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Publikationer 2000 2019

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2018

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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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).

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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).

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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).

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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.

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2015

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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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).

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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).

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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

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).

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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, s. 399-407 10 s. (Lecture Notes in Computer Science; vol. 7256).

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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. (red.). Springer-Verlag, s. 384-395 (Lecture Notes in Computer Science; vol. 7434).

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2011

Indexing Finite Language Representation of Population Genotypes

Sirén, J., Välimäki, N. & Mäkinen, V., 2011, Algorithms in Bioinformatics: 11th International Workshop, WABI 2011. Przytycka, T. M. & Sagot, M-F. (red.). Springer, s. 270-281 (Lecture Notes in Bioinformatics; vol. 6833).

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2010

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).

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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., 2010, ICDE 2010: 26th IEEE International Conference on Data Engineering. IEEE Computer Society, s. 417-428 12 s.

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2009

Storage and retrieval of individual genomes

Mäkinen, V., Navarro, G., Sirén, J. & Välimäki, N., 2009, Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009. Batzoglou, S. (red.). Springer, s. 121-137 17 s. (Lecture Notes in Computer Science; nr. 5541).

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2008

An(other) entropy-bounded compressed suffix tree

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

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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).

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Fast index based filters for music retrieval

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

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On self-indexing images: image compression with added value

Mäkinen, V. & Navarro, G., 2008, Data Compression Conference: DCC 2008. s. 422-431 10 s.

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Run-length compressed indexes are superior for highly repetitive sequence collections

Sirén, J., Välimäki, N., Mäkinen, V. & Navarro, G., 2008, String Processing and Information Retrieval: 15th International Symposium, SPIRE 2008. Amir, A., Turpin, A. & Moffat, A. (red.). Springer, s. 164-175 12 s. (Lecture Notes in Computer Science; nr. 5280).

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Space-efficient string mining under frequency constraints

Fischer, J., Mäkinen, V. & Välimäki, N., 2008, Eighth IEEE International Conference on Data Mining, ICDM 2008, 15-19 December, 2008, Pisa, Italy: IEEE Computer Society 2008. s. 193-202 10 s.

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Storage and retrieval of individual genomes (extended abstract)

Mäkinen, V., Navarro, G., Siren, J. & Välimäki, N., 2008, Dagstuhl seminar proceedings. 14 s. (Dagstuhl seminar proceedings; nr. 08261).

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2007

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).

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Implicit compression boosting with applications to self-indexing

Mäkinen, V. & Navarro, G., 2007, String Processing and Information Retrieval. Springer, s. 229-241 13 s. (Lecture notes in computer science; vol. 4726).

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Space-efficient algorithms for document retrieval

Välimäki, N. & Mäkinen, V., 2007, Combinatorial pattern matching. s. 205-215 11 s.

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2006

Dynamic entrocopy-compressed sequences and full-text indexes

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

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Position-restricted substring searching

Mäkinen, V. & Navarro, G., 2006, LATIN 2006: THEORETICAL INFORMATICS. s. 703-714 12 s. (Lecture Notes in Computer Science; vol. 3887).

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2005

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

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Flexible music retrieval in sublinear time

Fredriksson, K., Mäkinen, V. & Navarro, G., 2005, Proceedings of the Prague Stringology Conference (PSC 2005). Department of Computer Science and Engineering, Faculty of Electrical Engineering, Czech Technical University, s. 174-189

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Maximum Line-Pair Stabbing Problem and its Variations

Böcker, S. & Mäkinen, V., 2005, Proceedings of the 21st European Workshop on Computational Geometry. s. 183–186 4 s.

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Practical Implementation of Rank and Select Queries

González, R., Grabowski, S., Mäkinen, V. & Navarro, G., 2005, Poster Proceedings of 4th International Workshop on Efficient and Experimental Algorithms .

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Succinct Suffix Arrays Based on Run-Length Encoding

Mäkinen, V. & Navarro, G., 2005, Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM 2005). Springer-Verlag, s. 45-56 (LNCS; vol. 3537).

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2004

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).

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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).

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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).

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Finding Missing Patterns

Inenaga, S., Kivioja, T. & Mäkinen, V., 2004, Proceedings of the 4th International Workshop on Algorithms in Bioinformatics (WABI 2004). Springer-Verlag, s. 463-474 (LNCS; vol. 3240).

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First Huffman, Then Burrows-Wheeler: A Simple Alphabet-Independent FM-index

Grabowski, S., Mäkinen, V. & Navarro, G., 2004, Proceedings of the 11th International Conference on String Processing and Information Retrieval (SPIRE 2004). Springer-Verlag, s. 210-211 (LNCS; vol. 3246).

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Rotation and Lighting Invariant Template Matching

Fredriksson, K., Mäkinen, V. & Navarro, G., 2004, Proceedings of the 6th Latin American Symposium on Theoretical Informatics (LATIN 2004). Springer-Verlag, s. 39-48 (LNCS; vol. 2976).

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2003

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).

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Geometric algorithms for transposition invariant content-based music retrieval

Ukkonen, E., Lemström, K. & Mäkinen, V., 2003, Proc. 4th International Conference on Music Information Retrieval. Hoos, H. & Bainbridge, D. (red.). s. 193-199

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On Minimizing Pattern Splitting in Multi-track String Matching

Lemström, K. & Mäkinen, V., 2003, Unknown host publication. Springer-Verlag, s. 237-253 (LNCS; vol. 2676).

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The C-BRAHMS Project

Lemström, K., Mäkinen, V., Pienimäki, A., Turkia, M. & Ukkonen, E., 2003, Proc. 4th International Conference on Music Information Retrieval. Hoos, H. & Bainbridge, D. (red.). s. 237-238

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2002

Local Similarity Based Point-Pattern Matching

Mäkinen, V. & Ukkonen, E., 2002, Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching (CPM 2002). Springer-Verlag, s. 115-132 (LNCS; vol. 2373).

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2001

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).

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Trade Off Between Compression and Search Times in Compact Suffix Array

Mäkinen, V., 2001, Proceedings of the Third International Workshop on Algorithm Engineering and Experimentation (ALENEX 2001). Springer-Verlag, s. 189-201 (LNCS; vol. 2153).

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Using Edit Distance in Point-Pattern Matching

Mäkinen, V., 2001, Proceedings of the 8th International Symposium on String Processing and Information Retrieval (SPIRE 2001). IEEE Computer Society, s. 153-161

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