Kristoffer Sahlin
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Explore the profile of Kristoffer Sahlin including associated specialties, affiliations and a list of published articles.
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26
Citations
1023
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Recent Articles
1.
Baudeau T, Sahlin K
Nucleic Acids Res
. 2024 Aug;
52(17):e82.
PMID: 39149898
Viral subgenomic RNA (sgRNA) plays a major role in SARS-COV2's replication, pathogenicity, and evolution. Recent sequencing protocols, such as the ARTIC protocol, have been established. However, due to the viral-specific...
2.
Karami M, Soltani Mohammadi A, Martin M, Ekim B, Shen W, Guo L, et al.
Bioinformatics
. 2024 Apr;
40(4).
PMID: 38579261
Motivation: Substrings of length k, commonly referred to as k-mers, play a vital role in sequence analysis. However, k-mers are limited to exact matches between sequences leading to alternative constructs....
3.
Tomaszkiewicz M, Sahlin K, Medvedev P, Makova K
Genome Biol Evol
. 2023 Nov;
15(11).
PMID: 37967251
Y chromosomal ampliconic genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families...
4.
Namias A, Sahlin K, Makoundou P, Bonnici I, Sicard M, Belkhir K, et al.
Comput Struct Biotechnol J
. 2023 Aug;
21:3656-3664.
PMID: 37533804
The importance of gene amplifications in evolution is more and more recognized. Yet, tools to study multi-copy gene families are still scarce, and many such families are overlooked using common...
5.
Ekim B, Sahlin K, Medvedev P, Berger B, Chikhi R
Genome Res
. 2023 Jul;
33(7):1188-1197.
PMID: 37399256
DNA sequencing data continue to progress toward longer reads with increasingly lower sequencing error rates. We focus on the critical problem of mapping, or aligning, low-divergence sequences from long reads...
6.
Petri A, Sahlin K
Bioinformatics
. 2023 Jun;
39(39 Suppl 1):i222-i231.
PMID: 37387174
Motivation: With advances in long-read transcriptome sequencing, we can now fully sequence transcripts, which greatly improves our ability to study transcription processes. A popular long-read transcriptome sequencing technique is Oxford...
7.
Sahlin K, Baudeau T, Cazaux B, Marchet C
Genome Biol
. 2023 Jun;
24(1):133.
PMID: 37264447
It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the...
8.
Maier B, Sahlin K
Genome Res
. 2023 May;
33(7):1162-1174.
PMID: 37217253
Seed design is important for sequence similarity search applications such as read mapping and average nucleotide identity (ANI) estimation. Although -mers and spaced -mers are likely the most well-known and...
9.
Tomaszkiewicz M, Sahlin K, Medvedev P, Makova K
bioRxiv
. 2023 Mar;
PMID: 36993458
Y-chromosomal Ampliconic Genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has...
10.
Sahlin K
Genome Biol
. 2022 Dec;
23(1):260.
PMID: 36522758
Read alignment is often the computational bottleneck in analyses. Recently, several advances have been made on seeding methods for fast sequence comparison. We combine two such methods, syncmers and strobemers,...