Bernhard Bein
bernhardbein.bsky.social
Bernhard Bein
@bernhardbein.bsky.social
PhD student in comparative genomics @ Senckenberg and Goethe University Frankfurt
Pinned
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:🧵
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
Reposted by Bernhard Bein
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...
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...
www.biorxiv.org
October 2, 2025 at 9:16 PM
Reposted by Bernhard Bein
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]
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 ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
Reposted by Bernhard Bein
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...
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...
www.biorxiv.org
September 10, 2025 at 7:34 AM
Reposted by Bernhard Bein
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
‘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.
go.nature.com
September 3, 2025 at 3:34 PM
#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...
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...
www.medrxiv.org
September 3, 2025 at 11:06 AM
Reposted by Bernhard Bein
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!
August 19, 2025 at 8:32 PM
Reposted by Bernhard Bein
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! 🙂
July 24, 2025 at 8:00 AM
Reposted by Bernhard Bein
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 ....
Breaking the cold chain: solutions for room temperature preservation of mosquitoes leading to high quality reference genomes https://www.biorxiv.org/content/10.1101/2025.07.03.662936v1
July 7, 2025 at 7:20 AM
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
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...
zookeys.pensoft.net
July 6, 2025 at 8:18 PM
Reposted by Bernhard Bein
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...
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...
www.frontiersin.org
July 3, 2025 at 5:33 PM
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
May 20, 2025 at 2:37 PM
Reposted by Bernhard Bein
#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
April 23, 2025 at 8:11 AM
Reposted by Bernhard Bein
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🙏!
April 17, 2025 at 10:40 AM
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!
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...
onlinelibrary.wiley.com
March 21, 2025 at 2:26 PM
Reposted by Bernhard Bein
🐙 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
March 3, 2025 at 2:11 PM
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
February 24, 2025 at 8:22 AM
Reposted by Bernhard Bein
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...
February 14, 2025 at 10:20 PM
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:🧵
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
February 10, 2025 at 3:26 PM
Reposted by Bernhard Bein
Glad to see our preprint out! We reconstructed diet evolution in bats and support ancestral omnivory of the ecologically diverse bat family Phyllostomidae.
We have a new @biorxivpreprint #preprint on dietary #Evolution across phyllostomid #bats 🦇: https://www.biorxiv.org/content/10.1101/2025.02.04.636560v1
Comprehensive phylogenetic reconstructions support ancestral omnivory in the ecologically diverse bat family Phyllostomidae
Adaptive radiations often occur with an early burst of ecological diversification, which requires not only various available niches but also a generalist ancestor with wide ecological niche breadths. However, ancestral generalism remains hard to test in empirical cases. The New World leaf-nosed bats (family Phyllostomidae) represent an unparalleled mammalian adaptive radiation with diverse dietary niches including arthropods, blood, terrestrial vertebrates, nectar, and fruits. However, when and how often phyllostomid bats transitioned from insectivory to fruit or nectar feeding remains unclear. Here we tested the hypotheses of ancestral insectivory versus ancestral omnivory in Phyllostomidae (141 species) using improved trait reconstructions based on multi-response phylogenetic threshold models, while explicitly accounting for phylogenetic uncertainty. Our results indicate that complementary fruit feeding has fully evolved at the early burst of the phyllostomid radiation and started to evolve in the most recent common ancestor of the family, supporting the ancestral omnivory hypothesis. In addition, fruit feeding probably evolved before nectar eating in Phyllostomidae, in contrast to the claims of previous studies. Extending this analysis to all bat families (621 species) reveals independent evolution of ancestral fruit feeding in four families, namely the Pteropodidae (Old World fruit bats) and three families from the Noctilionoidea superfamily. Despite the ancestral omnivory of these fruit-eating families, only Phyllostomidae and Pteropodidae show high species diversity and evolved predominant and strict fruit feeding. Therefore, our results reveal that ancestral generalism (i.e., omnivory) may be a precondition of but does not necessarily lead to adaptive radiations which also require subsequent niche partitioning and speciation. ### Competing Interest Statement The authors have declared no competing interest.
www.biorxiv.org
February 8, 2025 at 6:52 AM
Reposted by Bernhard Bein
‼️These #PSMC #peaks are #artifacts‼️

Seen #PSMC results like this🤔?
They are caused by ill-set parameters, #very #common, and #easy #to #solve!

For details see 🧵& OA paper @currentbiology.bsky.social
🙂🐢🧬🎉!

cell.com/current-biol...
Avoidable false PSMC population size peaks occur across numerous studies
Hilgers et al. detect and solve a common artifact in PSMC and related methods for historical population size inference. Analyses of real and simulated genomes show that ill-set default parameters fals...
cell.com
February 7, 2025 at 8:14 AM
Reposted by Bernhard Bein
With the new #PacBio Ampli-Fi protocol, you can now sequence genomes with as little as 1 ng of DNA! Paired with our #HiFisequencing technology, it provides a powerful solution for assembling high-quality genomes with exceptional accuracy. #PAG32
January 13, 2025 at 9:49 PM