Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

Congratulations to Rayan Chiki, (Institut Pasteur) head of the “Sequence Bioinformatics” unit, for securing the ERC Proof of Concept 2025 for his project ENZYMINER! 👏 ‪@rayan.chiki.bsky.social #Bioinformatics

We have officially started #HitSeq track @hitseq.bsky.social at #ISMBECCB2025. Francisco de la Vega, introduces our first #keynote speaker Valentina Boeva @valboeva.bsky.social with her talk: "Learning variant effects on chromatin accessibility and 3D structure without matched Hi-C data"

Meet our amazing sponsor PacBio @pacbio.bsky.social for @hitseq.bsky.social track at #ISMBECCB2025 represented by Elizabeth Tseng with her talk "Bioinformatics analysis for long-read RNA sequencing: challenges and promises" #hitseq #iscb #sequencing #application #iverpool #uk

Dont miss any of our #LongTREC communications at #ISMBECCB2025. Download this flyer to make catching all the latest & hottest long-read transcriptomics research simple. @anaconesa.bsky.social

@hitseq.bsky.social is kicking off with our first keynote @valboeva.bsky.social talking about "Learning variant effects on chromatin accessibility and 3D structure without matched Hi-C data". #ISMBECCB2025

📽️ Next in the LongTREC Series: Mahmud Sami Aydin! Sami is a Doctoral Candidate at @stockholm-uni.bsky.social , working under the supervision of @ksahlin.bsky.social .In this video, Sami shares his research and his role in the broader LongTREC collaboration across Europe. #AlgorithmDevelopment

Paper alert! We present Oreo a tools that reorder long reads datasets in a way to compress them efficiently with ANY universal compressor like gz, zstd, xz ... TLDR: You can get state of the art compression WITHOUT a dedicated compressor/decompressor! academic.oup.com/bioinformati... A thread!

I worked with Thomas during a three months research visit during his PhD, and it resulted in a paper in NAR. I highly recommend him. doi.org/10.1093/nar/...

Thomas Baudeau defended his thesis on Studying the properties of viral long reads mapping methods - congrats docteur Baudeau you'll be deeply missed in the team. I'm very glad I got the chance to work with you. Thomas is also on the lookout for a postdoc 👀

🧵1/n Estimating mutation rates using k-mers is fast—but what happens when repeats dominate the genome? In a new preprint, Haonan Wu, Antonio Blanca, and myself propose a *repeat-aware* estimator that's accurate even in centromeres.

Hey yeast lovers. Do you like pangenomes? O'Donnel et al. 2023 produced T2T assemblies of different strains, including phased haplotypes for yeast. Here I selected 10 phased haplotypes and the S288C reference, and looked for the MST28 / YAR033W gene reported to contain SVs such as indels. 👇🏻👇🏻

@alexanderjpetri.bsky.social's isONclust3 algorithm is now published doi.org/10.1093/bioi.... isONclust3 performs de novo clustering of long-read cDNA sequencing data. A key step in reference-free transcriptome analysis.

@tolyan.bsky.social is our very last speaker, on randstrobes ( high sensitivity seeds ) and their evolution the multi context seeds

2 in a row for @ksahlin.bsky.social (👋🏻👏🏻), first is @alexanderjpetri.bsky.social on de novo clustering of long read RNA, a problem that brings memories...

🚨 Final Call! 🚨 The last day to submit abstracts for the HitSeq Special Track is April 17th! 🧬 📅 HitSeq is part of ISMB 2025, July 20–24, Liverppol, UK 🇬🇧 📢 Don’t miss your chance to present your work on high-throughput sequencing! Submit now 👉 www.iscb.org/ismbeccb2025... #HitSeq #ISMB2025

We are looking for an Associate professor in Mathematical statistics. Deadline to apply is June 1, 2025. More information: su.varbi.com/en/what:job/...

Strobealign v0.16.0 has been released. It comes with both runtime and accuracy improvements. Full changelog here github.com/ksahlin/stro...

