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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

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Bit-parallel sequence-to-graph alignment

Rautiainen, M., Mäkinen, V. & Marschall, T., 1 Oct 2019, In : Bioinformatics. 35, 19, p. 3599-3607 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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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

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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

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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

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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
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

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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

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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

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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

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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

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2016

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

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2015

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

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: 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

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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

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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 others, Qian, 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 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

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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

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

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2011

Algoritmitutkimuksen rooli bioinformatiikassa

Mäkinen, V., Jul 2011, In : Tietojenkäsittelytiede. 32, p. 10-15 6 p.

Research output: Contribution to journalArticleScientific

Fast scaffolding with small independent mixed integer programs

Salmela, L., Mäkinen, V., Välimäki, N., Ylinen, J. & Ukkonen, E., 2011, In : Bioinformatics. 27, 23, p. 3259-3265 7 p.

Research output: Contribution to journalArticleScientificpeer-review

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Missing pattern discovery

Angelov, S., Inenaga, S., Kivioja, T. & Mäkinen, V., 2011, In : Journal of Discrete Algorithms. 9, 2, p. 153-165 13 p.

Research output: Contribution to journalArticleScientificpeer-review

The Cycle Switching Graph of the Steiner Triple Systems of Order 19 is Connected

Kaski, P., Mäkinen, V. & Östergård, P. R. J., 2011, In : Graphs and Combinatorics. 27, 4, p. 539-546 8 p.

Research output: Contribution to journalArticleScientificpeer-review

2010

Filtering methods for content-based retrieval on indexed symbolic music databases

Lemstrom, K., Mikkila, N. & Makinen, V., 2010, In : Information Retrieval Journal. 13, p. 1-21 21 p.

Research output: Contribution to journalArticleScientificpeer-review

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: Contribution to journalArticleScientificpeer-review

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2009

Efficient construction of maximal and minimal representations of motifs of a string

Nicolas, F., Mäkinen, V. & Ukkonen, E., 2009, In : Theoretical Computer Science. 410 (2009), p. 2999-3005 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Engineering a Compressed Suffix Tree Implementation

Välimäki, N., Mäkinen, V., Gerlach, W. & Dixit, K., 2009, In : ACM Journal of Experimental Algorithmics. 14, 4.2, p. 4.2:1-4.2:23 23 p.

Research output: Contribution to journalArticleScientificpeer-review

Faster entropy-bounded compressed suffix trees

Fischer, J., Mäkinen, V. & Navarro, G., 2009, In : Theoretical Computer Science. 410 (2009), p. 5354-5364 11 p.

Research output: Contribution to journalArticleScientificpeer-review

2008

Combinatorial approaches for mass spectra recalibration

Böcker, S. & Mäkinen, V., 2008, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 5, 1, p. 91-100 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Dynamic entropy-compressed sequences and full-text indexes

Mäkinen, V. & Navarro, G., 2008, In : ACM Transactions on Algorithms. 4, 3, p. art. 32 38 p.

Research output: Contribution to journalArticleScientificpeer-review

Kauniita algoritmeja vääriin ongelmiin

Mäkinen, V., 14 Dec 2008, In : Luova : tiedettä & teknologiaa.

Research output: Contribution to journalArticleGeneral public

2007

Compressed full-text indexes

Navarro, G. & Mäkinen, V., 2007, In : ACM Computing Surveys. 39, 1, p. Article No. 2

Research output: Contribution to journalArticleScientificpeer-review

Compressed representations of sequences and full-text indexes

Ferragina, P., Manzini, G., Mäkinen, V. & Navarro, G., 2007, In : ACM Transactions on Algorithms. 3, 2, p. Art. 20

Research output: Contribution to journalArticleScientificpeer-review

Compressed suffix tree: a basis for genome-scale sequence analysis

Välimäki, N., Gerlach, W., Dixit, K. & Mäkinen, V., 2007, In : Bioinformatics. 23, 5, p. 629-630 2 p.

Research output: Contribution to journalArticleScientificpeer-review

Peak alignment using restricted edit distances

Mäkinen, V., 2007, In : Biomolecular engineering. 24, 3, p. 337-342 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Rank and select revisited and extended

Mäkinen, V. & Navarro, G., 2007, In : Theoretical Computer Science. 387, 3, p. 332-347 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Rotation and lighting invariant template matching

Fredriksson, K., Mäkinen, V. & Navarro, G., 2007, In : Information and Computation. 205, 7, p. 1096-1113 18 p.

Research output: Contribution to journalArticleScientificpeer-review

2006

A simple alphabet-independent FM-index

Grabowski, S., Navarro, G., Przywarski, R., Salinger, A. & Mäkinen, V., 2006, In : International Journal of Foundations of Computer Science. 17, 6, p. 1365-1384 20 p.

Research output: Contribution to journalArticleScientificpeer-review