Alex Warwick Vesztrocy

EdgeHOG: fine-grained ancestral gene order inference at tree-of-life scale

EdgeHOG infers ancestral gene order across the tree of life, producing 1,133 ancestral genomes and revealing conserved and rapidly evolving gene adjacencies.

Orthology inference at scale with FastOMA

FastOMA scales orthology inference to handle large genome datasets efficiently while maintaining accuracy.

Unveiling the Functional Fate of Duplicated Genes Through Expression Profiling and Structural Analysis

This study tests the least diverged orthologue conjecture by analyzing sequence and expression data across multiple species, finding that the least diverged orthologue tends to retain ancestral functions.

OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches

OMAmer improves protein subfamily assignment by using alignment-free methods and phylogenetic information, reducing misassignments compared to closest sequence approaches.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

The paper reports results from the CAFA3 challenge, showing improved computational protein function prediction and new annotations for over 1000 genes through experimental screens in C. albicans, P. aureginosa, and Drosophila.

OMA standalone: orthology inference among public and custom genomes and transcriptomes

OMA standalone is a tool for orthology inference across public and custom genomes, enabling analysis of both existing and user-provided data.