Absolute tour de force led by @ymalovichko.bsky.social, with contributions from many in the lab @leonhilgers.bsky.social @xuelingyi.bsky.social @mich-albertini.bsky.social Alejandro Gonzales-Irribarren, Evgeny Leushkin and many others Check #TOGA2 out: github.com/hillerlab/TO...

Had such a good time at @official-smbe.bsky.social talking about museum samples and comparative genomics. Many thanks to everyone who reached out to me and my supervisor for all her support @astridboehne.bsky.social. Special thanks to the Alexander-Koenig-Gesellschaft for funding my trip. #SMBE2026

For those interested in PacBio's SPRQ-Nx chemistry and reusable SMRT Cells: in the Genome of Sweden project, we moved from 2 to 3 acquisitions per SMRT Cell in June. The results are impressive—we’re now approaching 400 Gb HiFi yield from a single SMRT Cell!

Excellent dive into the bizarre world of turtles and how they completely reworked their bodyplan through gene loss by @leonhilgers.bsky.social #SMBE2026 Especially great detective work on the genes of interest!

If you are interested in #PacBio #HiFi sequencing of challenging specimens through long range #PCR amplification, check out my poster (Board 038, Blomster Salen) this evening between 6-8pm! #SMBE2026

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 ...

Drivers of cold adaptation and genome evolution in Antarctic fish, and a haplotype resolved assembly for an important model notothenioid species 🐟 🧬 Our new paper available on BioRxiv #BiodiversityGenomics #ColdAdaptation www.biorxiv.org/content/10.6...

And the winner is… Your 2026 International Mollusc of the Year is 𝘾𝙪𝙢𝙞𝙖 𝙞𝙣𝙩𝙚𝙧𝙩𝙚𝙭𝙩𝙖, the Vampire Snail! It will be the first blood-feeding mollusc to ever have its genome sequenced. Huge thanks to the nominators & @sgn.one for unlocking its DNA secrets! 🧬🩸 #IMOY26

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

Here's a genome from the Vertebrate Genomes Project (vertebrategenomespro...): a chromosome-level assembly for the false killer whale (Pseudorca crassidens)! 🐋 This resource advances cetacean research and conservation. Photo: Stefan Thiesen Buntrabe 1/2

New preprint out!!📜 We show that decades-old FFPE brain tissue archived in the unique Danish Brain Collection (up to 73 years old) can yield biologically informative genomes and transcriptomes. Read the full manuscript at: www.biorxiv.org/content/10.6... #RNA #DNA #FFPE #Brain

Lernt den Spitzenprädator Triplofusus giganteus kennen! 👹 Die Florida-Pferdemuschel ist mit einer Länge von bis zu 60 cm eine der größten fleischfressenden Schnecken der Welt. Sie nutzt ihren massiven Fuß, um ihre Beute zu „ersticken“. 🌊 Stimmt für den Atlantikriesen 👉 https://sgn.one/moty2026 🐚

I've always been fascinated with biodiversity, dreaming of discovering new species. That dream has finally come true: We found two new crab species tugged away in small streamlets in Guangdong! This journey started 7 years ago, huge thanks to Chao for taking me along! 🦀 🦀 🦀 doi.org/10.6620/ZS.2...

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

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 🧵

Truly breathtaking work here, building on the concept of targeted sequencing and turning it dynamic. Remains to be seen how QV will scale beyond human/mammalian data, but the future of routine T2T assemblies might be around the corner: www.nature.com/articles/s41...

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 ...

Our paper on foldback artifacts in long-read sequencing is now published in BMC Genomics! We introduce Breakinator to flag foldback and chimeric artifacts across library types, sequencers, and chemistries. Paper: link.springer.com/article/10.1... With Matthew Meyerson and @lh3lh3.bsky.social

Say hello to Nallo - our Nextflow pipeline for long-read WGS analysis!👋 It handles both ONT and PacBio data and we’re using this for rare disease and population projects in Sweden. A big team effort by Felix Lenner, Anders Jemt et al.🧬💻 academic.oup.com/bioinformati...

The last chapter of my PhD is finally out !!!! In the same species, on neighboring islands, we see radically different warning colors emerge. Evolution in action: Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio: Current Biology www.cell.com/current-biol...

Amazing to see read N50 in the 100s of kb: www.sciencedirect.com/science/arti... Also, optimizing the protocol for long-fragment DNA extraction must have been a mighty effort!

Just in time for Karneval, we present coelsch ! 🎭🥳 A platform-agnostic framework for single-cell recombination analysis. We study crossover variation in mutants & natural lines, identifying the largest natural inversion in A. thaliana to date! 📄 doi.org/10.64898/202... 🐱 github.com/schneeberger...

That looks great! To avoid errors due to starting with spotty gene annotations (gene loss vs. not annotated), I would suggest re-annotating every genome used with TOGA2 from the Hiller lab: github.com/hillerlab/TO... Many annotations out there are not optimal and TOGA2 has great power and accuracy.

📣 #Forschungsnews: Feine Unterschiede – 5 neue Krebsarten in der Nordsee entdeckt 🌊🦐 In der Deutschen Bucht, einem der weltweit bestuntersuchten Meeresgebiete, hat ein Senckenberg-Forschungsteam 5 neue Arten winziger Krebstiere nachgewiesen. Unbekannte Vielfalt vor der Haustür! 👉 https://sgn.one/1df

Excited to share our final accepted version of the CiFi method out today: www.nature.com/articles/s41...

