Leena Salmela
Overview
Explore the profile of Leena Salmela including associated specialties, affiliations and a list of published articles.
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Articles
29
Citations
726
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Recent Articles
1.
Diaz-Dominguez D, Leinonen M, Salmela L
Algorithms Mol Biol
. 2024 Apr;
19(1):14.
PMID: 38581000
Computing k-mer frequencies in a collection of reads is a common procedure in many genomic applications. Several state-of-the-art k-mer counters rely on hash tables to carry out this task but...
2.
Leinonen M, Salmela L
PLoS One
. 2023 Nov;
18(11):e0294415.
PMID: 38019768
K-mer-based analysis plays an important role in many bioinformatics applications, such as de novo assembly, sequencing error correction, and genotyping. To take full advantage of such methods, the k-mer content...
3.
Ma J, Caceres M, Salmela L, Makinen V, Tomescu A
Bioinformatics
. 2023 Jul;
39(8).
PMID: 37494467
Motivation: Aligning reads to a variation graph is a standard task in pangenomics, with downstream applications such as improving variant calling. While the vg toolkit [Garrison et al. (Variation graph...
4.
Freire B, Ladra S, Parama J, Salmela L
IEEE/ACM Trans Comput Biol Bioinform
. 2022 Jul;
20(2):1550-1562.
PMID: 35853050
During viral infection, intrahost mutation and recombination can lead to significant evolution, resulting in a population of viruses that harbor multiple haplotypes. The task of reconstructing these haplotypes from short-read...
5.
Walve R, Salmela L
BMC Bioinformatics
. 2022 May;
23(1):167.
PMID: 35525918
Background: De novo genome assembly typically produces a set of contigs instead of the complete genome. Thus additional data such as genetic linkage maps, optical maps, or Hi-C data is...
6.
Leinonen M, Salmela L
IEEE/ACM Trans Comput Biol Bioinform
. 2021 Sep;
PP.
PMID: 34529572
The extraction of k-mers from reads is an important task in many bioinformatics applications, such as all DNA sequence analysis methods based on de Bruijn graphs. These methods tend to...
7.
Walve R, Puglisi S, Salmela L
IEEE/ACM Trans Comput Biol Bioinform
. 2021 May;
PP.
PMID: 34057895
A key problem in processing raw optical mapping data (Rmaps) is finding Rmaps originating from the same genomic region. These sets of related Rmaps can be used to correct errors...
8.
Mukherjee K, Rossi M, Salmela L, Boucher C
Algorithms Mol Biol
. 2021 May;
16(1):6.
PMID: 34034751
Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical...
9.
Patro R, Salmela L
iScience
. 2021 Jan;
24(1):101956.
PMID: 33437938
DNA and RNA sequencing is a core technology in biological and medical research. The high throughput of these technologies and the consistent development of new experimental assays and biotechnologies demand...
10.
Freire B, Ladra S, Parama J, Salmela L
Bioinformatics
. 2020 Sep;
37(4):473-481.
PMID: 32926162
Motivation: RNA viruses exhibit a high mutation rate and thus they exist in infected cells as a population of closely related strains called viral quasispecies. The viral quasispecies assembly problem...