Kristoffer Sahlin

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] Open Access

Entropy predicts sensitivity of pseudo-random seeds.

Maier BD, Sahlin K

Genome Res - (-) - [2023-05-22; online 2023-05-22] Open Access

Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.

Tomaszkiewicz M, Sahlin K, Medvedev P, Makova KD

bioRxiv - (-) - [2023-03-18; online 2023-03-18]

Year 2022

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]

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] Open Access

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]

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]

Year 2021

Accurate spliced alignment of long RNA sequencing reads

Sahlin K, Mäkinen V

Bioinformatics 37 (24) 4643-4651 [2021-12-11; online 2021-07-24]

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]

Effective sequence similarity detection with strobemers

Sahlin K

Genome Res. 31 (11) 2080-2094 [2021-11-00; online 2021-10-19]

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]

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]

Year 2020

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]

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]

Year 2019

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]

Year 2018

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]

Year 2017

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

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

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

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

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

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

Improved gap size estimation for scaffolding algorithms

Kristoffer S, Nathaniel S, Joakim L, Lars A

Bioinformatics 28 (17) 2215–2222 [2012-09-01]