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Publications 2000 2019

2019

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

Open Access
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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

Open Access
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Linear time minimum segmentation enables scalable founder reconstruction

Norri, T., Cazaux, B., Kosolobov, D. & Mäkinen, V., 17 May 2019, In : Algorithms for Molecular Biology. 14, 15 p., 12.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP

Husic, E., Li, X., Hujdurovic, A., Mehine, M., Rizzi, R., Mäkinen, V., Milanic, M. & Tomescu, A. I., 1 Mar 2019, In : Bioinformatics. 35, 5, p. 769-777 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Sparse Dynamic Programming on DAGs with Small Width

Mäkinen, V., Tomescu, A. I., Kuosmanen, A., Paavilainen, T., Gagie, T. & Chikhi, R., May 2019, In : ACM Transactions on Algorithms. 15, 2, 21 p., 29.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2018

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

Open Access
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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

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

Open Access

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

Open Access
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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

Open Access
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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

Open Access
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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

Open Access
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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

2017

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

Open Access
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Algorithms and Data Structures for Sequence Analysis in the Pan-Genomic Era

Valenzuela, S. D. A., 9 Jun 2017, Helsinki: University of Helsinki. 74 p.

Research output: ThesisDoctoral ThesisCollection of Articles

Open Access

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

Third-generation RNA-sequencing analysis: graph alignment and transcript assembly with long reads

Kuosmanen, A., 20 Dec 2017, Helsinki: University of Helsinki. 133 p.

Research output: ThesisDoctoral ThesisCollection of Articles

Open Access

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

Open Access
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2016

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

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

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

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

Open Access
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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

Open Access
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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

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

2015

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

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

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

Open Access

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

Gap2Seq

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

Research output: Non-textual formSoftwareScientific

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

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

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

SNV-PPILP

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

Research output: Non-textual formSoftwareScientific

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

2014

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

Open Access
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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

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

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

Open Access
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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

Open Access
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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

2013

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

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

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

Open Access
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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

2012

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

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

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

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