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 TOGA2

Inferring 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...

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 Methods

Annevo uses deep learning to achieve unprecedented accuracy in eukaryotic gene annotation, approaching the performance of evidence-based methods.

nature.com

I hear you want novelty🦎->🐢, chromosome evolution 🧬, sex determination🩷, link population history📈 & climate🌏🌡️? Or you share my love for wonderfully weird animals? Side-necked turtle genomes reveal chromosomal dynamics, skeletal innovation and cancer resistance www.biorxiv.org/content/10.6... A 🧵

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 birds

High-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...

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 ...

🚀🧬🔥 Hot off the press — 2025! Don’t miss this must-read publication: bit.ly/4mJwFb7 This groundbreaking paper sets the stage for Earth BioGenome Project Phase II — where EBP is gearing up to scale genome sequencing 10× faster than ever before! 🌍✨

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

@tdcapellini.bsky.social · 11mo ago

1) I am delighted to present this terrific tour de force research conducted by my post-doc Dr. Gayani Senevirathne @gayani.bsky.social and published today in Nature - www.nature.com/articles/s41...

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...

You link #phenotype 🦜 to #genotype 🧬 with #comparative #genomics 💻? This #review is for you 📜: authors.elsevier.com/sd/article/S... We review new #methods, remaining #challenges and #future directions and highlight recent key studies. Thanks @hillermich.bsky.social! Please share! 🙂

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 - PacBio

The Ampli-Fi protocol is a new workflow that will enable HiFi sequencing from as little as 1 ng of genomic DNA.

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 Biology

Museum 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

Bernhard Bein@bernhardbein.bsky.social · last yr.

Thrilled to share our work on unlocking challenging specimens for @pacbio.bsky.social #HiFi sequencing, now out in Genome Biology! genomebiology.biomedcentral.com/articles/10.... We show that specimens that have been stored in ethanol for decades can still be amenable for long-read sequencing:🧵

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...

Xueling (Ling) Yi@xuelingyi.bsky.social · last yr.

Glad to see our preprint out! We reconstructed diet evolution in bats and support ancestral omnivory of the ecologically diverse bat family Phyllostomidae.

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...

I am writing a short #review about linking #phenotype to #genotype 🧬using #comparative #genomics. There is a lot of amazing work and I would love to hear about your favorite studies 🥇 from the last 2-3 years! ✉️ Pls also send your own work here (or DM)🙂!! Please #repost!!! 🔁 (just joined bsky)

an owl holding an envelope with a label that says ' envelope ' on it

ALT: an owl holding an envelope with a label that says ' envelope ' on it

media.tenor.com

A news article for a lay summary also: www.nature.com/articles/d41...

How flight helped bats become invincible to viruses

The mammals carry immune adaptations that emerged when their ancestors took to the skies.

nature.com

Finally online - Bat genomes illuminate adaptations to viral tolerance and disease resistance www.nature.com/articles/s41... @hillermich.bsky.social @virology.bsky.social @emmateeling.bsky.social

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 - Nature

A 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...

nature.com