Vikram Shivakumar

Must-see new tool from me and Alex! I hurt my back a few weeks ago and was confined to the couch. I used my "break" to play around with webassembly and ended up vibe-coding an AMAZING interactive dotplotter. Passed my prototype to Alex to clean up and extend. Check out his release thread!

Probably the most useful exploratory tool I’ve seen all in a web browser. It’s so quick and easy to use. Super cool stuff. And also an excellent teaching resource to show alignments and dotplots.

I’m excited to share our new preprint introducing HipHap, a tool for assigning long reads to haplotype-resolved diploid reference assemblies! With Max Marin, Matthew Meyerson, and @lh3lh3.bsky.social Preprint: www.biorxiv.org/content/10.6... 🧵 1/6

Congratulations to @benlangmead.bsky.social and @nathanielbrown.bsky.social on receiving a Best Paper Award for their work, “Bounding the Average Move Structure Query for Faster and Smaller RLBWT Permutations,” at the 24th Symposium on Experimental Algorithms!

Have you been thinking of submitting an abstract to Genome Informatics UK this year? You still have time! The deadline is October 5. We'll see you there. coursesandconferences.wellcomeconnectingscience.org/event/genome...

Shredtools is making it easier to explore regions across a pangenome by quickly finding matching genomic regions across hundreds of genomes. The tool can identify a gene region across 476 human genomes in approximately half a second.  Read more: www.biorxiv.org/content/10.6...

Pangenome coordinates can be complex... Shredtools offers a new approach using exact matches to query pangenome data efficiently. Its tools can extract syntenic regions across hundreds of genomes, making pangenome-scale exploration more accessible. pubmed.ncbi.nlm.nih.gov/42465356/

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...

📢 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!

ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies https://www.biorxiv.org/content/10.64898/2026.07.27.741037v1

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...

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!

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...