Kristoffer Sahlin
@ksahlin.bsky.social
Associate Professor at the Department of Mathematics, Stockholm University, and a Scilifelab Fellow. Algorithms, Modeling, Transcriptomics, Genomics.
Hobby runner 5000m 18:48 | 10k 37:40 | HM 1:27:43 | M 3:39:06
Hobby runner 5000m 18:48 | 10k 37:40 | HM 1:27:43 | M 3:39:06
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Kristoffer Sahlin
@ksahlin.bsky.social
· Apr 14
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
Strobealign v0.16.0 has been released. It comes with both runtime and accuracy improvements. Full changelog here github.com/ksahlin/stro...
Reposted by Kristoffer Sahlin
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.
September 25, 2025 at 1:21 PM
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.
Reposted by Kristoffer Sahlin
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
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
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
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
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
Reposted by Kristoffer Sahlin
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
@rayan.chiki.bsky.social
#Bioinformatics
July 24, 2025 at 3:10 PM
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
@rayan.chiki.bsky.social
#Bioinformatics
Reposted by Kristoffer Sahlin
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"
July 23, 2025 at 10:56 AM
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"
Reposted by Kristoffer Sahlin
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
July 23, 2025 at 4:00 PM
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
Reposted by Kristoffer Sahlin
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
@anaconesa.bsky.social
July 21, 2025 at 12:30 PM
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
@anaconesa.bsky.social
Reposted by Kristoffer Sahlin
@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
July 23, 2025 at 10:40 AM
@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
Reposted by Kristoffer Sahlin
📽️ 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
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
July 13, 2025 at 8:28 AM
📽️ 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
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
Reposted by Kristoffer Sahlin
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!
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
July 3, 2025 at 10:53 AM
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!
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/...
July 2, 2025 at 11:48 AM
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/...
Reposted by Kristoffer Sahlin
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 👀
June 30, 2025 at 4:36 PM
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 👀
Reposted by Kristoffer Sahlin
🧵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.
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.
A k-mer-based estimator of the substitution rate between repetitive sequences https://www.biorxiv.org/content/10.1101/2025.06.19.660607v1
June 25, 2025 at 1:19 PM
🧵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.
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.
Reposted by Kristoffer Sahlin
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.
👇🏻👇🏻
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.
👇🏻👇🏻
June 11, 2025 at 2:46 PM
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.
👇🏻👇🏻
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
May 8, 2025 at 1:04 PM
@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.
Reposted by Kristoffer Sahlin
@tolyan.bsky.social is our very last speaker, on randstrobes ( high sensitivity seeds ) and their evolution the multi context seeds
April 25, 2025 at 7:39 AM
@tolyan.bsky.social is our very last speaker, on randstrobes ( high sensitivity seeds ) and their evolution the multi context seeds
Reposted by Kristoffer Sahlin
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...
April 25, 2025 at 7:14 AM
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...
Reposted by Kristoffer Sahlin
🚨 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
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
April 16, 2025 at 10:53 PM
🚨 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
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
April 16, 2025 at 3:40 PM
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...
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
April 14, 2025 at 8:12 AM
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)
su.varbi.com/en/what:job/...
Application deadline: April 22. (1/3)
PhD student in Computational Mathematics
The Department of Mathematics at Stockholm University has with its long tradition of excellent research a prominent place in Scandinavian mathematics. The department consists of three divisions: Mathe
su.varbi.com
March 26, 2025 at 2:08 PM
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)
su.varbi.com/en/what:job/...
Application deadline: April 22. (1/3)
Reposted by Kristoffer Sahlin
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
Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome
March 17, 2025 at 6:30 AM
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
Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome
Reposted by Kristoffer Sahlin
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
March 4, 2025 at 6:56 AM
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
Reposted by Kristoffer Sahlin
🚀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
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
www.cs.helsinki.fi
February 6, 2025 at 3:12 PM
🚀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
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
Reposted by Kristoffer Sahlin
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.
Low mem construction. Spaced seeds. Optional crazy-low-mem search. More info on the horizon.
I've pushed a new version of Sufr, a #Rust implementation for fast parallel creation and searching of a suffix array. This release includes support for spaced seeds and searches requiring almost no RAM.
crates.io/crates/sufr
crates.io/crates/sufr
crates.io: Rust Package Registry
crates.io
January 7, 2025 at 11:39 PM
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.
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...
Multi-context seeds enable fast and high-accuracy read mapping
A key step in sequence similarity search is to identify seeds that are found in both the query and the reference sequence. A seed is a shorter substring (e.g., a k -mer) or pattern (e.g., a spaced k -...
www.biorxiv.org
December 13, 2024 at 11:06 AM
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...