Genome-scale algorithmics

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  1. On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy

    Kuosmanen, A. E., Sobih, A. A. M., Rizzi, R., Mäkinen, V. A. T. & Tomescu, A. I., 2016, Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies. Gilbert, J., Azhari, H., Ali, H., Quintão, C., Sliwa, J., Ruiz, C., Fred, A. & Gamboa, H. (eds.). SCITEPRESS Science And Technology Publications , p. 272-277 6 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  2. Gap Filling as Exact Path Length Problem

    Salmela, L., Sahlin, K., Mäkinen, V. & Tomescu, A. I., 9 May 2016, In : Journal of Computational Biology. 23, 5, p. 347-361 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Relations Between Greedy and Bit-Optimal LZ77 Encodings

    Kosolobov, D., 2018, Relations Between Greedy and Bit-Optimal LZ77 Encodings. Niedermeier, R. & Vallée, B. (eds.). Schloss Dagstuhl - Leibniz-Zentrum für Informatik, p. 46:1-46:14 14 p. 46. (Leibniz International Proceedings in Informatics (LIPIcs); vol. 96)

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  4. Crochemore’s String Matching Algorithm: Simplification, Extensions, Applications

    Kärkkäinen, J., Kempa, D. & Puglisi, S., 2013, Proceedings of the Prague Stringology Conference 2013. Holub, J. & Žďárek, J. (eds.). Czech Technical University in Prague, Department of Theoretical Computer Science, Faculty of Information Technology, p. 168-175 8 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  5. The representation of Boolean algebras in the spotlight of a proof checker

    Ceterchi, R., Omodeo, E. G. & Tomescu, A. I., 2014, Proceedings of the 29th Italian Conference on Computational Logic: Torino, Italy, June 16-18, 2014. Giordano, L., Gliozzi, V. & Pozzato, G. L. (eds.). CEUR Workshop Proceedings, p. 287-301 15 p. (CEUR Workshop Proceedings; vol. 1195)

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  6. LoRDEC: accurate and efficient long read error correction

    Salmela, L. & Rivals, E., 2014, In : Bioinformatics. 30, 24, p. 3506-3514 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  7. Closed Factorization

    Badkobeh, G., Bannai, H., Goto, K., I, T., Iliopoulos, C. S., Inenaga, S., Puglisi, S. J. & Sugimoto, S., 2014, Proceedings of the Prague Stringology Conference 2014, Prague, Czech Republic, September 1-3, 2014. Holub, J. & Zdárek, J. (eds.). Prague: Czech Technical University in Prague, Department of Theoretical Computer Science, Faculty of Information Technology, p. 162-168 7 p.

    Research output: Chapter in Book/Report/Conference proceedingChapterScientific

  8. 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: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

  9. Disentangled long-read de Bruijn graphs via optical maps

    Alipahani, B., Salmela, L., Puglisi, S. J., Muggli, M. & Boucher, C., 2017, 17th International Workshop on Algorithms in Bioinformatics, WABI 2017. Schwartz, R. & Reinert, K. (eds.). Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, p. 1:1-1:14 14 p. (Leibniz International Proceedings in Informatics; vol. 88)

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  10. Linear time construction of compressed text indices in compact space

    Belazzougui, D., Jun 2014, STOC '14- Proceedings of the 46th Annual ACM Symposium on Theory of Computing. Shmoys, D. B. (ed.). New York: ACM, p. 184-193 10 p. (Proceedings of the annual ACM Symposium on Theory of Computing)

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

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