Genome-scale algorithmics

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  1. Fast in-memory XPath search using compressed indexes

    Arroyuelo, D., Claude, F., Maneth, S., Mäkinen, V., Navarro, G., Nguyen, K., Sirén, J. & Välimäki, N. 2010 ICDE 2010: 26th IEEE International Conference on Data Engineering. IEEE Computer Society, p. 417-428 12 p.

    Research output: Scientific - peer-reviewConference contribution

  2. Approximate string matching with reduced alphabet

    Salmela, L. & Tarhio, J. 2010 Algorithms and applications: Essays dedicated to Esko Ukkonen on the occasion of his 60th birthday. Elomaa, T., Mannila, H. & Orponen, P. (eds.). Springer-Verlag, 11 p. (Lecture Notes in Computer Science; vol. 2010, no. 6060)

    Research output: Scientific - peer-reviewChapter

  3. Unified view of backward backtracking in short read mapping

    Mäkinen, V., Välimäki, N., Laaksonen , A. & Katainen , R. 2010 Algorithms and applications: Essays dedicated to Esko Ukkonen on the occasion of his 60th birthday. Elomaa, T., Mannila, H. & Orponen, P. (eds.). Springer-Verlag, 14 p. (Lecture Notes in Computer Science; vol. 2010, no. 6060)

    Research output: Scientific - peer-reviewChapter

  4. Storage and Retrieval of Highly Repetitive Sequence Collections

    Mäkinen, V., Navarro, G., Sirén, J. & Välimäki, N. 2010 In : Journal of Computational Biology. 17, 3, p. 281-308 28 p.

    Research output: Scientific - peer-reviewArticle

  5. Bit-parallel search algorithms for long patterns

    Durian, B., Peltola, H., Salmela, L. & Tarhio, J. 2010 Proceedings of the 9th International Symposium on Experimental Algorithms. Festa, P. (ed.). Springer-Verlag, p. 129-140 12 p. (Lecture Notes in Computer Science; vol. 2010, no. 6049)

    Research output: Scientific - peer-reviewConference contribution

  6. Correction of sequencing errors in a mixed set of reads

    Salmela, L. 2010 In : Bioinformatics. 26, 10, p. 1284-1290 7 p.

    Research output: Scientific - peer-reviewArticle

  7. Hybrid SHREC

    Salmela, L. 2010

    Research output: ScientificSoftware

  8. Approximate All-Pairs Suffix/Prefix Overlaps

    Välimäki, N., Ladra, S. & Mäkinen, V. 2010 CPM 2010: Proceedings of the 21st Annual Symposium on Combinatorial Pattern Matching . Germany: Springer-Verlag, Vol. 21, p. 76-87 (Lecture Notes in Computer Science; vol. 6129)

    Research output: Scientific - peer-reviewConference contribution

  9. Storage and retrieval of individual genomes

    Mäkinen, V., Navarro, G., Sirén, J. & Välimäki, N. 2009 Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009. Batzoglou, S. (ed.). Springer, p. 121-137 17 p. (Lecture Notes in Computer Science; no. 5541)

    Research output: Scientific - peer-reviewConference contribution

  10. Compressed suffix arrays for massive data

    Sirén, J. 2009 String Processing and Information Retrieval: 16th International Symposium, SPIRE 2009. Karlgren, J., Tarhio, J. & Hyyrö, H. (eds.). Springer, p. 63-74 12 p. (Lecture Notes in Computer Science; no. 5721)

    Research output: Scientific - peer-reviewConference contribution

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