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The #TOGA2 preprint is now at www.biorxiv.org/content/10.6.... Describes the new method and the comparative genomics resource (annotations, orthologs, gene losses/dups, retrogenes and more) generated using a total of 9420 TOGA2 runs for 2173 vertebrate genome assemblies.

Accurate, comprehensive gene annotation and ortholog identification across thousands of vertebrate genomes with TOGA2Inferring orthologs and annotating coding genes remain central challenges in genomics, evident by the growing gap between assembled and annotated genomes. TOGA (Tool to infer Orthologs from Genome Ali...www.biorxiv.org

Happy to announce the release of TOGA2 data for 68 turtle genomes, generated with a cryptodiran and a pleurodiran turtle reference. The combined TOGA2 annotation consistently improves annotation completeness compared with RefSeq. All data at genome.senckenberg.de/download/TOGA2. Genome browsers ...

We now have genome browsers on our UCSC mirror at genome.senckenberg.de for the 1033 mammal and 866 bird assemblies, showing spliceAi, reference-based and ref-integrated TOGA2 tracks. Tables with links to all browsers are genome.senckenberg.de/TOGA2Mammali... & genome.senckenberg.de/TOGA2Aves.html

I wrote a short Nature Methods News & Views piece on deep learning based gene finders such as ANNEVO. www.nature.com/articles/s41...

Learning genes deeply - Nature MethodsAnnevo uses deep learning to achieve unprecedented accuracy in eukaryotic gene annotation, approaching the performance of evidence-based methods.www.nature.com

Happy to share that our work with Ekaterina Osipova, @maggiemcko.bsky.social, Tim Sackton, Maude Baldwin & fantastic collaborators on convergent and lineage-specific genomic adaptations in sugar-feeding birds is published in Science www.science.org/doi/10.1126/.... While high sugar intake ...

Convergent and lineage-specific genomic changes shape adaptations in sugar-consuming birdsHigh-sugar diets cause human metabolic diseases, yet several bird lineages convergently adapted to feeding on sugar-rich nectar or fruits. We investigated the underlying molecular mechanisms in hummin...www.science.org

Happy to present TOGA2, developed by Yury Malovichko @ymalovichko.bsky.social, the faster, memory-efficient & more accurate TOGA1 successor (github.com/hillerlab/TO...). And annotations, orthologs & gene loss/dup data generated with 4 references for 883 placental mammal and with 5 refs for 676 ...

phenomenal work from Terry's lab !! And unbelievable that funding for such exciting work is cut.

Back from the Biology of Aging Gordon Research Conference. Fantastic meeting. Great to meet old friends and making new ones.

Happy to share our review on "Linking phenotype to genotype using comprehensive genomic comparisons" in Current Op with @leonhilgers.bsky.social. Summary of recent work and a discussion of the challenges ahead. www.sciencedirect.com/science/arti...

And @pacbio.bsky.social updated the ultralow protocol based on our results. Checkout www.pacb.com/blog/new-amp...

New Ampli-Fi ultra-low-input protocol will support HiFi sequencing from as little as 1 ng of DNA - PacBioThe Ampli-Fi protocol is a new workflow that will enable HiFi sequencing from as little as 1 ng of genomic DNA.www.pacb.com

Our work on long read sequencing of ethanol or difficult-to-sequence samples is out genomebiology.biomedcentral.com/articles/10..... Will help to sequence Earth's biodiversity @ebpgenome.bsky.social. w @bernhardbein.bsky.social & many great colleagues.

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens - Genome BiologyMuseum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protoco...genomebiology.biomedcentral.com

Checkout @xuelingyi.bsky.social manuscript on diet evolution in bats, with a focus on the super diverse Phyllostomid bat family. www.biorxiv.org/content/10.1...

To all #PSMC users. A prominent PSMC peak followed by a collapse is typically an artifact. @leonhilgers.bsky.social publiation in @currentbiology.bsky.social shows how to avoid this with simple parameter adjustments. www.cell.com/current-biol...

Happy to report that our work on immune system adaptations in bats is now out in @nature.com 🦇🧬 www.nature.com/articles/s41... @ariadnamorales.bsky.social @batresearch.bsky.social @virology.bsky.social @DGKontopoulos.ecoevo.social.ap.brid.gy @sgn.one @bat1kgenomes.bsky.social Read more ...

Bat genomes illuminate adaptations to viral tolerance and disease resistance - NatureA systematic analysis of 115 mammalian genomes, including 10 new bat genomes, reveals prevalent positive selection in immune genes in bats and shows key adaptations in the antiviral gene ISG15 that ai...www.nature.com