Sahlin K

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Family name Sahlin
Given name Kristoffer
Initials K
ORCID

ORCID 0000-0001-7378-2320
Affiliations Department of Mathematics, Science for Life Laboratory, Stockholm University, 106 91, Stockholm, Sweden.

32 publications

DOI Crossref
AEMB: efficient abundance estimation for metagenomic binning
Pan S, Tolstoganov I, Sahlin K, ..., Zhao XM, Coelho LP
- - (-) - [2025-08-01; online 2025-08-01]
PubMed DOI Crossref
cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads.
Petri AJ, Thi-Huyen Nguyen M, Rajwar A, Benson E, Sahlin K
PLoS ONE 20 (7) e0321246 [2025-07-24; online 2025-07-24]
Erik Benson Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
De novo clustering of large long-read transcriptome datasets with isONclust3.
Petri AJ, Sahlin K
Bioinformatics 41 (5) - [2025-05-06; online 2025-04-23]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads
Petri AJ, Thi-Huyen Nguyen M, Rajwar A, Benson E, Sahlin K
- - (-) - [2025-03-10; online 2025-03-10]
PubMed DOI Crossref
Improved sub-genomic RNA prediction with the ARTIC protocol.
Baudeau T, Sahlin K
Nucleic Acids Res. 52 (17) e82 [2024-09-23; online 2024-08-16]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Designing efficient randstrobes for sequence similarity analyses.
Karami M, Soltani Mohammadi A, Martin M, ..., Patro R, Sahlin K
Bioinformatics 40 (4) - [2024-03-29; online 2024-04-05]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
Designing efficient randstrobes for sequence similarity analyses
Karami M, Mohammadi AS, Martin M, ..., Patro R, Sahlin K
- - (-) - [2023-10-16; online 2023-10-16]
PubMed DOI Crossref
Efficient mapping of accurate long reads in minimizer space with mapquik.
Ekim B, Sahlin K, Medvedev P, Berger B, Chikhi R
Genome Res 33 (7) 1188-1197 [2023-07-00; online 2023-06-30]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Entropy predicts sensitivity of pseudorandom seeds.
Maier BD, Sahlin K
Genome Res 33 (7) 1162-1174 [2023-07-00; online 2023-05-22]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
isONform: reference-free transcriptome reconstruction from Oxford Nanopore data.
Petri AJ, Sahlin K
Bioinformatics 39 (39 Suppl 1) i222-i231 [2023-06-30; online 2023-06-30]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
mapquik: Efficient low-divergence mapping of long reads in minimizer space
Ekim B, Sahlin K, Medvedev P, Berger B, Chikhi R
- - (-) - [2022-12-23; online 2022-12-23]
PubMed DOI Crossref
Strobealign: flexible seed size enables ultra-fast and accurate read alignment.
Sahlin K
Genome Biol. 23 (1) 260 [2022-12-15; online 2022-12-15]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
Nanopore sequencing enables multigenic family reconstruction despite highly frequent PCR-induced recombination
Namias A, Sahlin K, Makoundou P, ..., Belkhir K, Weill M
- - (-) - [2022-11-15; online 2022-11-15]
DOI Crossref
Entropy predicts sensitivity of pseudo-random seeds
Maier BD, Sahlin K
- - (-) - [2022-10-17; online 2022-10-17]
PubMed DOI Crossref
Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment.
Pomerantz A, Sahlin K, Vasiljevic N, ..., Ogden R, Prost S
Nat Protoc 17 (6) 1415-1443 [2022-06-00; online 2022-04-11]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
A survey of mapping algorithms in the long-reads era
Sahlin K, Baudeau T, Cazaux B, Marchet C
- - (-) - [2022-05-22; online 2022-05-22]
PubMed DOI Crossref
Accurate spliced alignment of long RNA sequencing reads
Sahlin K, Mäkinen V
Bioinformatics 37 (24) 4643-4651 [2021-12-11; online 2021-07-24]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Effective sequence similarity detection with strobemers
Sahlin K
Genome Res. 31 (11) 2080-2094 [2021-11-00; online 2021-10-19]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
Flexible seed size enables ultra-fast and accurate read alignment
Sahlin K
- - (-) - [2021-06-20; online 2021-06-20]
PubMed DOI Crossref
Author Correction: Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis.
Sahlin K, Medvedev P
Nat Commun 12 (1) 992 [2021-02-08; online 2021-02-08]
PubMed DOI Crossref
NGSpeciesID: DNA barcode and amplicon consensus generation from long-read sequencing data.
Sahlin K, Lim MCW, Prost S
Ecol Evol 11 (3) 1392-1398 [2021-02-00; online 2021-01-11]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
Strobemers: an alternative to k-mers for sequence comparison
Sahlin K
- - (-) - [2021-01-29; online 2021-01-29]
PubMed DOI Crossref
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis.
Sahlin K, Medvedev P
Nat Commun 12 (1) 2 [2021-01-04; online 2021-01-04]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
Accurate spliced alignment of long RNA sequencing reads
Sahlin K, Mäkinen V
- - (-) - [2020-09-03; online 2020-09-03]
PubMed DOI Crossref
DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies.
Rangavittal S, Stopa N, Tomaszkiewicz M, ..., Makova KD, Medvedev P
BMC Genomics 20 (1) 641 [2019-08-09; online 2019-08-09]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon.
Sahlin K, Tomaszkiewicz M, Makova KD, Medvedev P
Nat Commun 9 (1) 4601 [2018-11-02; online 2018-11-02]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Structural Variation Detection with Read Pair Information: An Improved Null Hypothesis Reduces Bias.
Sahlin K, Frånberg M, Arvestad L
J. Comput. Biol. 24 (6) 581-589 [2017-06-00; online 2016-09-28]
Affiliated researcher Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Assembly scaffolding with PE-contaminated mate-pair libraries.
Sahlin K, Chikhi R, Arvestad L
Bioinformatics 32 (13) 1925-1932 [2016-07-01; online 2016-03-02]
Affiliated researcher Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Gap Filling as Exact Path Length Problem.
Salmela L, Sahlin K, Mäkinen V, Tomescu AI
J. Comput. Biol. 23 (5) 347-361 [2016-05-00; online 2016-03-09]
Affiliated researcher Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
BESST--efficient scaffolding of large fragmented assemblies.
Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L
BMC Bioinformatics 15 (1) 281 [2014-08-15; online 2014-08-15]
PubMed DOI Crossref
The Norway spruce genome sequence and conifer genome evolution.
Nystedt B, Street NR, Wetterbom A, ..., Lundeberg J, Jansson S
Nature 497 (7451) 579-584 [2013-05-30; online 2013-05-22]
PubMed DOI Crossref
Improved gap size estimation for scaffolding algorithms.
Sahlin K, Street N, Lundeberg J, Arvestad L
Bioinformatics 28 (17) 2215-2222 [2012-09-01; online 2012-08-28]
SciLifeLab Data Centre
Publications 9.5.1