Veli Mäkinen - RankMe

164 papers A* 3A 3B 28C 18Misc 4Journal 84Unranked 16

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Adaptive encodings for small and fast compressed suffix arrays. CoRR Diego Díaz-Domínguez, Veli Mäkinen
2026	J	`jnl`	Quantum Pattern Matching in Generalised Degenerate Strings. CoRR Massimo Equi, Md Rabiul Islam Khan, Veli Mäkinen
2025	B	`ed.`	36th Annual Symposium on Combinatorial Pattern Matching, CPM 2025, Milan, Italy, June 17-19, 2025 CPM Paola Bonizzoni, Veli Mäkinen
2025	J	`jnl`	Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs. Bioinform. Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
2025	—	`conf`	Graph Indexing Beyond Wheeler Graphs. The Expanding World of Compressed Data Jarno N. Alanko, Elena Biagi, Massimo Equi, Veli Mäkinen, Simon J. Puglisi, Nicola Rizzo, Kunihiko Sadakane, Jouni Sirén
2025	—	`conf`	On the Construction of Elastic Degenerate Strings. From Strings to Graphs, and Back Again Nicola Rizzo, Veli Mäkinen, Nadia Pisanti
2025	—	`conf`	Practical Colinear Chaining on Sequences Revisited. ISBRA (2) Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
2025	J	`jnl`	Practical colinear chaining on sequences revisited. CoRR Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
2024	J	`jnl`	Elastic founder graphs improved and enhanced. Theor. Comput. Sci. Nicola Rizzo, Massimo Equi, Tuukka Norri, Veli Mäkinen
2024	J	`jnl`	Finding maximal exact matches in graphs. Algorithms Mol. Biol. Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
2023	J	`jnl`	Algorithms and Complexity on Indexing Founder Graphs. Algorithmica Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
2023	J	`jnl`	Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. Bioinform. Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu
2023	C	`conf`	Chaining of Maximal Exact Matches in Graphs. SPIRE Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
2023	J	`jnl`	Chaining of Maximal Exact Matches in Graphs. CoRR Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
2023	J	`jnl`	Elastic Founder Graphs Improved and Enhanced. CoRR Nicola Rizzo, Massimo Equi, Tuukka Norri, Veli Mäkinen
2023	C	`conf`	Finding Maximal Exact Matches in Graphs. WABI Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
2023	J	`jnl`	Finding Maximal Exact Matches in Graphs. CoRR Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
2023	B	`conf`	From Bit-Parallelism to Quantum String Matching for Labelled Graphs. CPM Massimo Equi, Arianne Meijer-van de Griend, Veli Mäkinen
2023	—	`book`	Genome-Scale Algorithm Design: Bioinformatics in the Era of High-Throughput Sequencing (2nd edition). Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, Alexandru I. Tomescu
2023	J	`jnl`	Graphs cannot be indexed in polynomial time for sub-quadratic time string matching, unless SETH fails. Theor. Comput. Sci. Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
2023	J	`jnl`	On the Complexity of String Matching for Graphs. ACM Trans. Algorithms Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu, Roberto Grossi
2022	B	`conf`	Indexable Elastic Founder Graphs of Minimum Height. CPM Nicola Rizzo, Veli Mäkinen
2022	C	`conf`	Linear Time Construction of Indexable Elastic Founder Graphs. IWOCA Nicola Rizzo, Veli Mäkinen
2022	J	`jnl`	Linear Time Construction of Indexable Elastic Founder Graphs. CoRR Nicola Rizzo, Veli Mäkinen
2021	J	`jnl`	Accurate spliced alignment of long RNA sequencing reads. Bioinform. Kristoffer Sahlin, Veli Mäkinen
2021	B	`conf`	Algorithms and Complexity on Indexing Elastic Founder Graphs. ISAAC Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
2021	J	`jnl`	Algorithms and Complexity on Indexing Founder Graphs. CoRR Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
