iiinova — where your digital self keeps evolving

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Sina Majidian @sinamajidian.bsky.social · 06/11/2025

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...

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Ben Langmead @benlangmead.bsky.social · 03/11/2025

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...

Driveway at Cold Spring Harbor Lab, with conference attendees walking to a meal

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Mohsen Zakeri @mohsenzakeri.bsky.social · 02/11/2025

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.

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Ben Langmead @benlangmead.bsky.social · 21/10/2025

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?...

youtu.be

Move structure, part 1

YouTube video by Ben Langmead

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Giulio Ermanno Pibiri @jermp.bsky.social · 22/10/2025

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.

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Mohsen Zakeri @mohsenzakeri.bsky.social · 21/10/2025

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.com

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

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

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Mohsen Zakeri @mohsenzakeri.bsky.social · 09/10/2025

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

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Sina Majidian @sinamajidian.bsky.social · 20/08/2025

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

Anchor-based merging requires a common sequence (red) present in each partition. Multi-MUMs are merged by identifying overlaps between partition-specific matches in the anchor coordinate space, and a uniqueness threshold determines if a MUM is still unique in each partition after truncation. (B) String-based merging enables computation of multi-MUMs between partitions without a common sequence. An example tree (left) is shown, highlighting the use case where partial multi-MUMs specific to internal nodes (starred) can be computed by merging subclade- based partitions up a tree. (right) MUM overlaps are computed by running Mumemto on the MUM sequences, and the uniqueness threshold array ensures overlaps remain unique across the merged dataset. (C) An example Burrows-Wheeler Transform (BWT), matrix (BWM), and Longest Common Prefix (LCP) array, with sequence IDs for each suffix shown (ID). A non-maximal unique match (UM) is shown, and the uniqueness threshold for this match is found using the flanking LCP values. (D) A partial multi-MUM (in blue) is found in all-but-one sequence (excluded in red). Using two anchor sequences (red and orange), all-but-one partial MUMs can be computed using an augmented anchor-based merging method.

(A) Phylogeny of geographically diverse A. thaliana accessions (Lian et al. 2024), with broad geographical regions colored. Internal nodes are labeled with the coverage of partial multi-MUMs across the leaves of each node. Internal node partial MUMs are computed by merging subtree-based partitions progressively up the phylogeny. (B) Global multi-MUM synteny across the full dataset shown in blue (with inversions in green). Global MUMs are computed by merging all partitions together (representing the root node). Additionally, three geographically distinct subgroups are highlighted and partition-specific multi-MUMs (in purple, with inversions in pink) reveal local structural variation in centromeric regions.

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Rob Patro @robp.bsky.social · 20/08/2025

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!

wabiconf.github.io

WABI 2025

WABI Conference on Algorithms in Bioinformatics

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Rob Patro @robp.bsky.social · 30/06/2025

🧬🖥️ 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

zenodo.org

The piscem index

This manuscript provides a brief overview of the piscem index — a fast and compact index for the compacted, colored, reference (i.e., storing positional information about the input references) de Brui...

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Rob Patro @robp.bsky.social · 23/06/2025

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...

wabiconf.github.io

Recursive Parsing and Grammar Compression in the Era of Pangenomics

Talk by Christina Boucher - WABI 2025

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Mia Farrow @miafarrow.bsky.social · 20/06/2025

No war with Iran

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Kuan-Hao Chao @kuanhaochao.bsky.social · 17/06/2025

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.com

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

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Ben Langmead @benlangmead.bsky.social · 29/05/2025

Excellent work, Steven & Mohsen! See thread below

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Mohsen Zakeri @mohsenzakeri.bsky.social · 29/05/2025

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...

github.com

Release Movi Color · mohsenzakeri/Movi

This version introduces Movi Color. Movi rows are augmented with run colors, defined based on the origin of the suffixes within each run. The Movi Color index can be built by either an additional ...

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Vikram Shivakumar @vikramshivakumar.bsky.social · 27/05/2025

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

biorxiv.org

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...

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Rob Patro @robp.bsky.social · 07/05/2025

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!

wabiconf.github.io

WABI 2025

WABI Conference on Algorithms in Bioinformatics

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Arun Das @arun-das.bsky.social · 21/04/2025

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

arundas.org

Arun Das

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Igor Martayan @imartayan.bsky.social · 27/04/2025

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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Rob Patro @robp.bsky.social · 05/04/2025

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

wabiconf.github.io

WABI 2025

WABI Conference on Algorithms in Bioinformatics

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Rob Patro @robp.bsky.social · 12/03/2025

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

talks.cs.umd.edu

Talks

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Vikram Shivakumar @vikramshivakumar.bsky.social · 26/02/2025

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).

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recombseq.bsky.social @recombseq.bsky.social · 24/01/2025

🚨 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/

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Ben Langmead @benlangmead.bsky.social · 11/12/2024

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.

cell.com

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

Biocomputational method; Classification of bioinformatical subject; Genomic analysis

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Mohsen Zakeri @mohsenzakeri.bsky.social · 19/02/2024

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...

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Physalia-courses@ONLINE @physaliacourses.bsky.social · 17/11/2023

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!

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Mohsen Zakeri @mohsenzakeri.bsky.social · 07/11/2023

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.

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