!!!Reminders!!! Applications due Wed Aug 5 for the @jxtxFoundation scholarships for the @CSHL Biological Data Science conference. Abstracts due Aug 14 for consideration as a talk. #cshldata26 Apply for scholarship: bit.ly/jxtx-biodata26 Conference Info: bit.ly/cshl-biodata26

JXTX + CSHL 2026 Biological Data Science Scholarship

JXTX + CSHL 2026 Biological Data Science Scholarship

bit.ly

Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n

1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...

Complete Mutagenesis of the Genome and Proteome of ΦX174

The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...

biorxiv.org

1/ Excited to share our preprint ImpuT2T: a pangenome-based assembly patching tool ImpuT2T scaffolds draft human assemblies with a pangenome (HPRC2) and patches gaps by leveraging linkage disequilibrium and sequence identity between contigs and reference haplotypes Code: github.com/maojanlin/Im...

ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies

With improvements in sequencing and assembly have come many high-quality telomere-to-telomere assemblies and reference pangenomes. However, the long-read sequencing recipes needed for high quality ass...

biorxiv.org

📢 Genome Informatics 2026 (Hinxton UK + virtual, 2–4 Dec) is coming! Some confirmed speakers now listed: coursesandconferences.wellcomeconnectingscience.org/event/genome... Early-bird registration & bursary deadlines: 7 Sept. Abstract deadline: 5 Oct. Please submit your work & join us!

#zebrafish genome update: So for those of you waiting for RefSeq annotations to hit the GRCz12ab genome, UCSC has generated annotations via BLAST based on the RefSeq RNA's generated for TU.

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation https://www.biorxiv.org/content/10.64898/2026.07.21.739710v1

How did octopuses evolve novel traits? Rishav Mitra, Richard Han, Trey Scott, et al serendipitously discover a unique ribosome adaptation that increases the accuracy of protein synthesis and evolved alongside their elaborate nervous systems vs deep sea relatives. www.biorxiv.org/content/10.6...

🔥 Does switching to a pangenome reference actually improve your association study? We tested it, and the answer is yes, measurably. Our preprint is online now: "Pangenome-based human genome analysis improves trait association and genomic prediction": doi.org/10.64898/202...

Pangenome-based human genome analysis improves trait association and genomic prediction

The Human Pangenome Reference Consortium has generated 462 open-access reference genomes and a variation graph that represents differences among them, providing a substrate for pangenome-based analysi...

doi.org

Senior Bioinformatics Software Developer opening in my team in ONT's Applications department! Hybrid with a few days a week in our Oxford headquarters. We can sponsor visas! www.linkedin.com/jobs/view/44...

🚨 MANUSCRIPT ALERT 🚨 The VGP Phase I manuscript pre-print is now live on bioRxiv! 🧬 doi.org/10.64898/202... Over 8 years, the VGP generated reference genomes for more than 800 vertebrate species, spanning ~95% of vertebrate orders and delivering some of the highest-quality genomes ever produced.

Hi everyone! I'm excited to announce that our lab at UW will soon be recruiting a postdoc to work on DNA methylation signatures in rare disease. This will be a mostly computational position. Please share and reach out if interested! millerlaboratory.com

Complete diploid genomes anchored to the pangenome and interpreted with the help of AI models. Endorsed! We are very actively building towards this future for medical genetics 🔮

Alex Hoischen@ahoischen.bsky.social · last mo.

Excited to share our ‘perspective’ on significant impact long-read sequencing technologies, genome assemblies and better (AI-assisted) interpretation-tools will bring to our field of medical genetics – as we are entering an era of “near-perfect genome sequencing”. www.nature.com/articles/s41...

It's crazy that all of HPRCv2 (466 human genomes totalling 1.5Tbp) can be indexed in just 24GB! Or 36GB with ~single cache miss LF-mapping, which makes it *much* faster than the B-tree representation used by RopeBWT.

Ben Langmead@benlangmead.bsky.social · last mo.

Movi 2 has appeared (as an advance article) in Bioinformatics 🧬 Faster, leaner pangenome queries — half the memory of Movi 1, ~30% faster. Paper: academic.oup.com/bioinformati... Code: github.com/mohsenzakeri/Movi (1/6)

Movi 2 has appeared (as an advance article) in Bioinformatics 🧬 Faster, leaner pangenome queries — half the memory of Movi 1, ~30% faster. Paper: academic.oup.com/bioinformati... Code: github.com/mohsenzakeri/Movi (1/6)

Last chance to register for a Scalable genomics course this autumn! It will be a banger. With @katiejenike.bsky.social @richard-durbin.bsky.social @npmalfoy.bsky.social and @vikramshivakumar.bsky.social! coursesandconferences.wellcomeconnectingscience.org/event/scalab...

