- Our lab has published a couple of major papers in the past few months, which I would like to highlight in this thread! 🧵
- Structure-informed phylogenetic inference with FoldTree outperforms sequence-only trees on divergent proteins, and untangles RRNPPA quorum-sensing receptors across Gram-positive bacteria & phages. Work led by David Moi (www.linkedin.com/in/david-moi) Paper: doi.org/10.1038/s415...
- Testing the "least-diverged ortholog” conjecture on >1M structs + expression across 16 animals & 20 plants, the LDO tends to retain ancestral function while the other copy specialises. Work led by @irenejulca.bsky.social. Paper: doi.org/10.1101/gr.2... Free preprint: www.biorxiv.org/content/10.1...Oct 23, 2025 06:17
- EdgeHOG reconstructs ancestral gene order at Tree-of-Life scale in linear time. 2,845 genomes → 1,133 ancestors. Vontigs for LECA (~1.8 Ga). Also dates gene adjacencies & rearrangements. Sexual chroms stand out! Led by Charles Bernard (research.pasteur.fr/fr/member/ch...) doi.org/10.1038/s415...
- Gene annotations matter for downstream analyses: different structural gene-annotation pipelines yield markedly different orthology calls. We compare four strategies across species and argue for standards & QC before inference. Work led by @silviaprietob.bsky.social. Paper: doi.org/10.1093/bioi...