2021	J	`jnl`	Founder reconstruction enables scalable and seamless pangenomic analysis. Bioinform. Tuukka Norri, Bastien Cazaux, Saska Dönges, Daniel Valenzuela, Veli Mäkinen
2021	B	`conf`	Graphs Cannot Be Indexed in Polynomial Time for Sub-quadratic Time String Matching, Unless SETH Fails. SOFSEM Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
2020	B	`conf`	Chaining with Overlaps Revisited. CPM Veli Mäkinen, Kristoffer Sahlin
2020	J	`jnl`	Chaining with overlaps revisited. CoRR Veli Mäkinen, Kristoffer Sahlin
2020	J	`jnl`	Conditional Indexing Lower Bounds Through Self-Reducibility. CoRR Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
2020	C	`conf`	Linear Time Construction of Indexable Founder Block Graphs. WABI Veli Mäkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri, Alexandru I. Tomescu
2020	J	`jnl`	Linear Time Construction of Indexable Founder Block Graphs. CoRR Veli Mäkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri, Alexandru I. Tomescu
2020	J	`jnl`	Linear-time String Indexing and Analysis in Small Space. ACM Trans. Algorithms Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen, Veli Mäkinen
2020	B	`conf`	Scalable Reference Genome Assembly from Compressed Pan-Genome Index with Spark. BigData Altti Ilari Maarala, Ossi Arasalo, Daniel Valenzuela, Keijo Heljanko, Veli Mäkinen
2020	C	`conf`	Tailoring r-index for Document Listing Towards Metagenomics Applications. SPIRE Dustin Cobas, Veli Mäkinen, Massimiliano Rossi
2020	J	`jnl`	Tailoring r-index for metagenomics. CoRR Dustin Cobas, Veli Mäkinen, Massimiliano Rossi
2019	J	`jnl`	Applying the Positional Burrows-Wheeler Transform to all-pairs Hamming distance. Inf. Process. Lett. Veli Mäkinen, Tuukka Norri
2019	J	`jnl`	Bit-parallel sequence-to-graph alignment. Bioinform. Mikko Rautiainen, Veli Mäkinen, Tobias Marschall
2019	J	`jnl`	Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics. IEEE ACM Trans. Comput. Biol. Bioinform. Romeo Rizzi, Massimo Cairo, Veli Mäkinen, Alexandru I. Tomescu, Daniel Valenzuela
2019	C	`conf`	Linear Time Maximum Segmentation Problems in Column Stream Model. SPIRE Bastien Cazaux, Dmitry Kosolobov, Veli Mäkinen, Tuukka Norri
2019	J	`jnl`	Linear time minimum segmentation enables scalable founder reconstruction. Algorithms Mol. Biol. Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov, Veli Mäkinen
2019	J	`jnl`	MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP. Bioinform. Edin Husic, Xinyue Li, Ademir Hujdurovic, Miika Mehine, Romeo Rizzi, Veli Mäkinen, Martin Milanic, Alexandru I. Tomescu
2019	J	`jnl`	On the Complexity of Exact Pattern Matching in Graphs: Binary Strings and Bounded Degree. CoRR Massimo Equi, Roberto Grossi, Veli Mäkinen
2019	J	`jnl`	On the Complexity of Exact Pattern Matching in Graphs: Determinism and Zig-Zag Matching. CoRR Massimo Equi, Roberto Grossi, Alexandru I. Tomescu, Veli Mäkinen
2019	A*	`conf`	On the Complexity of String Matching for Graphs. ICALP Massimo Equi, Roberto Grossi, Veli Mäkinen, Alexandru I. Tomescu
2019	J	`jnl`	Sparse Dynamic Programming on DAGs with Small Width. ACM Trans. Algorithms Veli Mäkinen, Alexandru I. Tomescu, Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi
2018	J	`jnl`	A safe and complete algorithm for metagenomic assembly. Algorithms Mol. Biol. Nidia Obscura Acosta, Veli Mäkinen, Alexandru I. Tomescu
2018	J	`jnl`	Assembling Omnitigs using Hidden-Order de Bruijn Graphs. CoRR Diego Díaz-Domínguez, Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Gonzalo Navarro, Simon J. Puglisi
2018	J	`jnl`	Bidirectional Variable-Order de Bruijn Graphs. Int. J. Found. Comput. Sci. Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi
