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
- University Researcher Jarno Alanko
- Doctoral Researcher Pierfrancesco Martinello
- Research Assistant Martin Kostadinov
Alumni
- Postdoctoral Researcher Diego Díaz-Domínguez
- PhD Miika Leinonen
- Research Assistant Essi Tepponen
- PhD Riku Walve
- Research Assistant Silvia Nepšinská
- Postdoctoral Researcher Taku Onodera
Publications
Recent publications
- Xiao et al.: Oriented binding of transcription factors to nucleosomes remodels chromatin at human promoters. Accepted to Molecular Cell.
- D. Díaz-Domínguez, P. Martinello, T. Onodera, S.J. Puglisi, and L. Salmela: Contig model for variable-order de Bruijn graphs. In Proc. WABI 2026, International Conference on Algorithms for Bioinformatics (ed. N. El-Mabrouk, and F. Vandin), Leibniz International Proceedings in Informatics (LIPIcs) 390, Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, 2026, 4:1-4:190.
- 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.
- 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.
- 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