Leena Salmela
University Lecturer
Department of Computer Science
P. O. Box 68
(Pietari Kalmin katu 5)
FIN-00014 University
of Helsinki, FINLAND
Email: Firstname.Lastname@cs.Helsinki.FI
Room: A237
Research
Genome assembly
Determining the genomic sequence of an organism is a fundamental task in molecular biology. Current sequencing technologies are not able to read the whole genome at once but instead produce sets of short reads, i.e. fragments of the genome, which must then be assembled. We have previously worked on several phases of fragment assembly including sequencing error correction, scaffolding, and gap filling. Together with our biological collaborators we have sequenced and assembled the genome of the Glanville fritillary butterfly which is the first large genome sequenced in Finland. Currently we work on providing probabilistic guarantees for structural correctness of genome assembly.
De Bruijn graphs
The de Bruijn graph is an important data structure for processing data produced by second generation sequencing machines which produce short but accurate sequencing reads. We have used de Bruijn graphs to develop methods for e.g. sequencing error correction and gap filling. Our current projects include development of de Bruijn graphs suitable for third generation sequencing data.
People
- University Lecturer Leena Salmela
Alumni
- Postdoctoral Researcher Diego Díaz-Domínguez
- PhD Miika Leinonen
- Research Assistant Essi Tepponen
- PhD Riku Walve
- Research Assistant Silvia Nepšinská
- Taku Onodera (now assistant professor at University of Tokyo)
Publications
Recent publications
- L. Salmela: SAMA: a contig assembler with correctness guarantee. Algorithms for Molecular Biology, Volume 20, Article number 9, 2025.
- D. Díaz-Domínguez, M. Leinonen, and L. Salmela: Space-efficient computation of k-mer dictionaries for large values of k. Algorithms for Molecular Biology, Volume 19, Article number 14, 2024.
- M. Leinonen and L. Salmela: SAKE: Strobemer-assisted k-mer extraction. PLoS ONE, Volume 18, Issue 11, e0294415, 2023.
- D. Díaz-Domínguez and L. Salmela: Computing all-vs-all MEMs in grammar-compressed text. In Proc. SPIRE 2023, International symposium on String Processing and Information Retrieval (ed. F.M. Nardini, N. Pisanti, and R. Venturini), Lecture Notes in Computer Science 14240, Springer, 2023, 157-170.
- J. Ma, M. Cáceres, L. Salmela, V. Mäkinen, A.I. Tomescu: Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. Bioinformatics, Volume 39, Issue 8, btad460, 2023.
- D. Díaz-Domínguez, S. Dönges, S. Puglisi, and L. Salmela: Simple runs-bounded FM-index designs are fast. In Proc. SEA 2023, International Symposium on Experimental Algorithms (ed. L. Georgiadis), Leibniz International Proceedings in Informatics (LIPIcs) 265, Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, 2023, 7:1-7:16..
- B. Freire, S. Ladra, J.R. Paramá, and L. Salmela: ViQUF: De novo viral quasispecies reconstruction using unitig-based flow networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 20, 2023, 1550-1562.
Software