Veli Mäkinen

RSS feed of this list

  1. Sparse Dynamic Programming on DAGs with Small Width

    Mäkinen, V., Tomescu, A. I., Kuosmanen, A., Paavilainen, T., Gagie, T. & Chikhi, R., Feb 2019, In : ACM transactions on algorithms.. 15, 2, p. Article No. 29 21 p.

    Research output: Contribution to journalArticleScientificpeer-review

  2. Applying the Positional Burrows–Wheeler Transform to All-Pairs Hamming distance

    Mäkinen, V. & Norri, T., Jun 2019, In : Information Processing Letters. 146, p. 17-19 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics

    Rizzi, R., Cairo, M., Mäkinen, V., Tomescu, A. I. & Valenzuela, D., Feb 2019, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 1, p. 23-30 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  4. Bidirectional Variable-Order de Bruijn Graphs

    Belazzougui, D., Gagie, T., Mäkinen, V., Previtali, M. & Puglisi, S. J., Dec 2018, In : International Journal of Foundations of Computer Science. 29, 8, p. 1279-1295 17 p.

    Research output: Contribution to journalArticleScientificpeer-review

  5. Minimum Segmentation for Pan-genomic Founder Reconstruction in Linear Time

    Norri, T., Cazaux, B., Kosolobov, D. & Mäkinen, V., 2018, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Parida, L. & Ukkonen, E. (eds.). Dagstuhl: Schloss Dagstuhl Leibniz Center for Informatics, p. 15:1-15:15 15 p. (Leibniz International Proceedings in Informatics (LIPIcs); vol. 113).

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

  6. Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer

    Katainen, R., Donner, I., Cajuso, T., Kaasinen, E., Palin, K., Mäkinen, V., Aaltonen, L. A. & Pitkänen, E., Nov 2018, In : Nature Protocols. 13, 11, p. 2580-2600 21 p.

    Research output: Contribution to journalArticleScientificpeer-review

  7. Editorial: Special Issue on "Combinatorial Algorithms" (IWOCA 2016)

    Makinen, V. & Puglisi, S. J., Aug 2018, In : Theory of Computing Systems. 62, 6, p. 1349-1350 2 p.

    Research output: Contribution to journalEditorialScientific

  8. A safe and complete algorithm for metagenomic assembly

    Acosta, N. O., Mäkinen, V. & Tomescu, A. I., 7 Feb 2018, In : Algorithms for Molecular Biology. 13, 12 p., 3.

    Research output: Contribution to journalArticleScientificpeer-review

  9. Towards pan-genome read alignment to improve variation calling

    Valenzuela, D., Norri, T., Välimäki, N., Pitkänen, E. & Mäkinen, V., 9 May 2018, In : BMC Genomics. 19, 8 p., 87.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Variant genotyping with gap filling

    Walve, R., Salmela, L. & Mäkinen, V., 8 Sep 2017, In : PLoS One. 12, 9, 12 p., e0184608.

    Research output: Contribution to journalArticleScientificpeer-review

  11. Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended

    Kuosmanen, A., Paavilainen, T., Gagie, T., Chikhi, R., Tomescu, A. & Mäkinen, V., Apr 2018, Research in Computational Molecular Biology : 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings. Raphael, B. J. (ed.). Cham: Springer International Publishing AG, p. 105-121 17 p. (Lecture Notes in Bioinformatics; vol. 10812).

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

  12. Interval scheduling maximizing minimum coverage

    Mäkinen, V., Staneva, V., Tomescu, A. I., Valenzuela, D. & Wilzbach, S., 10 Jul 2017, In : Discrete Applied Mathematics. 225, p. 130-135 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Evaluating approaches to find exon chains based on long reads

    Kuosmanen, A., Norri, T. & Mäkinen, V., May 2018, In : Briefings in Bioinformatics. 19, 3, p. 404-414 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  14. A framework for space-efficient read clustering in metagenomic samples

    Alanko, J., Cunial, F., Belazzougui, D. & Mäkinen, V., 14 Mar 2017, In : BMC Bioinformatics. 18, Suppl 3, 12 p., 59.

    Research output: Contribution to journalArticleScientificpeer-review

  15. Computational pan-genomics: status, promises and challenges

    The Computational Pan-Genomics Consortium, Mäkinen, V. A. T. & Valenzuela, S. D. A., Jan 2018, In : Briefings in Bioinformatics. 19, 1, p. 118-135 18 p.

    Research output: Contribution to journalArticleScientificpeer-review

  16. Combinatorial Algorithms: 27th International Workshop, IWOCA 2016, Helsinki, Finland, August 17-19, 2016, Proceedings

    Mäkinen, V. (ed.), Puglisi, S. J. (ed.) & Salmela, L. (ed.), 2016, Cham: Springer International Publishing . 434 p. (Theoretical Computer Science and General Issues; vol. 9843)

    Research output: Book/ReportAnthology or special issueScientificpeer-review

  17. Fully Dynamic de Bruijn Graphs

    Belazzougui, D., Gagie, T., Mäkinen, V. & Previtali, M., 2016, String Processing and Information Retrieval: 23rd International Symposium, SPIRE 2016, Beppu, Japan, October 18-20, 2016, Proceedings. Springer, p. 145-152 8 p. (Lecture Notes in Computer Science; vol. 9954).

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

  18. Identification of Variant Compositions in Related Strains Without Reference

    Rautiainen, M., Salmela, L. & Mäkinen, V., 2016, Algorithms for Computational Biology: Third International Conference, AlCoB 2016, Trujillo, Spain, June 21-22, 2016, Proceedings. Botón-Fernández, M., Martín-Vide, C., Santander-Jiménez, S. & Vega-Rodríguez, M. A. (eds.). Springer International Publishing , p. 158-170 13 p. (Lecture Notes in Computer Science; vol. 9702).

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

  19. Bidirectional Variable-Order de Bruijn Graphs

    Belazzougui, D., Gagie, T., Mäkinen, V. A. T., Previtali, M. & Puglisi, S. J., 2016, Theoretical informatics: LATIN 2016: 12th Latin American Symposium, Ensenada, Mexico, April 11-15, 2016 : proceedings. Kranakis, E., Navarro, G. & Chávez, E. (eds.). Berlin: Springer, p. 164-178 9 p. (Lecture Notes in Computer Science; vol. 9644).

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

  20. 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

Previous 1 2 3 4 5 6 7 Next