Veli Mäkinen

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  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

  21. MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows

    Sobih, A. A. M., Tomescu, A. I. & Mäkinen, V. A. T., 8 Apr 2016, Research in Computational Molecular Biology: 20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings. Singh, M. (ed.). Cham: Springer International Publishing AG, p. 111-121 11 p. (Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science); vol. 9649).

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

  22. 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

  23. Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly

    Tomescu, A. I., Gagie, T., Popa, A., Rizzi, R., Kuosmanen, A. E. & Mäkinen, V. A. T., Dec 2015, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 12, 6, p. 1345-1354 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  24. SNV-PPILP

    van Rens, K., Mäkinen, V. A. T. & Tomescu, A. I., 2015

    Research output: Non-textual formSoftwareScientific

  25. Repeat- and error-aware comparison of deletions

    Wittler, R., Marschall, T., Schönhuth, A. & Mäkinen, V., Sep 2015, In : Bioinformatics. 31, 18, p. 2947-2954 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  26. Compressed Suffix Array

    Belazzougui, D., Mäkinen, V. A. T. & Valenzuela, S. D. A., 2015, Encyclopedia of Algorithms. Kao, M-Y. (ed.). New York: Springer, 6 p.

    Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

  27. Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing

    Mäkinen, V. A. T., Belazzougui, D., Cunial, F. & Tomescu, A. I., May 2015, Cambrigde University Press. 391 p.

    Research output: Book/ReportBookScientificpeer-review

  28. Diploid Alignments and Haplotyping

    Mäkinen, V. & Valenzuela, D., 2015, Bioinformatics Research and Applications: 11th International Symposium, ISBRA 2015, Norfolk, USA, June 6-9, 2015, Proceedings . Harrison, R., Li, Y. & Măndoiu, I. (eds.). Cham: Springer International Publishing AG, p. 235-246 12 p. (Lecture notes in computer science; vol. 9096)(LNCS sublibrary. SL 8, Bioinformatics).

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

  29. Fast in-memory XPath search using compressed indexes

    Arroyuelo, D., Claude, F., Maneth, S., Mäkinen, V., Navarro, G., Nguyen, K., Sirén, J. & Välimäki, N., Mar 2015, In : Software: Practice & Experience. 45, 3, p. 399-434 36 p.

    Research output: Contribution to journalArticleScientificpeer-review

  30. Gap2Seq

    Salmela, L. M., Sahlin, K., Mäkinen, V. A. T. & Tomescu, A. I., 2015

    Research output: Non-textual formSoftwareScientific

  31. SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP

    van Rens, K. E., Mäkinen, V. & Tomescu, A. I., 1 Apr 2015, In : Bioinformatics. 31, 7, p. 1133-1135 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  32. Gap filling as exact path length problem

    Salmela, L., Sahlin, K., Mäkinen, V. & Tomescu, A. I., 2015, Research in Computational Molecular Biology : 19th Annual International Conference, RECOMB 2015, Warsaw, Poland, April 12-15, 2015, Proceedings . Przytycka, T. M. (ed.). Cham: Springer International Publishing AG, p. 281-292 12 p. (Lecture Notes in Bioinformatics; vol. 9029).

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

  33. Editorial: Special Issue on Algorithms for Sequence Analysis and Storage

    Mäkinen, V., 2014, In : Algorithms. 7, 1, p. 186-187

    Research output: Contribution to journalArticleScientific

  34. Indexing Graphs for Path Queries with Applications in Genome Research

    Sirén, J., Välimäki, N. & Mäkinen, V., 2014, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 11, 2, p. 375-388 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  35. Recombination-aware alignment of diploid individuals

    Mäkinen, V. & Valenzuela, D., 2014, In : BMC Genomics. 15, Suppl 6, p. S15 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  36. On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly

    Rizzi, R., Tomescu, A. I. & Mäkinen, V., 10 Sep 2014, In : BMC Bioinformatics. 15, S9, p. S5

    Research output: Contribution to journalArticleScientificpeer-review

  37. The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

    Ahola, V., Lehtonen, R., Somervuo, P., Salmela, L., Koskinen, P., Rastas, P., Valimaki, N., Paulin, L., Kvist, J., Wahlberg, N., Tanskanen, J., Hornett, E. A., Ferguson, L. C., Luo, S., Cao, Z., de Jong, M. A., Duplouy, A., Smolander, O-P., Vogel, H., McCoy, R. C. & 27 othersQian, K., Wong, S. C., Zhang, Q., Ahmad, F., Haukka, J. K., Joshi, A., Salojarvi, J., Wheat, C. W., Grosse-Wilde, E., Hughes, D., Katainen, R., Pitkanen, E., Ylinen, J., Waterhouse, R. M., Turunen, M., Vaharautio, A., Ojanen, S. P., Schulman, A. H., Taipale, M., Lawson, D., Ukkonen, E., Makinen, V., Goldsmith, M. R., Holm, L., Auvinen, P., Frilander, M. J. & Hanski, I., Sep 2014, In : Nature Communications. 5, 9 p., 4737.

