Olga Zhaxybayeva

Bacterial growth temperature as a horizontally acquired polygenic trait

The paper identifies 68 genes in Thermotogota bacteria correlated with optimal growth temperature, showing these genes are often horizontally transferred and involved in metabolism and regulation.

Homology detection using a protein secondary structure-based large language model

The paper introduces ProSSL, a Transformer-based model using protein secondary structure to detect homology, outperforming traditional sequence-based methods in identifying distant homologs.

Machine-learning classification suggests that many alphaproteobacterial prophages may instead be gene transfer agents

The paper uses a machine-learning classifier to distinguish gene transfer agents from viral homologs in alphaproteobacterial genomes, finding that many prophage predictions are likely GTAs.