Day 2: bringing the consortium researchers & experts together is on the theme of Functional & comparative genomics Keynote #StefanMundlos: Functional Genomics of Bat Limb Development With Genome Chalk team talks #LucasCanesin, #YuryMalovichko, #AlejandroGonzales, #BernhardBein & #MicheleAlbertini

⚡ We've released a new version of rdeval! v0.0.8 includes full support for @pacbio.bsky.social CiFi read preprocessing, visualization report improvements, and upgrades to performance and parallelization! 🔗 Release notes and source code: github.com/vgl-hub/rdev...

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 ...

📢 New #preprint alert 📢 https://www.biorxiv.org/content/10.1101/2025.11.18.689136v1 Several lineages of #birds and #mammals appear to have independently gained or lost the ability to enter #torpor. 🧵1/4

Preprint Alert! 🦥 We produced complete genomes for 2 Xenarthra and placed them in a mammalian comparative framework. We found that Xenarthra harbour the largest number of retrocopies in mammals! www.biorxiv.org/content/10.1...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

New preprint! With PureTarget we achieved >1000× coverage of targets with ~5kb PacBio reads at QV39. This enabled high-resolution analysis of CRISPR-Cas9 outcomes Key finding: Some CRISPR-mutations may only emerge in the second generation, due to germ cell mosaicism www.biorxiv.org/content/10.1...

A common type of ant in Europe breaks a fundamental rule in biology: its queens can produce male offspring that are a whole different species go.nature.com/4mOb5T9

#PacBio #ULI #HiFi sequencing goes clinical: Really cool paper showing that Ultra-low input (ULI) HiFi sequencing can help cancer diagnostics. Only emphasizes how interdisciplinary the ULI field is ( #museomics, #single-cell #sequencing, #diagnostics etc) www.medrxiv.org/content/10.1...

The poster session was really great and lots of fun @eseb2025.bsky.social! Many interesting discussions and ideas! Thanks to everyone who stopped by at my poster! Looking forward to more interesting talks and posters in the following days!

🔗 https://doi.org/10.1093/bioinformatics/btaf416 💻️ rdeval code: https://github.com/vgl-hub/rdeval (3/3)

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! 🙂

new from the lab -- we investigate 100% ethanol, DMSO salt solution (DESS), EDTA, RNAlater, and AllProtect as possible approaches for short term room temperature preservation of mosquito HMW DNA, nuclei for Hi-C, and RNA towards high quality reference genome creation. the key findings/tips are ....

6 years ago, a dream came true when Chao took me along on a field trip to look for freshwater crabs in Guangdong. Now, the new species we found is formally described (𝘔𝘦𝘨𝘢𝘱𝘭𝘦𝘰𝘯𝘶𝘮 𝘺𝘢𝘯𝘨𝘥𝘰𝘯𝘨𝘦𝘯𝘴𝘦 in the article). Congrats!! zookeys.pensoft.net/articles.php... #FreshwaterCrab #Biodiversity #Potamidae

The Cetacean Genomes Project is happy to share a milestone publication, presenting the first 18 reference-quality, chromosome-resolved genomes of whales, dolphins and porpoises across the cetacean tree of life. www.frontiersin.org/journals/mar...

Exciting news! Good to see that findings from our study on ethanol-preserved specimens are now applied to formalin-fixed cancer samples. Looking forward to more of these interdisciplinary applications regarding amplification-aided sequencing (i. e. scWGA). #PCRAmplification #LongReadSequencing

#ERGAReads | Thinking of sequencing a genome in your lab? 🧬 This review offers practical guidance on how to start a #genome project for non-model species - covering DNA extraction, sequencing tech, costs, and more! 🔗 rdcu.be/eiHRG @sgn.one @leibnizlib.bsky.social #biodiversity #genomics

Still no reading material for the Easter break🌞🌻🐰? Then I have a suggestion: "Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide" (lnkd.in/dsRmSBDE). It was a pleasure to work on this new publication with TilmanSchell & @lpodsiadlowski.bsky.social🙏!

Research about ultra-low input DNA seq and MDA I recently found: 1. MDA on pg input DNA for ONT rapid seq of pathogens + Tool to detect concatemers doi.org/10.1111/1755... 2. MDA for metagenomics of low biomass samples doi.org/10.1093/isme... Exciting Stuff, small inputs + ampli. going strong!

🐙 Jetzt abstimmen: Molluske des Jahres 2025! 🐌 5 beeindruckende Weichtiere stehen im Finale. Dem Gewinner-Weichtier winkt die Entschlüsselung seines kompletten Genoms! 🧬🏆 Erfahrt mehr über die Kandidaten und stimmt bis zum 31.3. für euren Favoriten ab 👉 moty.senckenberg.science

𝗖𝗿𝗮𝗰𝗸𝗶𝗻𝗴 𝘁𝗵𝗲 𝗠𝗼𝗹𝗹𝘂𝘀𝗰 𝗖𝗼𝗱𝗲: A ground-breaking study in @science.org unravels the evolutionary history of molluscs: tinyurl.com/MolluscTree @sgn.one @sigwartae.bsky.social @kmkocot.bsky.social @squamiferum.bsky.social @vans-gonzalez.bsky.social @cgreve.bsky.social @mkyapchiongco.bsky.social

This looks extremely promising and it works with smallish amounts of input DNA. Why? Because it applies long range PCR amplification with 'polC' (KOD Xtreme™ Hot Start DNA polymerase) that we investigated in depth here: genomebiology.biomedcentral.com/articles/10.... #PacBio #HiFiSequencing #PCR

With @katiejenike.bsky.social and a bunch more of our fellow k-mer enthusiasts, we put together a manuscript on k-mers in biodiversity genomics. A guide if you will, that covers k-mers from basics to some really funky stuff... genome.cshlp.org/content/35/2...

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:🧵

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