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/

The RECOMB-Seq 2026 program is now available! Join us May 24–25 in Thessaloniki, Greece, for two days of cutting-edge biological sequence analysis, with keynotes by Camille Marchet (CNRS) and Manolis Kellis (MIT). Full schedule: recomb-seq.github.io/seq2026/prog... #RECOMBseq

Two more days to submit your abstract for a short talk or poster at RECOMB-Seq 2026. See instructions at recomb-seq.github.io/seq2026/call...

10 days left to apply. Stockholm has great employment conditions and benefits. Looking forward to your application!

Kristoffer Sahlin@ksahlin.bsky.social · 5mo ago

𝗣𝗼𝘀𝘁𝗱𝗼𝗰 𝗮𝗻𝗱 𝗣𝗵𝗗 𝗽𝗼𝘀𝗶𝘁𝗶𝗼𝗻𝘀 𝗶𝗻 𝗖𝗼𝗺𝗽𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝗮𝗹 𝗚𝗲𝗻𝗼𝗺𝗶𝗰𝘀 / 𝗔𝗹𝗴𝗼𝗿𝗶𝘁𝗵𝗺𝗶𝗰 𝗕𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝘀 I am currently recruiting for both: 🔹 Postdoc position su.varbi.com/what:job/job... 🔹 PhD position su.varbi.com/en/what:job/... Please share with anyone who might be interested!

Abstract deadline approaching for #HitSeq26 at #ISMB2026: April 9 ⏰🧬💻 If you are developing new algorithms, methods, or tools for high-throughput sequencing data, please submit an abstract for a chance to present a talk or poster at the meeting in Washington, DC, July 12-16.

𝗣𝗼𝘀𝘁𝗱𝗼𝗰 𝗮𝗻𝗱 𝗣𝗵𝗗 𝗽𝗼𝘀𝗶𝘁𝗶𝗼𝗻𝘀 𝗶𝗻 𝗖𝗼𝗺𝗽𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝗮𝗹 𝗚𝗲𝗻𝗼𝗺𝗶𝗰𝘀 / 𝗔𝗹𝗴𝗼𝗿𝗶𝘁𝗵𝗺𝗶𝗰 𝗕𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝘀 I am currently recruiting for both: 🔹 Postdoc position su.varbi.com/what:job/job... 🔹 PhD position su.varbi.com/en/what:job/... Please share with anyone who might be interested!

Postdoktor i Beräkningsbiologi

Matematiska institutionen består av cirka 120 forskare, lärare och administrativ personal och är organiserad i tre huvudsakliga avdelningar: Matematik, Matematisk statistik och Beräkningsmatematik

su.varbi.com

⏰ Last chance! Register your submission with a placeholder abstract for #RECOMBSeq TODAY. Final paper due March 15, 2026, 23:59 AoE Submit now 👉 recomb-seq.github.io/seq2026/call...

1/ Our paper on Multi-Context Seeds is now out, with @tolyan.bsky.social spearheading the work and contributions from Nicolas and @marcelm.net. We introduce a new seeding concept that improves read alignment accuracy while maintaining speed. link.springer.com/article/10.1...

Multi-context seeds enable fast and high-accuracy read mapping - Genome Biology

A key step in sequence similarity search is to identify shared seeds between a query and a reference sequence. A well-known tradeoff is that longer seeds offer fast searches but reduce sensitivity in ...

link.springer.com

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result

DSB Program is out ! Seems incredible (as ever) dsb-meeting.github.io/DSB2026/

Strobealign v0.17.0 is out! github.com/ksahlin/stro...

Release Version 0.17.0 · ksahlin/strobealign

Changes #504: Introduce collinear chaining as the new default mapping and alignment method, replacing NAMs. This reproduces the Minimap2 chaining algorithm providing better mapping accuracy. NAMs ...

github.com

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.

1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.

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

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 11mo ago

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

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!

OReO: optimizing read order for practical compression

AbstractMotivation. Recent advances in high-throughput and third-generation sequencing technologies have created significant challenges in storing and mana

academic.oup.com

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/...

Improved sub-genomic RNA prediction with the ARTIC protocol

Abstract. Viral subgenomic RNA (sgRNA) plays a major role in SARS-COV2’s replication, pathogenicity, and evolution. Recent sequencing protocols, such as th

doi.org

Camille Marchet ⚡@camillemrcht.bsky.social · last yr.

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 👀

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.

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

A k-mer-based estimator of the substitution rate between repetitive sequences https://www.biorxiv.org/content/10.1101/2025.06.19.660607v1

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.

De novo clustering of large long-read transcriptome datasets with isONclust3

AbstractMotivation. Long-read sequencing techniques can sequence transcripts from end to end, greatly improving our ability to study the transcription proc

doi.org

@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/...

Associate Professor in Mathematical Statistics

With its long tradition of excellent research, the Department of Mathematics at Stockholm University has a prominent place in Scandinavian mathematics. The department consists of three divisions: math

su.varbi.com

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

Release v0.16.0 · ksahlin/strobealign

Changelog #476: Improve accuracy by enabling (by default) a variant of multi-context seeds: When no regular seeds - which consist of two strobes - can be found for the entire query, strobealign no...

github.com