2018	J	`jnl`	Editorial: Special Issue on "Combinatorial Algorithms" (IWOCA 2016). Theory Comput. Syst. Veli Mäkinen, Simon J. Puglisi
2018	J	`jnl`	Evaluating approaches to find exon chains based on long reads. Briefings Bioinform. Anna Kuosmanen, Tuukka Norri, Veli Mäkinen
2018	C	`conf`	Minimum Segmentation for Pan-genomic Founder Reconstruction in Linear Time. WABI Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov, Veli Mäkinen
2018	J	`jnl`	Minimum Segmentation for Pan-genomic Founder Reconstruction in Optimal Time. CoRR Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov, Veli Mäkinen
2018	J	`jnl`	Towards pan-genome read alignment to improve variation calling. BMC Genom. Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen, Veli Mäkinen
2018	B	`conf`	Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. RECOMB Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
2017	J	`jnl`	A framework for space-efficient read clustering in metagenomic samples. BMC Bioinform. Jarno Alanko, Fabio Cunial, Djamal Belazzougui, Veli Mäkinen
2017	J	`jnl`	Interval scheduling maximizing minimum coverage. Discret. Appl. Math. Veli Mäkinen, Valeria Staneva, Alexandru I. Tomescu, Daniel Valenzuela, Sebastian Wilzbach
2017	J	`jnl`	Speeding up Dynamic Programming on DAGs through a Fast Approximation of Path Cover. CoRR Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
2016	B	`conf`	Bidirectional Variable-Order de Bruijn Graphs. LATIN Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi
2016	C	`ed.`	Combinatorial Algorithms - 27th International Workshop, IWOCA 2016, Helsinki, Finland, August 17-19, 2016, Proceedings IWOCA Veli Mäkinen, Simon J. Puglisi, Leena Salmela
2016	—	`ch.`	Compressed Suffix Array. Encyclopedia of Algorithms Djamal Belazzougui, Veli Mäkinen, Daniel Valenzuela
2016	—	`ch.`	Compressed Text Indexing. Encyclopedia of Algorithms Veli Mäkinen, Gonzalo Navarro
2016	J	`jnl`	Diploid Alignment is NP-hard. CoRR Romeo Rizzi, Massimo Cairo, Veli Mäkinen, Daniel Valenzuela
2016	C	`conf`	Fully Dynamic de Bruijn Graphs. SPIRE Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali
2016	J	`jnl`	Fully Dynamic de Bruijn Graphs. CoRR Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali
2016	J	`jnl`	Gap Filling as Exact Path Length Problem. J. Comput. Biol. Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu
2016	—	`conf`	Identification of Variant Compositions in Related Strains Without Reference. AlCoB Mikko Rautiainen, Leena Salmela, Veli Mäkinen
2016	J	`jnl`	Linear-time string indexing and analysis in small space. CoRR Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen, Veli Mäkinen
2016	B	`conf`	MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows. RECOMB Ahmed Sobih, Alexandru I. Tomescu, Veli Mäkinen
2016	—	`conf`	On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy. BIOINFORMATICS Anna Kuosmanen, Ahmed Sobih, Romeo Rizzi, Veli Mäkinen, Alexandru I. Tomescu
2016	—	`ch.`	Point Pattern Matching. Encyclopedia of Algorithms Veli Mäkinen, Esko Ukkonen
2015	—	`conf`	Diploid Alignments and Haplotyping. ISBRA Veli Mäkinen, Daniel Valenzuela
2015	J	`jnl`	Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly. IEEE ACM Trans. Comput. Biol. Bioinform. Alexandru I. Tomescu, Travis Gagie, Alexandru Popa, Romeo Rizzi, Anna Kuosmanen, Veli Mäkinen
2015	J	`jnl`	Fast in-memory XPath search using compressed indexes. Softw. Pract. Exp. Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
2015	B	`conf`	Gap Filling as Exact Path Length Problem. RECOMB Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu
2015	—	`book`	Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing. Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, Alexandru I. Tomescu
