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Kristoffer Sahlin

@ksahlin.bsky.social

750 followers 150 following 23 posts

Assistant Professor at the Department of Mathematics, Stockholm University, and a Scilifelab Fellow. Algorithms, Modeling, Transcriptomics, Genomics. Amateur runner 5000m 18:48 | 10k 37:40 | HM 1:28:34 | M 3:39:06

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Kristoffer Sahlin @ksahlin.bsky.social · Apr 14

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

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Reposted by Kristoffer Sahlin

Paul Medvedev @pashadag.bsky.social · 13d

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.

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Reposted by Kristoffer Sahlin

Jim Shaw @jimshaw.bsky.social · Sep 7

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

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Sep 7

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

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Reposted by Kristoffer Sahlin

Institut Pasteur | 130 years of biomedical research @pasteur.fr · Jul 24

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

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Kristoffer Sahlin @ksahlin.bsky.social · Jul 25

Incredible! 👏

Reposted by Kristoffer Sahlin

HiTSeq 2025 Conference @hitseq.bsky.social · Jul 23

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"

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Reposted by Kristoffer Sahlin

HiTSeq 2025 Conference @hitseq.bsky.social · Jul 23

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

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Reposted by Kristoffer Sahlin

LongTREC @longtrec.bsky.social · Jul 21

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

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Reposted by Kristoffer Sahlin

Ana Conesa @anaconesa.bsky.social · Jul 23

@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

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Reposted by Kristoffer Sahlin

LongTREC @longtrec.bsky.social · Jul 13

📽️ 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

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Reposted by Kristoffer Sahlin

Antoine Limasset @npmalfoy.bsky.social · Jul 3

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

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Kristoffer Sahlin @ksahlin.bsky.social · Jul 2

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/...

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Reposted by Kristoffer Sahlin

Camille Marchet ⚡ @camillemrcht.bsky.social · Jun 30

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 👀

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Reposted by Kristoffer Sahlin

Paul Medvedev @pashadag.bsky.social · Jun 25

🧵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 · Jun 25

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

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Reposted by Kristoffer Sahlin

Camille Marchet ⚡ @camillemrcht.bsky.social · Jun 11

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.

👇🏻👇🏻

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Kristoffer Sahlin @ksahlin.bsky.social · May 9

Congrats 👏👏

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Kristoffer Sahlin @ksahlin.bsky.social · May 8

IMO it matters a lot as a 'first impression'

Kristoffer Sahlin @ksahlin.bsky.social · May 8

I did only very minor impl. contributions, but from my (non-expert) view, I like that (1) it installs easily (also on a MacBook) and (2) no header files. Felt much easier to get started with than, e.g., C++. I never truly learned good .h/.cpp practices, and I could never get OpenMP/g++ working well

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Kristoffer Sahlin @ksahlin.bsky.social · May 8

Also, it's in Rust! Tool available at github.com/aljpetri/isO...

GitHub - aljpetri/isONclust3: De novo clustering of long transcript reads into genes

De novo clustering of long transcript reads into genes - GitHub - aljpetri/isONclust3: De novo clustering of long transcript reads into genes

github.com

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Kristoffer Sahlin @ksahlin.bsky.social · May 8

As for results, isONclust3 handles a 37M reads PacBio dataset from a revio machine in under 10h while other algorithms fail (>256Gb mem or >120h runtime). On the other datasets, isONclust3 has comparable or better accuracy than the other benchmarked tools.

Kristoffer Sahlin @ksahlin.bsky.social · May 8

The algorithm follows isONclust's algorithm in the general structure (greedy minimizer matching) but adds three key concepts: high confidence minimizers, on-the-fly cluster information update, and iterative (post-)cluster merging.

Kristoffer Sahlin @ksahlin.bsky.social · May 8

The motivation to develop this algorithm came from the inability of other algorithms to process recent large datasets (10-100M reads) from Revio or PromethION machines.

Kristoffer Sahlin @ksahlin.bsky.social · May 8

@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

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Reposted by Kristoffer Sahlin

Camille Marchet ⚡ @camillemrcht.bsky.social · Apr 25

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

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Kristoffer Sahlin @ksahlin.bsky.social · Apr 25

Oh the good ol’ carnac/isonclust(1) times :)

Reposted by Kristoffer Sahlin

Camille Marchet ⚡ @camillemrcht.bsky.social · Apr 25

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...

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