Bernhard Bein

Targeted sequencing and iterative assembly of near-complete genomes - Nature Communications Long-read sequencing enables high-quality genome assemblies, but challenges remain. Here, the authors introduce Cornetto, a method that improves assembly quality, enables genome sequencing from saliva...

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...

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...

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 ...

Detecting foldback artifacts in long-reads - BMC Genomics Long-read sequencing data is useful for detecting large and complex structural variations; however, technical artifacts can lead to false structural variant calls. In our analyses, we became aware of ...

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

Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis AbstractMotivation. Long-read sequencing (LRS) is increasingly used for human medical research and clinical diagnostics, due to its capacity to generate co

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...

Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio Aguilar-Gómez et al. use exome sequencing of 347 strawberry poison frogs to uncover the genetic basis of color variation. They identify that kit, ttc39b, and bco1 underlie blue-red, yellow-red, and gr...

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...

Nanopore ultra-long sequencing and adaptive sampling spur plant complete telomere-to-telomere genome assembly The pursuit of complete telomere-to-telomere (T2T) genome assembly in plants, challenged by genomic complexity, has been advanced by Oxford Nanopore T…

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.

Vergrößerte Aufnahme der fünf neu entdeckten Krebstiere eingefärbt in Rot, Orange, Gelb, Türkis und Blau vor schwarzem Hintergrund.

Vergrößerte Aufnahme eines der neu entdeckten, blass-weißen Krebstiere, einmal von oben, einmal von der Seite vor schwarzem Hintergrund.

📣 #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

Retrocopy formation and domestication shape genome evolution in sloths and other xenarthrans Xenarthrans, comprising sloths, anteaters, and armadillos, represent one of the most morphologically and physiologically specialised mammalian clades, yet the genomic basis of their adaptations remain...

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...

A complete diploid human genome benchmark for personalized genomics Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

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]

Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads Background: Genetic mosaicism is a consequence of CRISPR-Cas9 genome editing that is difficult to study, especially when it involves structural variants occurring at low frequency. A comprehensive ana...

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...

‘Almost unimaginable’: these ants are different species but share a mother Ant queens of one species clone ants of another to create hybrid workers that do their bidding.

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

Whole-genome variant detection in long-read sequencing data from ultra-low input patient samples Long-read sequencing provides a more complete view of the genome than short-read sequencing, with advantages in the detection of structural variants, tandem repeats, and small variants (single nucleot...

#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!

GitHub - vgl-hub/rdeval: Multithreaded read analysis Multithreaded read analysis. Contribute to vgl-hub/rdeval development by creating an account on GitHub.

🔗 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 ....

Four new freshwater crab species of the genus Megapleonum Huang, Shih & Ahyong, 2018 (Crustacea, Decapoda, Potamidae) from Guangdong, China Four new species of the poorly known genus Megapleonum Huang, Shih & Ahyong, 2018, are described from Guangdong Province, China: Megapleonum falx sp. nov. from Huizhou City, M. yangdongense sp. no...

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

Frontiers | Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life Reference genomes from representative species across families provide the critical infrastructure for research and conservation. The Cetacean Genomes Project...

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🙏!

Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing Multiple displacement amplification (MDA) outperforms conventional PCR in long fragment and whole-genome amplification, making it attractive to couple MDA with long-read sequencing of samples with li...

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!

Ein Kraken der Gattung Muusoctopus schwimmt am Meeresgrund

Ein Blauer Drache (Glaucus atlanticus), eine leuchtend blaue Meeresnacktschnecke, schwebt in dunklem Wasser. Seine fingerartigen Fortsätze erstrecken sich symmetrisch vom Körper. Darunter ist eine blau-weiße, kreisförmige Kolonie einer Staatsqualle zu sehen.

Eine Hawaiische Schwarzfuß-Napfschnecke (Cellana exarata) guckt mit ausgestreckten Fühlern aus ihrer Muschelschale heraus, die auf sandigem Boden nahe einer dunklen Felswand liegt.

🐙 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