2015	J	`jnl`	Interval scheduling maximizing minimum coverage. CoRR Veli Mäkinen, Valeria Staneva, Alexandru I. Tomescu, Daniel Valenzuela
2015	J	`jnl`	Repeat- and error-aware comparison of deletions. Bioinform. Roland Wittler, Tobias Marschall, Alexander Schönhuth, Veli Mäkinen
2015	J	`jnl`	SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP. Bioinform. Karen E. van Rens, Veli Mäkinen, Alexandru I. Tomescu
2014	J	`jnl`	Editorial: Special Issue on Algorithms for Sequence Analysis and Storage. Algorithms Veli Mäkinen
2014	J	`jnl`	Indexing Graphs for Path Queries with Applications in Genome Research. IEEE ACM Trans. Comput. Biol. Bioinform. Veli Mäkinen, Niko Välimäki, Jouni Sirén
2014	J	`jnl`	Multi-pattern matching with bidirectional indexes. J. Discrete Algorithms Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Niko Välimäki
2014	J	`jnl`	On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly. BMC Bioinform. Romeo Rizzi, Alexandru I. Tomescu, Veli Mäkinen
2014	J	`jnl`	Towards the ground truth: Exact algorithms for bioinformatics research (NII Shonan Meeting 2014-2). NII Shonan Meet. Rep. Sebastian Böcker, Gunnar W. Klau, Veli Mäkinen, Hon Wai Leong
2013	C	`conf`	A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. WABI Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen
2013	J	`jnl`	A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. CoRR Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen
2013	J	`jnl`	A novel min-cost flow method for estimating transcript expression with RNA-Seq. BMC Bioinform. Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen
2013	J	`jnl`	Haploid to diploid alignment for variation calling assessment. BMC Bioinform. Veli Mäkinen, Jani Rahkola
2013	A	`conf`	Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform. ESA Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen, Veli Mäkinen
2012	J	`jnl`	Approximate all-pairs suffix/prefix overlaps. Inf. Comput. Niko Välimäki, Susana Ladra, Veli Mäkinen
2012	—	`conf`	Efficient Path Kernels for Reaction Function Prediction. BIOINFORMATICS Markus Heinonen, Niko Välimäki, Veli Mäkinen, Juho Rousu
2012	B	`conf`	Forbidden Patterns. LATIN Johannes Fischer, Travis Gagie, Tsvi Kopelowitz, Moshe Lewenstein, Veli Mäkinen, Leena Salmela, Niko Välimäki
2012	B	`conf`	Indexed Multi-pattern Matching. LATIN Travis Gagie, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Leena Salmela, Jorma Tarhio
2012	Misc	`conf`	Multi-pattern Matching with Bidirectional Indexes. COCOON Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Niko Välimäki
2012	J	`jnl`	Normalized N50 assembly metric using gap-restricted co-linear chaining. BMC Bioinform. Veli Mäkinen, Leena Salmela, Johannes Ylinen
2011	J	`jnl`	Fast scaffolding with small independent mixed integer programs. Bioinform. Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen
2011	C	`conf`	Indexing Finite Language Representation of Population Genotypes. WABI Jouni Sirén, Niko Välimäki, Veli Mäkinen
2011	J	`jnl`	Missing pattern discovery. J. Discrete Algorithms Stanislav Angelov, Shunsuke Inenaga, Teemu Kivioja, Veli Mäkinen
2011	J	`jnl`	The Cycle Switching Graph of the Steiner Triple Systems of Order 19 is Connected. Graphs Comb. Petteri Kaski, Veli Mäkinen, Patric R. J. Östergård
2010	B	`conf`	Approximate All-Pairs Suffix/Prefix Overlaps. CPM Niko Välimäki, Susana Ladra, Veli Mäkinen
2010	A*	`conf`	Fast in-memory XPath search using compressed indexes. ICDE Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
2010	J	`jnl`	Filtering methods for content-based retrieval on indexed symbolic music databases. Inf. Retr. Kjell Lemström, Niko Mikkilä, Veli Mäkinen
