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Publikationer 2000 2019

Advantages of Backward Searching: Efficient Secondary Memory and Distributed Implementation of Compressed Suffix Arrays

Mäkinen, V., Navarro, G. & Sadakane, K., 2004, Proceedings of the 15th International Symposium on Algorithms and Computation (ISAAC 2004). Springer-Verlag, s. 681-692 (LNCS; vol. 3341).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

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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Algorithms for Transposition Invariant String Matching

Mäkinen, V., Navarro, G. & Ukkonen, E., 2003, Proceedings of the 20th Annual Symposium on Theoretical Aspects of Computer Science (STACS 2003): Proceedings of the 20th Annual Symposium on Theoretical Aspects of Computer Science (STACS 2003). Springer-Verlag, s. 191-202 (LNCS; vol. 2607).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Algoritmitutkimuksen rooli bioinformatiikassa

Mäkinen, V., jul 2011, I : Tietojenkäsittelytiede. 32, s. 10-15 6 s.

Forskningsoutput: TidskriftsbidragArtikelVetenskaplig

An(other) entropy-bounded compressed suffix tree

Fischer, J., Mäkinen, V. & Navarro, G., 2008, Combinatorial pattern matching. s. 152-165 14 s.

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

An Alphabet-Friendly FM-Index

Ferragina, P., Manzini, G., Mäkinen, V. & Navarro, G., 2004, Proceedings of the 11th International Conference on String Processing and Information Retrieval (SPIRE 2004). Springer-Verlag, s. 150-160 (LNCS; vol. 3246).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

An in-memory XQuery/XPath engine over a compressed structured text representation

Bonifati, A., Leighton, G., Mäkinen, V., Maneth, S., Navarro, G. & Pugliese, A., 2008, Dagstuhl seminar proceedings. Böttcher, S., Lohrey, M., Maneth, S. & Rytter, W. (red.). 17 s. (Dagstuhl Seminar Proceedings; nr. 08261).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskaplig

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

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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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

Approximate All-Pairs Suffix/Prefix Overlaps

Välimäki, N., Ladra, S. & Mäkinen, V., 2010, CPM 2010: Proceedings of the 21st Annual Symposium on Combinatorial Pattern Matching . Germany: Springer-Verlag, Vol. 21. s. 76-87 (Lecture Notes in Computer Science; vol. 6129).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Approximate Matching of Run-length Compressed Strings

Mäkinen, V., Navarro, G. & Ukkonen, E., 2003, I : Algorithmica. 35, 4, s. 347–369

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Approximate Matching of Run-Length Compressed Strings

Mäkinen, V., Navarro, G. & Ukkonen, E., 2001, Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching (CPM 2001). Springer-Verlag, s. 31-49 (LNCS; vol. 2089).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

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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A simple alphabet-independent FM-index

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

A simple alphabet-independent FM-index

Grabowski, S., Mäkinen, V., Navarro, G. & Salinger, A., 2005, Proceedings of the Prague Stringology Conference (PSC 2005). Department of Computer Science and Engineering, Faculty of Electrical Engineering, Czech Technical University, s. 231-245

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

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

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

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

Combinatorial approaches for mass spectra recalibration

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Compact Suffix Array

Mäkinen, V., 2000, Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching (CPM 2000). Springer-Verlag, s. 305-319 (LNCS; vol. 1848).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Compact Suffix Array — A Space-efficient Full-text Index

Mäkinen, V., 2003, I : Fundamenta Informaticae. 56, 1-2, s. 191–210

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Compressed Compact Suffix Arrays

Mäkinen, V. & Navarro, G., 2004, Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching (CPM 2004). Springer-Verlag, s. 420-433 (LNCS; vol. 3109).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Compressed full-text indexes

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Compressed full-text indexes

Navarro, G. & Mäkinen, V., 2006, Santiago: University of Chile, Department of Computer Science. 66 s.

Forskningsoutput: Bok/rapportBokVetenskapligPeer review

Compressed representations of sequences and full-text indexes

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Compressed suffix array

Mäkinen, V., 2008, Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, s. 174-176 3 s.

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKapitelVetenskapligPeer review

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

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

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Compressed text indexing

Mäkinen, V. & Navarro, G., 2008, Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, s. 176-178 3 s.

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKapitelVetenskapligPeer 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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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

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).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Dynamic entrocopy-compressed sequences and full-text indexes

Mäkinen, V. & Navarro, G., 2006, Combinatorial pattern matching. s. 306-317 12 s.

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Dynamic entropy-compressed sequences and full-text indexes

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Dynamic entropy-compressed sequences and full-text indexes

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

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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Editorial: Special Issue on Algorithms for Sequence Analysis and Storage

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

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

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

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Engineering a Compressed Suffix Tree Implementation

Välimäki, N., Gerlach, W., Dixit, K. & Mäkinen, V., 2007, Experimental Algorithms. Springer-Verlag, s. 217-228 12 s. (LNCS; vol. 4525).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Engineering a Compressed Suffix Tree Implementation

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

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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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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Faster entropy-bounded compressed suffix trees

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Fast index based filters for music retrieval

Lemström, K., Mikkilä, N. & Mäkinen, V., 2008, ISMIR 2008. s. 677-682 6 s.

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

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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