Evolutionary Dynamics

Bioinformatics and Computational Biology

 Dra. Ildefonso Cases Díaz

Associate Investigator

 

Summary

 

Our research focuses on the development and application of artificial intelligence methods to build computational representations of biological entities, including proteins, genes, regulatory regions, cells, and organisms. These representations transform complex biological objects into numerical spaces where they can be compared, organized, and analyzed using mathematical and computational approaches.

A central goal of our work is to understand what biological information is encoded within these representations. In particular, we investigate how properties such as molecular function, evolutionary relationships, biological diversity, and the organization of cellular systems are embedded in these representation spaces, enabling the exploration of biological principles that are not readily apparent from the original data.

Another major area of research involves the development of predictive tools based on these representations. These approaches enable the transfer of knowledge between related proteins, genes, or cells, overcoming some of the limitations of traditional methods that rely exclusively on sequence similarity or homology.

Finally, these representations are used as tools to address fundamental questions in evolutionary and functional biology. These include the study of evolutionary convergence, the emergence of novel biological functions, the organization of protein functional landscapes, and the identification of large-scale evolutionary patterns. The ultimate goal is to use artificial intelligence not only as a predictive tool, but also as a framework for understanding how biological information is organized and evolves.

 

 

Relevant publications

 

 

  • Fernández R, Valverde S, Bombarely A, Cases I, Handley SA, Rojas AM. (2026) Rethinking molecular evolution through protein language model embeddings. Trends Genet.  Jun 15:S0168-9525(26)00141-1. doi: 10.1016/j.tig.2026.05.014.
     
  • Martínez-Redondo,G.I., Perez-Canales F.M., Carbonetto B., Fernández J.M., Barrios-Núñez I., Vázquez-Valls M., Cases, I. , Rojas A.M. and Fernández R (2025) FANTASIA leverages language models to decode the functional dark proteome across the Animal Tree of Life . Commun Biol.14;8(1):1227. doi: 10.1038/s42003-025-08651-2
     
  • Cases I., Martínez-Redondo G.I., Fernández R. and Rojas AM. (2025) Functional annotation of proteomes using protein language models: a High-throughput implementation of the ProtTrans model. Methods in Molecular Biology, 2941:127-137, doi: 10.1007/978-1-0716-4623-6_8
     
  • Maya-Miles D, García-Martínez J, Cases I, Pasión R, de la Cruz J, Pérez-Ortín JE, Muñoz-Centeno MC, Chávez S. (2025) Regulation of transcription elongation anticipates alternative gene expression strategies across the cell cycle. PLoS One. 7;20(5):e0317650. doi: 10.1371/journal.pone.0317650
     
  • Verdugo-Sivianes EM, Espinosa-Sánchez A, Cases I, Rojas AM, Otero-Albiol D, Romero L, Blanco JR, Carnero A. (2024) MEG8 as an antagonistic pleiotropic mechanism in breast cancer. Cell Death Discov.  Dec 20;10(1):509. doi: 10.1038/s41420-024-02272-0. PMID: 39706842; PMCID: PMC11662018.
     
  • Barrios-Núñez,I., Martínez-Redondo,G.I., Medina-Burgos, P., Cases I *., Fernández, R.*, Rojas A.M.* (2024) Decoding functional proteome information in model organisms using protein language models. NAR Genomics and Bioinformatics, 6, 3, doi:10.1093/nargab/lqae078
     
  • Rueda AD, Salvador-Martínez I, Sospedra-Arrufat I, Alcaina-Caro A, Fernández-Miñán A, Burgos-Ruiz AM, Cases I, Mohedano A, Tena JJ, Heyn H, Lopez-Rios J, Nusspaumer G.(2024 ) The cellular landscape of the endochondral bone during the transition to extrauterine life. Immunol Cell Biol. Feb;102(2):131-148. doi: 10.1111/imcb.12718.
     
  • Marlétaz F, de la Calle-Mustienes E, Acemel RD, Paliou C, Naranjo S, Martínez-García PM, Cases I, Sleight VA, Hirschberger C, Marcet-Houben M, Navon D, Andrescavage A, Skvortsova K, Duckett PE, González-Rajal Á, Bogdanovic O, Gibcus JH, Yang L, Gallardo-Fuentes L, Sospedra I, Lopez-Rios J, Darbellay F, Visel A, Dekker J, Shubin N, Gabaldón T, Nakamura T, Tena JJ, Lupiáñez DG, Rokhsar DS, Gómez-Skarmeta JL. (2023) The little skate genome and the evolutionary emergence of wing-like fins. Nature. Apr;616(7957):495-503. doi: 10.1038/s41586-023-05868-1. Epub 2023 Apr 12. PMID: 37046085
     
  • Fragoso-Luna A, Romero-Bueno R, Eibl M, Ayuso C, Muñoz-Jiménez C, Benes V, Cases I, Askjaer P. (2023) Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in Caenorhabditis elegans. Genetics. 223(1):iyac166. doi: 10.1093/genetics/iyac166
     
  • Leon A, Subirana L, Magre K, Cases I, Tena JJ, Irimia M, Gomez-Skarmeta JL, Escrivá H, Bertrand S. (2022) Gene Regulatory Networks of Epidermal and Neural Fate Choice in a Chordate. Mol Biol Evol. 39(4):msac055. doi: 10.1093/molbev/msac055.