Ben Langmead @benlangmead.bsky.social delivers the official opening for this year's Genome Informatics Conference #GI2025 at Cold Spring Harbor Laboratory. List of talks and posters: meetings.cshl.edu/abstracts.as...

As our beloved Genome Informatics 2025 (#gi2025) approaches, I'm moved to share some photos from past years at CSHL. A couple more photos coming in a reply below...

We’re all so proud of Steven Tan! He’s a super talented undergraduate at JHU. Thanks to the incredible support of @benlangmead.bsky.social, I had the opportunity to help guide this work, and I really loved it. Many thanks also to @sinamajidian.bsky.social for his valuable collaboration and input.

Ben Langmead@benlangmead.bsky.social · 10mo ago

Huge congratulations to Steven Tan, a superb undergraduate junior at JHU CS whose first-author paper "Movi Color: fast and accurate taxonomic classification with the move structure" won best paper at ACM-BCB. Please check it out: www.biorxiv.org/content/10.1.... Congrats, Steven!!

Very excited about Movi 2! Excellent work by Mohsen here. FYI, I have a series of 5 videos on the move structure starting with this one: youtu.be/REniD2dKf6A?...

Move structure, part 1

YouTube video by Ben Langmead

youtu.be

Mohsen Zakeri@mohsenzakeri.bsky.social · 10mo ago

1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...

Great work and congrats to all authors! 🥳 Can't wait to read the preprint. Just for reference: a Fulgor index ⚡ on the same HPRC collection takes 8.26 GB (not in its most succinct representation). Fulgor, however, can be regarded as a "lossy" method here since it is based on kmers.

Mohsen Zakeri@mohsenzakeri.bsky.social · 10mo ago

5/6 On the 466 haplotypes from the 2nd release of HPRC, the fastest Movi 2 index is under 50 GB. It can be reduced to 24 GB while remaining over 3x faster than SPUMONI. Movi 2 is smaller and faster than ropebwt3, although it computes PMLs, which are easier to get than the SMEMs found by ropebwt3.

1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...

GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes

Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi

github.com

An awesome opportunity, strongly recommended to anyone looking for a postdoc in algorithms and genomics!

Rob Patro@robp.bsky.social · 10mo ago

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j.... If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

EvANI benchmarking workflow for evolutionary distance estimation academic.oup.com/bib/article/... An great teamwork by @mohsenzakeri.bsky.social, @stephenhwang.bsky.social and me, with the excellent mentorship of @benlangmead.bsky.social

EvANI benchmarking workflow for evolutionary distance estimation

Abstract. Advances in long-read sequencing technology have led to a rapid increase in high-quality genome assemblies. These make it possible to compare gen

academic.oup.com

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

The 25th iteration of the excellent Conference for Algorithms in Bioinformatics (WABI) starts tomorrow at UMD @umdscience.bsky.social at the Brendan Iribe Center. You can find details at the website wabiconf.github.io/2025/. We'll use the tag #WABI25 for the meeting!

🧬🖥️ In addition to an update to oarfish, a new version (0.14.0) of piscem (zenodo.org/records/1509...) has just been released. This version pulls in some of the latest improvements to sshash by @jermp.bsky.social! 1/2

The second keynote address at WABI '25 will be by Christina Boucher. She will talk about "Recursive Parsing and Grammar Compression in the Era of Pangenomics". PFP (& RPFP) has enabled tremendous advances in representation & indexing; this will be an exciting talk! wabiconf.github.io/2025/talks/t...

No war with Iran

Excited to introduce LiftOn – an open-source tool for accurate, scalable liftover of genome annotations (GFF) across assemblies. 🚀 👉 Code & community: github.com/Kuanhao-Chao... It’s been incredibly rewarding building this for the genomics community. Can’t wait for your feedback and contributions!

GitHub - Kuanhao-Chao/LiftOn: 🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies

🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies - Kuanhao-Chao/LiftOn

github.com

JHU Computer Science@jhucompsci.bsky.social · last yr.

Supported by the NIH, JHU researchers including @kuanhaochao.bsky.social, @stevensalzberg.bsky.social, & @celineh2ooo.bsky.social have created LiftOn, a software tool that can transfer annotations between the genomes of different species to map out new genomes far more quickly than current methods.

Excellent work, Steven & Mohsen! See thread below

Mohsen Zakeri@mohsenzakeri.bsky.social · last yr.

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...

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...

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

Movi Color: fast and accurate long-read classification with the move structure https://www.biorxiv.org/content/10.1101/2025.05.22.655637v1

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

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...

biorxiv.org

The deadline for WABI 2025 has been extended (but is still rapidly approaching) wabiconf.github.io/2025/ * abstract deadline: May 12 (AoE) * paper deadline: May 15 (AoE) Consider submitting your exciting algorithmic bioinformatics work to the WABI conference!

I'll also be on the job market this summer, so please reach out if you're interested! You can find out more about me at these links: LinkedIn: www.linkedin.com/in/arun96/ Personal Website: arundas.org

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...

Hey #genomics, #bioinformatics & #algorithms peeps 💻🧬. If you haven't seen the CfP for WABI '25 yet, check out the website wabiconf.github.io/2025/. It will be held at UMD @umdscience.bsky.social with Broňa Brejová & myself as co-chairs! Submit your exciting & late-breaking algorithmic work to WABI

On Thurs, March 13 at 9AM (ET), @noorpratap.bsky.social will be defending his dissertation! If you want to learn more about tree-based quantification & differential testing, or scATAC-seq preprocessing; tune in! Talk link: umd.zoom.us/j/9873133564... Abstract: talks.cs.umd.edu/talks/4137

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).

🚨 Keynotes at RECOMB-seq 2025! 🚨 🌟 Alicia Oshlack – computational transcriptomics @aliciao.bsky.social 🌟 Rayan Chikhi – sequencing data structures @rayanchikhi.bsky.social 🗓️ Dates: April 24–25, 2025 📍 Seoul, South Korea recomb-seq.github.io/speakers/

Very excited to see Movi (by @mohsenzakeri.bsky.social) now out in iScience: www.cell.com/iscience/ful.... Movi builds on the "move structure" pangenome index, a compressed full-text index and close cousin to r-index. Compared to r-index, the move structure is simpler and more cache-efficient.

Movi: A fast and cache-efficient full-text pangenome index

Biocomputational method; Classification of bioinformatical subject; Genomic analysis

cell.com

1/4 A new version of Movi uses memory prefetching to achieve a degree of latency hiding, improving the speed even further over the version I wrote about in November. Movi is now 30 times faster than SPUMONI to compute pseudo matching lengths for ONT reads. www.biorxiv.org/content/10.1...

We had an amazing time delving into #RNAseq data analysis with R and Bioconductor for the past 3 weeks! Huge thanks to Ludwig Geistlinger and @mikelove.bsky.social for the incredible sessions. Special shoutout to our active and dynamic attendees—you made the course truly exceptional!

1/5 We (Nate Brown, @oahmed.bsky.social, Travis Gagie, and @benlangmead.bsky.social) developed Movi, a cache-efficient full-text pangenome index.  It's the fastest full-text index for pangenomes, particularly appropriate for adaptive sampling where time budget is important.

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 3y ago

Movi: a fast and cache-efficient full-text pangenome index https://www.biorxiv.org/content/10.1101/2023.11.04.565615v1