    Research output: Contribution to journalArticleScientificpeer-review

  38. Dynamic entropy-compressed sequences and full-text indexes

    Mäkinen, V. & Navarro, G., 2006, In : Lecture Notes in Computer Science. 4009, p. 306-317 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  39. Multi-pattern matching with bidirectional indexes

    Gog, S., Karhu, K., Kärkkäinen, J., Mäkinen, V. & Välimäki, N., 2014, In : Journal of Discrete Algorithms. 24, p. 26-39 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  40. A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths

    Tomescu, A. I., Kuosmanen, A., Rizzi, R. & Mäkinen, V., 2013, Algorithms in Bioinformatics: 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings. Darling, A. & Stoye, J. (eds.). Springer-Verlag, p. 85-98 (Lecture Notes in Computer Science; no. 8126).

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

  41. Versatile succinct representations of the bidirectional Burrows-Wheeler transform

    Belazzougui, D., Cunial, F., Kärkkäinen, J. & Mäkinen, V., 2013, Algorithms – ESA 2013: 21st Annual European Symposium, Sophia Antipolis, France, September 2-4, 2013. Proceedings. Bodlaender, H. L. & Italiano, G. F. (eds.). Springer-Verlag, p. 133-144 (Lecture Notes in Computer Science; vol. 8125).

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

  42. Haploid to diploid alignment for variation calling assessment

    Mäkinen, V. & Rahkola, J., Oct 2013, In : BMC Bioinformatics. 14, (Suppl 15):S13, 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  43. A novel min-cost flow method for estimating transcript expression with RNA-Seq

    Tomescu, A. I., Kuosmanen, A., Rizzi, R. & Mäkinen, V., 10 Apr 2013, In : BMC Bioinformatics. 14, (Suppl 5):S15, 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  44. Efficient Path Kernels for Reaction Function Prediction

    Heinonen, M., Välimäki, N., Mäkinen, V. & Rousu, J., 2012, 3rd International Conference on Bioinformatics Models, Methods and Algorithms, 1-4 Feb 2012, Algarve, Portugal.: Proceedings. 6 p.

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

  45. Detection of Viruses in Sweetpotato from Honduras and Guatemala Augmented by Deep-Sequencing of Small-RNAs

    Kashif, M., Pietila, S., Artola, K., Jones, R. A. C., Tugume, A. K., Makinen, V. & Valkonen, J. P. T., Oct 2012, In : Plant Disease. 96, 10, p. 1430-1437 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  46. Normalized N50 Assembly Metric using Gap-Restricted Co-Linear Chaining

    Mäkinen, V., Salmela, L. & Ylinen, J., 3 Oct 2012, In : BMC Bioinformatics. 13, p. 255 5 p.

    Research output: Contribution to journalArticleScientificpeer-review

  47. Approximate all-pairs suffix/prefix overlaps

    Välimäki, N., Ladra, S. & Mäkinen, V., 2012, In : Information and Computation. 213, p. 49-58 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  48. Multi-Pattern Matching with Bidirectional Indexes

    Gog, S., Karhu, K., Kärkkäinen, J., Mäkinen, V. & Välimäki, N., 2012, Computing and Combinatorics: 18th Annual International Conference, COCOON 2012, Sydney, Australia, August 20-22, 2012. Proceedings. Gudmundsson, J., Mestre, J. & Viglas, T. (eds.). Springer-Verlag, p. 384-395 (Lecture Notes in Computer Science; vol. 7434).

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

  49. Forbidden Patterns

    Fischer, J., Gagie, T., Kopelowitz, T., Lewenstein, M., Mäkinen, V., Salmela, L. & Välimäki, N., 2012, LATIN 2012: Theoretical Informatics: 10th Latin American Symposium, Arequipa, Peru, April 16-20, 2012. Proceedings. Fernández-Baca, D. (ed.). Springer-Verlag, p. 327-337 (Lecture Notes in Computer Science; vol. 7256).

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

  50. Indexed Multi-Pattern Matching

    Gagie, T., Karhu, K., Kärkkäinen, J., Mäkinen, V., Salmela, L. & Tarhio, J., 2012, LATIN 2012: Theoretical Informatics: 10th Latin American Symposium, Arequipa, Peru, April 16-20, 2012. Proceedings. Springer-Verlag, p. 399-407 10 p. (Lecture Notes in Computer Science; vol. 7256).

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

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