Jarno Alanko received his PhD in 2020 at the University of Helsinki under the supervision of Veli Mäkinen. During 2020-2022, he worked as a post-doctoral researcher with professor Travis Gagie at Dalhousie University and professor Keijo Heljanko at the University of Helsinki.
Alanko’s work focuses on compact data structures for bioinformatics applications. Research highlights include the generalization of the concept of tunneling to Wheeler graphs, an optimal solution to the repeat-free minimum spectrum-preserving string set problem, and introduction of the concept of the Spectral Burrows-Wheeler transform for succinct indexing of k-mer spectra.
Alanko is also the lead developer in the Themisto project to build pseudoalignment index structures scalable to hundreds of thousands of bacterial genomes. The Themisto pseudoaligner has been used to develop bacterial genomic epidemiology with mixed samples and to study the pathogen competition in neonatal gut colonisation.
Sample of publications
[1] Jarno Alanko, Elena Biagi, Joel Mackenzie, Simon Puglisi. 2025. Batched k-mer lookup on the Spectral Burrows-Wheeler Transform. In R. Chowdhury, J. Berry, K. Hanauer, & B. Ren (Eds.), 2025 Proceedings of the Symposium on Algorithm Engineering and Experiments (ALENEX) (pp. 95 - 106). (Proceedings of the Workshop on Algorithm Engineering and Experiments). Society for Industrial and Applied Mathematics.
[2] Jarno N. Alanko, Philip Bille, Inge Li Gørtz, Gonzalo Navarro, Simon J. Puglisi. 2025. Compact Data Structures for Collections of Sets. In A. Conte, A. Conte, A. Marino, G. Rosone, J. S. Vitter, & J. S. Vitter (Eds.), From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday Article 6 (OpenAccess Series in Informatics; Vol. 132). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing.
[3] Jarno N. Alanko, Elena Biagi, Simon J. Puglisi. 2025. Finimizers: Variable-Length Bounded-Frequency Minimizers for k-mer Sets. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 22(2), 899-910.
[4] Jarno N. Alanko, Elena Biagi, Massimo Equi, Veli Mäkinen, Simon J. Puglisi, Nicola Rizzo, Kunihiko Sadakane, Jouni Sirén. 2025. Graph Indexing Beyond Wheeler Graphs. In P. Ferragina, T. Gagie, & G. Navarro (Eds.), The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday Article 13 (OpenAccess Series in Informatics; Vol. 131). Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
[5] Jarno N. Alanko, Ruben Becker, Davide Cenzato, Travis Gagie, Sung-Hwan Kim, Bojana Kodric, Nicola Prezza. 2025. The Trie Measure, Revisited. In P. Bonizzoni, & V. Makinen (Eds.), 36th Annual Symposium On Combinatorial Pattern Matching, Cpm 2025 (Leibniz International Proceedings In Informatics; Vol. 331). Schloss Dagstuhl Leibniz Center for Informatics.