We are hiring PhD students in Computational Mathematics and Mathematics at Stockholm University in various subjects: su.varbi.com/en/what:job/... Application deadline: April 22. (1/3)

We are looking for PhD students! Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome

Thrilled to see our Perspective on long-read transcriptomics Published in Advance in @genomeresearch.bsky.social, with #AdamFrankish and @carolinamonzo.bsky.social. We discuss the opportunities and challenges of LRS to uncover Transcript Divergence and for Genome Annotation. tinyurl.com/bdeteu4j

🚀Exciting PhD Opportunity🚀 Are you passionate about: 🧬 Graph algorithms for real-world genome sequencing? 💻 Writing efficient, reusable code & libraries? 🌲 Exploring stunning Nordic nature? This PhD position is for YOU! 🎓✨ 📅 Apply by March 2 #PhD #ComputerScience #Bioinformatics #GraphAlgorithms

Still in beta, so possible minor API changes ... but our Suffix Array library (in Rust) is ready for business. Builds on lovely ideas in CaPS-SA from @robp.bsky.social. Low mem construction. Spaced seeds. Optional crazy-low-mem search. More info on the horizon.

Strobealign v0.15.0 is released: (1) Allows more indexed contigs (2^32), (2) adds a mode --mcs which increase accuracy (paper on mcs www.biorxiv.org/content/10.1...). --mcs is still non-default in this release until we optimize it a bit more. Full changelog here github.com/ksahlin/stro...

🚨You've got to read this one. 🚨

Hi Bluesky! Live from the Seqbim workshop, our yearly national workshop on sequence bioinformatics. We started with a strobecool keynote by @ksahlin.bsky.social ! He overviewed strobemers, and related developments.

U Arizona Computer Science is seeking to fill 6 (six ... six!) new faculty positions cs.arizona.edu/currently-op... If you like warm winters, hikes in the desert, bread that doesn't get moldy, and a great scientific environment ... come to Tucson

I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics) go.bsky.app/TRWCnZs

Strobealign v0.12.0 is released and available on conda. It has (quantified) improvements related to metagenomic coverage-based applications, such as better uniformly distributed reads in the case of perfect repeats. See the full changelog here github.com/ksahlin/stro...

I'm recruiting PhD students for Oct 24 start at University of Bath. Fully funded for UK students only. If interested in developing data structures/algorithms for bacterial genomics, or exploring plasmid epidemiology, or ML/AI on bacterial/phage geno/pheno data, give me a call!

Interested in doing a PhD with me in Sweden? Experimental+computational genomics skills and/or interests? We have an open position! Great environment at KTH on @SciLifeLab campus, staff benefits, well-funded project, close interactions with our New York team. kth.varbi.com/en/what:job/...

What is your all-time favorite data structure, and why? Respond or quote "skeet", and let us know what data structure we should all appreciate more! 🧬🖥

When “you’re on my list” has a different meaning. The list of alternative reviewer suggestions of course. 😈

I wrote a blog post a while back on a silly problem: how does the average contig length for an assembly relate to its N50? I "proved": N50 = (s * average contig length) for a constant s under exponentially distributed lengths. Interestingly, "s" = 1.6783469... and this is exact, not approximate

Excited to share our preprint introducing MGX 2.0, which adds metagenome (co-)assembly (including binning and bin assessment) as well as de novo metatranscriptome assembly.

What's a paper in algorithmic bioinformatics that you found inspirational or cool that maybe others don't know about? Reply and share a link. Extra points if it's not a paper written by close colleagues :)

Wow, just discovered this book recently published: Pearles of Algorithm Engineering. I've been wishing for a book like this! www.cambridge.org/core/books/p...

Whaaat, no bookmarks feature 👀 where should I store all the papers I never read 😳

"Minmers are a generalization of minimizers that enable unbiased local jaccard estimation" aka MashMap3 with Bryce Kille, @erikg.bsky.social, and @treangen.bsky.social is now accepted in Bioinformatics! Many thanks to the reviewers for their very careful reviews doi.org/10.1093/bioi...