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  1. 22. sij

    Theory part of our work with Kristoffer Sahlin out:

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  2. proslijedio/la je Tweet
    19. pro 2019.
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  3. 11. stu 2019.

    Linear-time string indexing and analysis in small space. Accepted to ACM TALG. 52 pages, featuring a DAG of dependencies between Lemmas and Theorems. New standard created. Preprint:

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    23. ruj 2019.

    1 PhD & 2 Postdoc positions available in at , part of my new research group, funded by (Safe and Complete Algorithms for Bioinformatics). Graph and string algorithms for assembly and pan-genomes. Apply:

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  5. 4. ruj 2019.

    Congratulations Alexandru Tomescu, one of the nine highlighted ERC Grantees!

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  6. 11. lip 2019.

    At Dagstuhl, celebrating 25 years of BWT and 50th Birthday of my most frequent co-author with proper cake for the occasion. Thanks Travis et al. for great organisation!

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  7. 10. lip 2019.

    I guess I should co-author more often with my PhD students, as they write some good stuff (congrats Jarno!)

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  8. 30. svi 2019.

    Thanks and for great talks and twitter coverage at Finnish Bioinformatics Day 2019!

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    29. svi 2019.

    At Helsinki Bioinformatics Day organized by 's lab, reviews the literature of sets of k-mer sets (SBT, Bigsi, Mantis, etc..)

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  10. 27. svi 2019.
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  11. 19. tra 2019.

    "On the Complexity of String Matching for Graphs" accepted to ICALP 2019. My first ICALP paper! Joint work with Massimo Equi, Roberto Grossi and Alexandru Tomescu.

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    18. tra 2019.
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    9. ožu 2019.

    Super fast bit-parallel sequence to graph alignment! Speedup over cell-by-cell methods 3- to 20-fold, depending on the graph. In the meantime, we added banding and seeding, but more on that later. With and Mikko Rautiainen.

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  14. 13. velj 2019.

    Anyone wants to learn how to apply PBWT? We wrote this educational note: . There is an implementation included of the basic mechanism, and it makes a nice study project to continue with implementing the given all-pairs Hamming distance algorithm.

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  15. 11. velj 2019.

    Even deterministic variation graphs are hard to index under SETH:

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  16. 17. sij 2019.

    We shed some light on why it is hard to index variation graphs:

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  17. 8. pro 2018.

    Thanks et al. for great collaboration, editor for the fast processing, and reviewers for remarks that made us work hard in presenting the framework in a more general setting.

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  18. 8. pro 2018.

    Sparse Dynamic Programming on DAGs with Small Width just accepted to ACM TALG. This is an extended version of a paper I presented in RECOMB 2018 in April. Smooth operation I would say.

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    16. lis 2018.

    Our manuscript on BasePlayer - an open-source, cross-platform tool for genomic variant analysis in NGS data - is out in Nature Protocols!

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    Kolumni: Huhujen mukaan hallituksen seuraavat uudistukset kohdistuvat kulttuuriin: Fiktioloikka2018 nostaa Suomen kirjallisuuden huipputasolle

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