2010	J	`jnl`	Indexing Finite Language Representation of Population Genotypes CoRR Jouni Sirén, Niko Välimäki, Veli Mäkinen
2010	J	`jnl`	Pattern Kits CoRR Travis Gagie, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Leena Salmela
2010	J	`jnl`	Storage and Retrieval of Highly Repetitive Sequence Collections. J. Comput. Biol. Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki
2010	—	`conf`	Unified View of Backward Backtracking in Short Read Mapping. Algorithms and Applications Veli Mäkinen, Niko Välimäki, Antti Laaksonen, Riku Katainen
2009	J	`jnl`	Efficient construction of maximal and minimal representations of motifs of a string. Theor. Comput. Sci. François Nicolas, Veli Mäkinen, Esko Ukkonen
2009	J	`jnl`	Engineering a compressed suffix tree implementation. ACM J. Exp. Algorithmics Niko Välimäki, Veli Mäkinen, Wolfgang Gerlach, Kashyap Dixit
2009	J	`jnl`	Fast In-Memory XPath Search over Compressed Text and Tree Indexes CoRR Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
2009	J	`jnl`	Faster entropy-bounded compressed suffix trees. Theor. Comput. Sci. Johannes Fischer, Veli Mäkinen, Gonzalo Navarro
2009	B	`conf`	Storage and Retrieval of Individual Genomes. RECOMB Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki
2008	—	`conf`	An In-Memory XQuery/XPath Engine over a Compressed Structured Text Representation. Structure-Based Compression of Complex Massive Data Angela Bonifati, Gregory Leighton, Veli Mäkinen, Sebastian Maneth, Gonzalo Navarro, Andrea Pugliese
2008	B	`conf`	An(other) Entropy-Bounded Compressed Suffix Tree. CPM Johannes Fischer, Veli Mäkinen, Gonzalo Navarro
2008	J	`jnl`	Combinatorial Approaches for Mass Spectra Recalibration. IEEE ACM Trans. Comput. Biol. Bioinform. Sebastian Böcker, Veli Mäkinen
2008	—	`ch.`	Compressed Suffix Array. Encyclopedia of Algorithms Veli Mäkinen
2008	—	`ch.`	Compressed Text Indexing. Encyclopedia of Algorithms Veli Mäkinen, Gonzalo Navarro
2008	J	`jnl`	Dynamic entropy-compressed sequences and full-text indexes. ACM Trans. Algorithms Veli Mäkinen, Gonzalo Navarro
2008	—	`conf`	Fast Index Based Filters for Music Retrieval. ISMIR Kjell Lemström, Niko Mikkilä, Veli Mäkinen
2008	B	`conf`	On Self-Indexing Images - Image Compression with Added Value. DCC Veli Mäkinen, Gonzalo Navarro
2008	—	`ch.`	Point Pattern Matching. Encyclopedia of Algorithms Veli Mäkinen, Esko Ukkonen
2008	C	`conf`	Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections. SPIRE Jouni Sirén, Niko Välimäki, Veli Mäkinen, Gonzalo Navarro
2008	A*	`conf`	Space Efficient String Mining under Frequency Constraints. ICDM Johannes Fischer, Veli Mäkinen, Niko Välimäki
2008	—	`conf`	Storage and Retrieval of Individual Genomes. Structure-Based Compression of Complex Massive Data Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki
2007	J	`jnl`	Compressed full-text indexes. ACM Comput. Surv. Gonzalo Navarro, Veli Mäkinen
2007	J	`jnl`	Compressed representations of sequences and full-text indexes. ACM Trans. Algorithms Paolo Ferragina, Giovanni Manzini, Veli Mäkinen, Gonzalo Navarro
2007	J	`jnl`	Compressed suffix tree - a basis for genome-scale sequence analysis. Bioinform. Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit, Veli Mäkinen
2007	—	`conf`	Engineering a Compressed Suffix Tree Implementation. WEA Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit, Veli Mäkinen
2007	C	`conf`	Implicit Compression Boosting with Applications to Self-indexing. SPIRE Veli Mäkinen, Gonzalo Navarro
2007	J	`jnl`	Rank and select revisited and extended. Theor. Comput. Sci. Veli Mäkinen, Gonzalo Navarro
2007	J	`jnl`	Rotation and lighting invariant template matching. Inf. Comput. Kimmo Fredriksson, Veli Mäkinen, Gonzalo Navarro
