The Use of Weighted Least Squares Test Statistic in Branch and Topology Testing. - Borys Wróbel; Rafael Sanjuán; Andrés Moya; Fernando González-Candelas (Spanish Bioinformatics Conference, 2004)

Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes. - Jeff Clune; Dusan Misevic; Charles Ofria; Richard E. Lenski; Santiago F. Elena; Rafael Sanjuán (PLoS Comput. Biol., 2008)

Shape Matters: Effect of Point mutations on RNA secondary Structure. - Susanna C. Manrubia; Rafael Sanjuán (Adv. Complex Syst., 2013)

The role of spatial structure in the evolution of viral innate immunity evasion: A diffusion-reaction cellular automaton model. - Ernesto Segredo-Otero; Rafael Sanjuán (PLoS Comput. Biol., 2020)

DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models. - Robby Concha-Eloko; Michiel Stock; Bernard De Baets; Yves Briers; Rafael Sanjuán; Pilar Domingo-Calap; Dimitri Boeckaerts (PLoS Comput. Biol., 2024)