, mention that we are also devoting an important part of our efforts to the fundamental study of epigenetic processes, to reach a full picture of which phenomena contribute to the generation of phenotype and, more precisely, of clinical phenotype. 

Selected publications

- Jain S, Trinidad M,..., De la Cruz X, ..., Suhr T, Clark W T 2025 'Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A', Human Genetics, vol. 144, pp 295–308.

Selected research activities

In 2025, we participated in the CAGI 7 challenges with outstanding results, ranking 1st in two out of four challenges and 3rd–5th in the remaining two, being the only group to achieve two first-place positions. These results position our group at the forefront of applying artificial intelligence to genetic variant pathogenicity interpretation and led to an invited presentation at the CAGI 7 conference.