Ildefonso Cases

Keywords protein language models evolutionary bioinformatics deep learning phylogenetics genomics machine learning Get full text access Log in, subscribe or purchase for full access. References 1. Shaw, R. ... Evaluating pretrained protein language model embeddings as proxies for functional similarity J. Mol. Evol. 2025; 93:765-776 2. Tule, S. ... Do protein language models learn phylogeny? Brief. Bioinform. 2024; 26, bbaf047 3. Cao, Z. ...

Abstract Protein functional annotation is crucial in biology, but many protein-coding genes remain uncharacterized, especially in non-model organisms. FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) integrates protein language models for large-scale functional annotation. Applied to ~1000 animal proteomes, FANTASIA predicts functions to virtually all proteins, including up to 50% that remained unannotated by traditional homology-based methods.

Abstract A growing body of evidence supports the idea that RNA polymerase II (RNAP II) activity during transcription elongation can be regulated to control transcription rates. Using genomic run-on and RNAP II chromatin immunoprecipitation, we measured both active and total RNAP II across the bodies of genes at three different stages of the mitotic cell cycle in Saccharomyces cerevisiae: G1, S, and G2/M.