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Publikationer 2000 2019

2019

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

Mäkinen, V. & Norri, T., jun 2019, I : Information Processing Letters. 146, s. 17-19 3 s.

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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, I : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 1, s. 23-30 8 s.

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Linear time minimum segmentation enables scalable founder reconstruction

Norri, T., Cazaux, B., Kosolobov, D. & Mäkinen, V., 17 maj 2019, I : Algorithms for Molecular Biology. 14, 15 s., 12.

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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, I : Bioinformatics. 35, 5, s. 769-777 9 s.

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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., maj 2019, I : ACM Transactions on Algorithms. 15, 2, 21 s., 29.

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2018

A safe and complete algorithm for metagenomic assembly

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

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Bidirectional Variable-Order de Bruijn Graphs

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Computational pan-genomics: status, promises and challenges

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

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

Makinen, V. & Puglisi, S. J., aug 2018, I : Theory of Computing Systems. 62, 6, s. 1349-1350 2 s.

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Evaluating approaches to find exon chains based on long reads

Kuosmanen, A., Norri, T. & Mäkinen, V., maj 2018, I : Briefings in Bioinformatics. 19, 3, s. 404-414 11 s.

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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. (red.). Dagstuhl: Schloss Dagstuhl Leibniz Center for Informatics, s. 15:1-15:15 15 s. (Leibniz International Proceedings in Informatics (LIPIcs); vol. 113).

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Towards pan-genome read alignment to improve variation calling

Valenzuela, D., Norri, T., Välimäki, N., Pitkänen, E. & Mäkinen, V., 9 maj 2018, I : BMC Genomics. 19, 8 s., 87.

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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. (red.). Cham: Springer International Publishing AG, s. 105-121 17 s. (Lecture Notes in Bioinformatics; vol. 10812).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

2017

A framework for space-efficient read clustering in metagenomic samples

Alanko, J., Cunial, F., Belazzougui, D. & Mäkinen, V., 14 mar 2017, I : BMC Bioinformatics. 18, Suppl 3, 12 s., 59.

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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 s.

Forskningsoutput: AvhandlingDoktorsavhandlingSamling av artiklar

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Interval scheduling maximizing minimum coverage

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

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

Kuosmanen, A., 20 dec 2017, Helsinki: University of Helsinki. 133 s.

Forskningsoutput: AvhandlingDoktorsavhandlingSamling av artiklar

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Variant genotyping with gap filling

Walve, R., Salmela, L. & Mäkinen, V., 8 sep 2017, I : PLoS One. 12, 9, 12 s., e0184608.

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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. (red.). Berlin: Springer, s. 164-178 9 s. (Lecture Notes in Computer Science; vol. 9644).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

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

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

Forskningsoutput: Bok/rapportAntologi eller special utgåvaVetenskapligPeer 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, s. 145-152 8 s. (Lecture Notes in Computer Science; vol. 9954).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Gap Filling as Exact Path Length Problem

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

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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. (red.). Springer International Publishing , s. 158-170 13 s. (Lecture Notes in Computer Science; vol. 9702).

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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. (red.). Cham: Springer International Publishing AG, s. 111-121 11 s. (Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science); vol. 9649).

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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. (red.). SCITEPRESS Science And Technology Publications , s. 272-277 6 s.

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

2015

Compressed Suffix Array

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

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKapitelVetenskapligPeer 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. (red.). Cham: Springer International Publishing AG, s. 235-246 12 s. (Lecture notes in computer science; vol. 9096)(LNCS sublibrary. SL 8, Bioinformatics).

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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, I : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 12, 6, s. 1345-1354 10 s.

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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, I : Software: Practice & Experience. 45, 3, s. 399-434 36 s.

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Gap2Seq

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

Forskningsoutput: Icke-textbaserad outputProgramvaraVetenskaplig

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. (red.). Cham: Springer International Publishing AG, s. 281-292 12 s. (Lecture Notes in Bioinformatics; vol. 9029).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer 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., maj 2015, Cambrigde University Press. 391 s.

Forskningsoutput: Bok/rapportBokVetenskapligPeer review

Repeat- and error-aware comparison of deletions

Wittler, R., Marschall, T., Schönhuth, A. & Mäkinen, V., sep 2015, I : Bioinformatics. 31, 18, s. 2947-2954 8 s.

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer 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, I : Bioinformatics. 31, 7, s. 1133-1135 3 s.

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

SNV-PPILP

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

Forskningsoutput: Icke-textbaserad outputProgramvaraVetenskaplig

2014

Editorial: Special Issue on Algorithms for Sequence Analysis and Storage

Mäkinen, V., 2014, I : Algorithms. 7, 1, s. 186-187

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Indexing Graphs for Path Queries with Applications in Genome Research

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

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Multi-pattern matching with bidirectional indexes

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

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

Rizzi, R., Tomescu, A. I. & Mäkinen, V., 10 sep 2014, I : BMC Bioinformatics. 15, S9, s. S5

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Recombination-aware alignment of diploid individuals

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

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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 andraQian, 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, I : Nature Communications. 5, 9 s., 4737.

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer 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. (red.). Springer-Verlag, s. 85-98 (Lecture Notes in Computer Science; nr. 8126).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer 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, I : BMC Bioinformatics. 14, (Suppl 5):S15, 10 s.

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Haploid to diploid alignment for variation calling assessment

Mäkinen, V. & Rahkola, J., okt 2013, I : BMC Bioinformatics. 14, (Suppl 15):S13, 6 s.

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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. (red.). Springer-Verlag, s. 133-144 (Lecture Notes in Computer Science; vol. 8125).

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2012

Approximate all-pairs suffix/prefix overlaps

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer 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., okt 2012, I : Plant Disease. 96, 10, s. 1430-1437 8 s.

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer 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 s.

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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. (red.). Springer-Verlag, s. 327-337 (Lecture Notes in Computer Science; vol. 7256).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review