2007	B	`conf`	Space-Efficient Algorithms for Document Retrieval. CPM Niko Välimäki, Veli Mäkinen
2006	J	`jnl`	A Simple Alphabet-independent Fm-index. Int. J. Found. Comput. Sci. Szymon Grabowski, Gonzalo Navarro, Rafal Przywarski, Alejandro Salinger, Veli Mäkinen
2006	B	`conf`	Dynamic Entropy-Compressed Sequences and Full-Text Indexes. CPM Veli Mäkinen, Gonzalo Navarro
2006	J	`jnl`	Flexible Music Retrieval in Sublinear Time. Int. J. Found. Comput. Sci. Kimmo Fredriksson, Veli Mäkinen, Gonzalo Navarro
2006	B	`conf`	Position-Restricted Substring Searching. LATIN Veli Mäkinen, Gonzalo Navarro
2005	Misc	`conf`	A simple alphabet-independent FM-index. PSC Szymon Grabowski, Veli Mäkinen, Gonzalo Navarro, Alejandro Salinger
2005	—	`conf`	Combinatorial Approaches for Mass Spectra Recalibration. Computational Proteomics Sebastian Böcker, Veli Mäkinen
2005	Misc	`conf`	Flexible music retrieval in sublinear time. PSC Kimmo Fredriksson, Veli Mäkinen, Gonzalo Navarro
2005	C	`conf`	Maximum line-pair stabbing problem and its variations. EuroCG Sebastian Böcker, Veli Mäkinen
2005	J	`jnl`	On minimizing pattern splitting in multi-track string matching. J. Discrete Algorithms Kjell Lemström, Veli Mäkinen
2005	B	`conf`	Succinct Suffix Arrays Based on Run-Length Encoding. CPM Veli Mäkinen, Gonzalo Navarro
2005	J	`jnl`	Succinct Suffix Arrays based on Run-Length Encoding. Nord. J. Comput. Veli Mäkinen, Gonzalo Navarro
2005	J	`jnl`	Transposition invariant string matching. J. Algorithms Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen
2004	B	`conf`	Advantages of Backward Searching - Efficient Secondary Memory and Distributed Implementation of Compressed Suffix Arrays. ISAAC Veli Mäkinen, Gonzalo Navarro, Kunihiko Sadakane
2004	C	`conf`	An Alphabet-Friendly FM-Index. SPIRE Paolo Ferragina, Giovanni Manzini, Veli Mäkinen, Gonzalo Navarro
2004	B	`conf`	Compressed Compact Suffix Arrays. CPM Veli Mäkinen, Gonzalo Navarro
2004	C	`conf`	Finding Missing Patterns. WABI Shunsuke Inenaga, Teemu Kivioja, Veli Mäkinen
2004	C	`conf`	First Huffman, Then Burrows-Wheeler: A Simple Alphabet-Independent FM-Index. SPIRE Szymon Grabowski, Veli Mäkinen, Gonzalo Navarro
2004	B	`conf`	Rotation and Lighting Invariant Template Matching. LATIN Kimmo Fredriksson, Veli Mäkinen, Gonzalo Navarro
2003	A	`conf`	Algorithms for Transposition Invariant String Matching. STACS Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen
2003	J	`jnl`	Approximate Matching of Run-Length Compressed Strings. Algorithmica Veli Mäkinen, Esko Ukkonen, Gonzalo Navarro
2003	J	`jnl`	Compact Suffix Array - A Space-Efficient Full-Text Index. Fundam. Informaticae Veli Mäkinen
2003	—	`conf`	Geometric algorithms for transposition invariant content based music retrieval. ISMIR Esko Ukkonen, Kjell Lemström, Veli Mäkinen
2003	Misc	`conf`	Matching Numeric Strings under Noise. PSC Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen
2003	B	`conf`	On Minimizing Pattern Splitting in Multi-track String Matching. CPM Kjell Lemström, Veli Mäkinen
2003	—	`conf`	Sweepline the Music! Computer Science in Perspective Esko Ukkonen, Kjell Lemström, Veli Mäkinen
2003	—	`conf`	The C-BRAHMS project. ISMIR Kjell Lemström, Veli Mäkinen, Anna Pienimäki, Mika Turkia, Esko Ukkonen
2002	B	`conf`	Local Similarity Based Point-Pattern Matching. CPM Veli Mäkinen, Esko Ukkonen
2001	B	`conf`	Approximate Matching of Run-Length Compressed Strings. CPM Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen
2001	A	`conf`	Trade Off Between Compression and Search Times in Compact Suffix Array. ALENEX Veli Mäkinen
2001	C	`conf`	Using Edit Distance in Point-Pattern Matching. SPIRE Veli Mäkinen
2000	B	`conf`	Compact Suffix Array. CPM Veli Mäkinen