T2T roadshow this week! ✈️ Monday, ESHG talk on personalized genomes and Robertsonians ✈️ Wednesday, Sanger ToL talk on great ape acrocentric chromosomes 🚂 Thursday, QMUL talk on a little bit of both 🚇 Friday, London reunion with T2T legend @sergeynurk.bsky.social 🎉

Now published: journals.plos.org/plosbiology/...

What sets the mutation rate of a cell type in an animal species?

Mutation rates per generation are strikingly similar across germlines of animals and across at least one somatic cell type, suggesting a key role for natural selection in shaping mutation rates. This ...

journals.plos.org

Molly Przeworski@mollyprz.bsky.social · 8mo ago

Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social, @natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n

We are excited to share our pan-pangenome paper! This is a long time coming work of my postdoc with the incredible @psudmant.bsky.social, and a stellar group of people! I hope you enjoy reading it! And I am excited to talk more more about it this week at #PEQG26!! www.biorxiv.org/content/10.6...

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

Complete, haplotype-resolved genome assemblies have provided unprecedented insight into the evolution of structurally complex, rapidly evolving regions of human genomes; however, population-scale pang...

biorxiv.org

🦋🌿High-quality genomes begin with quality biological material. 🐝 Before sequencing, each species is identified, documented, collected, and preserved to ensure integrity. For insects, this requires field expertise, taxonomy, and preservation workflows. Biodiversity genomics starts with the specimen🐞

T2T assemblies for nearly all major Y chromosome haplogroups courtesy of a collab between @humanpangenome.bsky.social and HGSVC! What was once the hardest human chromosome to finish can now be routinely assembled thanks to ONT + Verkko www.biorxiv.org/content/10.6...

A big preprint from my group! Muller Elements are considered to be conserved in flies. We tested it by reconstructing the ancestral dipteran karyotype using 340 chromosomal genomes and suprise suprise, they're not... Led by @juliagries.bsky.social and Sam Ebdon. www.biorxiv.org/content/10.6... 🧵👇

🧬New from @ahoischen.bsky.social & co! 📄HiFi sequencing accurately identifies clinically relevant variants in paralogous genes

HiFi sequencing accurately identifies clinically relevant variants in paralogous genes

Long-read HiFi genome sequencing combined with Paraphase enables comprehensive detection of all clinically relevant variant types in paralogous genes. It resolves “dark” regions while enabling haploty...

cell.com

Old friend and new @jhucompsci.bsky.social colleague @benlangmead.bsky.social visited the NIH today and presented a great talk on pangenomes and BWT at exactly the level I need to hear it 🚣 🚣 🚣 😆 Thank you Ben!

Revamped the teaching materials site. Light/dark mode switch at the top. More consistent, compact presentation of all the materials. + Icons and such! www.langmead-lab.org/teaching.html

Off to the first of five “Summer of Nanopore” workshops. More than 100 faculty across the U.S. be trained, joining a growing network of educators making genome sequencing a routine part of classroom learning and research experiences. Box 1 of 3; water surveillance mobile lab!

Some thoughts on where AI in genomics stands right now, building on a symposium we recently hosted at UChicago. Seven points, ranging from why scaling DNA models hasn't delivered, to why metadata is the real bottleneck, to the weird backlash against AI in academia open.substack.com/pub/blekhman...

Seven points on the current state of AI in genomics

A grounded take from the messy middle of an AI revolution

open.substack.com

1/ There is a bill going through the New York State legislature that would transform our ability to provide medical genetics care: www.nysenate.gov/legislation/...

NY State Assembly Bill 2025-A3229A

Prohibits insurance companies from discriminating based on genetic predisposition including refusing to issue or renew, charging any increased rate, or restricting any length of coverage; prohibits insurers from requiring genetic testing.

nysenate.gov

Don't miss the ASHG annual meeting abstract submission deadline, just one week away! This year's meeting will be held in Montreal, October 20–24. The deadline is earlier than in previous years, so be sure to submit and share your research: ashgmeeting.ashg.org/programs/abs... #ASHG26 #ASHG2026