Reposted by Tomas BrunaKatharina Hoff @katharinahoff.bsky.social · 29/04/2026Post 1/2 Our new preprint is out! 🧬 We’ve extended #Tiberius for accurate ab initio gene prediction across the eukaryotic tree, including Plants, Fungi, Insects, and Diatoms. doi.org/10.64898/202...doi.org 11211
Reposted by Tomas BrunaKatharina Hoff @katharinahoff.bsky.social · 11/04/2026BRAKER4 is about to hatch. It now also covers functional annotation for protein sequences... #genomeannotation 2125
Reposted by Tomas BrunaJohn Lovell @jotlovell.bsky.social · 30/01/2026This article is now published! academic.oup.com/nargab/artic... We’ve added a few new analyses. First off, we show that, while gene presence absence variation (PAV) scales with evolutionary distance in both plants and animals, the base level and rate of accrual are both twice as high in plants.academic.oup.comEvolutionary and methodological considerations when interpreting gene presence–absence variation in pangenomesAbstract. While graph-based pangenomes have become a standard and interoperable foundation for comparisons across multiple reference genomes, integrating p 22417
Reposted by Tomas BrunaKatharina Hoff @katharinahoff.bsky.social · 24/10/2025With help of international colleagues at @jgi.doe.gov, @oregonstate.edu, and @stockholm-uni.bsky.social, we are relasing new parameters for Tiberius. Thx to Lars Gabriel, @tomasbruna.bsky.social, Samuel Talbot, @chriswheat.bsky.social, @masta.bsky.social - and many others. github.com/Gaius-August...github.comRelease v1.1.7 · Gaius-Augustus/Tiberius⚠️ New Models available: Diatoms Eudicotyledons Lepidoptera Monocotyledonae Mucoromycota Saccharomycota Sordariomycota Several bugfixes. 0104
Tomas Bruna @tomasbruna.bsky.social · 21/08/2025Big thanks to @axelvisel.bsky.social for sharing! For full consideration, please apply by September 2. 021
Reposted by Tomas BrunaJohn Lovell @jotlovell.bsky.social · 18/08/2025Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts. We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1... 34219
