Vikram Shivakumar
@vikramshivakumar.bsky.social
📤 148
📥 120
📝 22
PhD Student @ JHU Langmead Lab
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.
add a skeleton here at some point
2 days ago
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Vikram Shivakumar
Sina Majidian
4 days ago
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
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Vikram Shivakumar
Sina Majidian
4 days ago
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!
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Looking forward to lots of great talks from JHU folks at CSHL this week!
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5 days ago
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Vikram Shivakumar
Adam Phillippy
about 1 month ago
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. 🦒...
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Vikram Shivakumar
Adam Phillippy
about 1 month ago
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]...
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Vikram Shivakumar
Sina Majidian
about 2 months ago
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)
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Vikram Shivakumar
Sina Majidian
3 months ago
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
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Vikram Shivakumar
Rob Patro
3 months ago
Vikram Shivakumar telling us about "Partitioned Multi-MUM finding for scalable pangenomics"
#WABI25
! So many kinds of matches!
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Vikram Shivakumar
Liana Lareau
3 months ago
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...
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Protein language models reveal evolutionary constraints on synonymous codon choice
Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...
https://www.biorxiv.org/content/10.1101/2025.08.05.668603
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reposted by
Vikram Shivakumar
Petra Korlević
3 months ago
#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
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Vikram Shivakumar
4 months ago
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!
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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)
4 months ago
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Really excited to see this published! To more mum-finding 🍻
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5 months ago
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reposted by
Vikram Shivakumar
Rob Patro
5 months ago
🖥️🧬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!
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We are what we index; a primer for the Wheeler Graph era
Talk by Ben Langmead - WABI 2025
https://wabiconf.github.io/2025/talks/talk1/
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reposted by
Vikram Shivakumar
Mohsen Zakeri
5 months ago
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...
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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
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Partitioned Multi-MUM finding for scalable pangenomics
Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We prev...
https://www.biorxiv.org/content/10.1101/2025.05.20.654611v1
6 months ago
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reposted by
Vikram Shivakumar
Arun Das
6 months ago
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:
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reposted by
Vikram Shivakumar
Sara Carioscia
6 months ago
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
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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 👀
6 months ago
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reposted by
Vikram Shivakumar
Igor Martayan
7 months ago
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...
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Vikram Shivakumar
Nature Methods
8 months ago
Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications.
www.nature.com/articles/s41...
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Vikram Shivakumar
Bohan Ni
8 months ago
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...
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Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
https://genome.cshlp.org/content/early/2025/03/19/gr.279323.124.abstract
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reposted by
Vikram Shivakumar
Ben Langmead
8 months ago
Scenes from
#StandUpForScience2025
in DC today. Huge contingent from Johns Hopkins, and also from UMD & DC/Virginia Unis.
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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).
9 months ago
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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.
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Mumemto: efficient maximal matching across pangenomes
Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts ...
https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1
10 months ago
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Vikram Shivakumar
bioRxiv Bioinfo
10 months ago
Mumemto: efficient maximal matching across pangenomes
https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1
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