Gemma I. Martínez‐Redondo

The paper investigates genomic mechanisms underlying independent transitions to terrestrial life across species, finding lineage-specific gene changes that converge functionally.

This paper introduces FANTASIA, a tool using protein language models to annotate functions for thousands of animal proteomes, uncovering previously unknown functions across species.

The paper shows that clitellates experienced a burst of genomic rearrangements leading to loss of macrosynteny with marine annelids and new chromosomal interactions.

MATEdb2 provides high-quality proteomes for nearly 1000 animal species to enhance phylogenomic research by reducing computational effort and standardizing data formats.

This study compares protein language models and deep learning methods for decoding functional information from proteomes of model organisms, finding language models more precise and informative.