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, a project I pursued during my time at the NIH (1993-1997) and the UCL (1997-2000). After joining ICREA, this topic became the main focus of my activities (PCB, 2001-2009; IBMB-CSIC, 2009-2012). Over time, my interests shifted towards studying translational problems in biomedicine. 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. Our efforts have recently gained international recognition after our participation in the CAGI contest, where we have achieved second place on two occasions (Enigma and ARSA challenges, in 2018-2019 and 2023-2024, respectively).

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 state-of-the-art machine learning 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

– Aguirre S, Pappa S, Serna-Pujol N, Padilla N, Iacobucci S, Nacht AS, Vicent GP, Jordan A, de la Cruz X & Martínez-Balbás MA 2024, ‘PHF2-mediated H3K9me balance orchestrates heterochromatin stability and neural progenitor proliferation‘, Embo reports 25:3486-3505.
– Porras, LM et al. 2024, ‘A New Set of in Silico Tools to Support the Interpretation of ATM Missense Variants Using Graphical Analysis‘, Journal of molecular diagnostics, 26: 17-28.

Selected research activities

I have actively promoted the use of AI in healthcare through various activities:
  • Jan 2024: Delivered the talk ‘When the Future is Now: The Rising Contribution of AI to the Clinical Understanding of Genetic Variability’ at the XI International Conference BIFI 2024, Zaragoza, Spain.
  • Jun 2024: Co-organizer ‘Jornada sobre l’ús de la IA en Recerca Biomèdica’ at Vall d’Hebron Hospital, Barcelona, Spain.
  • Oct 2024: Taught a 10-hour degree course on Machine Learning for Pathogenicity Prediction at the University of Bologna, Italy.
  • Oct 2024: Participated in the ‘Back to Fundamentals of Research: Interdisciplinarity Roundtable’ at ISA, Bologna, Italy, with the talk ‘Pathogenicity Prediction Using AI Tools.’
  • Dec 2024: Organized a visit for Biomedicine degree students from the Universitat Internacional de Catalunya (UIC) to our laboratory to share our research on AI/ML applications in pathogenicity prediction