Kristoffer Sahlin

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SciLifeLab Fellow since 2020.

Primary: Shown in the list of current labels.

Year 2025

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

Year 2024

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

Year 2023

PubMed DOI Crossref
Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.
Tomaszkiewicz M, Sahlin K, Medvedev P, Makova KD
Genome Biol Evol 15 (11) - [2023-11-01; online 2023-11-15]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Nanopore sequencing of PCR products enables multicopy gene family reconstruction.
Namias A, Sahlin K, Makoundou P, ..., Belkhir K, Weill M
Comput Struct Biotechnol J 21 (-) 3656-3664 [2023-07-16; online 2023-07-16]
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
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
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
PubMed DOI Crossref
A survey of mapping algorithms in the long-reads era.
Sahlin K, Baudeau T, Cazaux B, Marchet C
Genome Biol. 24 (1) 133 [2023-06-01; online 2023-06-01]
Kristoffer Sahlin SciLifeLab Fellow

Year 2022

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
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

Year 2021

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
Safety in multi-assembly via paths appearing in all path covers of a DAG.
Caceres M, Mumey B, Husic E, ..., Sahlin K, Tomescu AII
IEEE/ACM Trans Comput Biol Bioinform PP (-) - [2021-11-30; online 2021-11-30]
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
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
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

Year 2020

DOI Crossref
Chaining with Overlaps Revisited
Sahlin K, Mäkinen V
31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020) 161 (-) 25:1--25:12 [2020-06-09; online 2020-06-09]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm.
Sahlin K, Medvedev P
J. Comput. Biol. 27 (4) 472-484 [2020-04-00; online 2020-03-16]
Kristoffer Sahlin SciLifeLab Fellow

Year 2019

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

Year 2018

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

Year 2017

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

Year 2016

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

Year 2014

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]
Affiliated researcher Kristoffer Sahlin SciLifeLab Fellow

Year 2013

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]
Affiliated researcher Kristoffer Sahlin SciLifeLab Fellow

Year 2012

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]
Affiliated researcher Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
Improved gap size estimation for scaffolding algorithms
Kristoffer S, Nathaniel S, Joakim L, Lars A
Bioinformatics 28 (17) 2215–2222 [2012-09-01]
Kristoffer Sahlin SciLifeLab Fellow
SciLifeLab Data Centre
Publications 9.5.1