1/ Excited to share the newest tool in the pangenome MUMiverse: Shredtools! Shredtools enables a user to navigate the pangenome coordinate system with multi-MUMs. More in the thread🧵 Code: github.com/vikshiv/shredtools Interactive tool for querying HPRC assemblies: vikshiv.github.io/shredtools

JOB ALERT! I'm hiring two postdocs in Computational Genomics to join our lab in beautiful Gothenburg, Sweden. Please share and repost! CGRLab.github.io/research/

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...

Very bittersweet for me too. I’ll always be grateful for your mentorship and for the amazing lab and community I’ve been fortunate to grow alongside over the years. I’ll definitely miss Baltimore and the wonderful genomics community at Hopkins. Looking forward to the next chapter in Cambridge!

Thank you! And thanks to all the wonderful people at JHU I’ve had the pleasure of working with during my PhD. And of course, to my advisor @benlangmead.bsky.social and my super supportive thesis committee members @aphillippy.bsky.social and @mikeschatz.bsky.social. Excited to 🇺🇸 -> 🇬🇧 soon!

1/ Excited to share my first first-author preprint from my PhD! We introduce Perseus, a lineage-aware confidence estimation framework for taxonomic classification in long-read metagenomics. Preprint: www.biorxiv.org/content/10.6... Code: github.com/matnguyen/Pe...

As an alternative to the h-index, I made the Mentorship Index (M-index) to proxy a scientist's contribution to mentoring junior scientists. Ex. M10-index = # last-author publications where the first author had < 10 pubs. Calculate yours: jef.works/Mentorship-I... Blog: jef.works/blog/2026/03... 🧵👇

New tool from @alexsweeten.bsky.social to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates" 📄 www.biorxiv.org/content/10.6... 📦 github.com/marbl/anianns

I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt: employment.utah.edu/salt-lake-ci...

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

Really excited to see our new work in scaling Mumemto to any size pangenome published in Genome Research this morning. And right on cue with the great opportunity to present this work at #GI2025 this week.

Nicole Brown gave a fantastic talk on Identifying introgressions across pangenomes with Panagram It uses k-mer conservation to annotate genomic variation across hundreds of genomes, followed by normalization of k-mer profiles to identify introgression events github.com/kjenike/pana... #GI2025

Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0 Code: github.com/vikshiv/mume... Very efficient pangenome visualization tool, revealing synteny and variations!

Looking forward to lots of great talks from JHU folks at CSHL this week!

If that’s not enough, we threw in a complete, T2T giraffe genome! Giraffe genomes are pretty cool. Almost all of their chromosomes are Robertsonian fusions of the typically telocentric ruminant chromosomes. 🐄 vs. 🦒...

Last week we were in the Washington Post for our characterization of Robertsonian chromosomes. This week we are entering our 10th day of being shut down and all of our research is on hold. To help me feel not-so-bad, here is a thread of some studies we released right before the shutdown 🧵 [1/n]...

Excited to share our EvANI benchmarking workflow, published in Briefings in Bioinformatics doi.org/10.1093/bib/... Computing average nucleotide identity (ANI) is neither conceptually nor computationally trivial. Its definition has evolved over years, with different meanings and assumptions (1/5)

Great talk by Vikram @vikramshivakumar.bsky.social on studying pangenomes and synteny visualization in #WABI25 Github: github.com/vikshiv/mume... First paper: genomebiology.biomedcentral.com/articles/10.... Second: www.biorxiv.org/content/10.1... #WABI2025

Vikram Shivakumar telling us about "Partitioned Multi-MUM finding for scalable pangenomics" #WABI25! So many kinds of matches!

This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...

#SciArt doodle of @vikramshivakumar.bsky.social's talk yesterday at the @sangerinstitute.bsky.social on MUMs* *maximal unique matches in pangenomes, now if you did that on sequenced moms you could do mummoms

Excited to share our new preprint on detecting foldback artifacts in long reads with my advisors Matthew Meyerson and @lh3lh3.bsky.social ! Stop by poster C-180 on Wednesday at ISMB/ECCB2025 to learn more and chat!

If you’re in Liverpool, stop by my poster A217 at ISMB/EECB 2025, and chat about all things pangenomes, MUMs, and alignment (and the Beatles or Oasis-mania)

Really excited to see this published! To more mum-finding 🍻

🖥️🧬We're thrilled to announce that one of our keynote speakers at #WABI2025 will be the inimitable @benlangmead.bsky.social! wabiconf.github.io/2025/talks/t... Ben's keynote is titled "We are what we index; a primer for the Wheeler Graph era", & it's sure to be a whirlwind tour of full-text indexing!

1/5 We introduce Movi Color, led by Steven Tan (a brilliant undergrad member of Langmead lab) for taxonomic and multi-class classification. It uses a full-text index based on the move structure and does not rely on predefined values (like k-mer length) for index building. github.com/mohsenzakeri...

Excited to share a new update to Mumemto, scaling MUM and conserved element finding to any size pangenome! Preprint out now w/ @benlangmead.bsky.social. Mumemto scales to the new HPRC v2 release and beyond, and can merge in future assemblies without any recomputation! 1/n

Our pre-print on investigating variation in South Asian genomes is now out! Thank you to @mikeschatz.bsky.social, @rajivmccoy.bsky.social and @aabiddanda.bsky.social for all their work on this. 🧵 A thread on the key results and takeaways from our work:

If you are here at #bog25 please check out my poster (number 87) tonight! 😁 Showing our work on common variation associated with aneuploidy in human embryos

Excited to share our latest work on comparing and visualizing multiple genome assemblies to identify conservation and structural variation in pangenomes with Mumemto! Check out poster 250 at #bog25 if you are here. New preprint coming very soon 👀

Next up is Nathaniel Brown from @benlangmead.bsky.social's group presenting col-bwt, a new algorithm for computing chain statistics using multi-maximal unique matches. www.biorxiv.org/content/10.1...

Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications. www.nature.com/articles/s41...

Happy to share our work characterizing functional rare SVs in rare diseases with long-read genome sequencing and transcriptomic outlier data: genome.cshlp.org/content/earl...

Scenes from #StandUpForScience2025 in DC today. Huge contingent from Johns Hopkins, and also from UMD & DC/Virginia Unis.

We ran Mumemto on 474 human assemblies from @humanpangenome.bsky.social to find syntenic regions using MUMs. Mumemto scales remarkably well to large pangenomes thanks to compressed-space algos! It took under 2 days across 7 nodes (each using ~500 GB memory).

Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.

Mumemto: efficient maximal matching across pangenomes https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1