Compact Suffix Array. - Veli Mäkinen (CPM, 2000)

Trade Off Between Compression and Search Times in Compact Suffix Array. - Veli Mäkinen (ALENEX, 2001)

Using Edit Distance in Point-Pattern Matching. - Veli Mäkinen (SPIRE, 2001)

Local Similarity Based Point-Pattern Matching. - Veli Mäkinen; Esko Ukkonen (CPM, 2002)

Sweepline the Music! - Esko Ukkonen; Kjell Lemström; Veli Mäkinen (Computer Science in Perspective, 2003)

The C-BRAHMS project. - Kjell Lemström; Veli Mäkinen; Anna Pienimäki; Mika Turkia; Esko Ukkonen (ISMIR, 2003)

Geometric algorithms for transposition invariant content based music retrieval. - Esko Ukkonen; Kjell Lemström; Veli Mäkinen (ISMIR, 2003)

Algorithms for Transposition Invariant String Matching. - Veli Mäkinen; Gonzalo Navarro 001; Esko Ukkonen (STACS, 2003)

Matching Numeric Strings under Noise. - Veli Mäkinen; Gonzalo Navarro 001; Esko Ukkonen (Stringology, 2003)

Approximate Matching of Run-Length Compressed Strings. - Veli Mäkinen; Esko Ukkonen; Gonzalo Navarro 001 (Algorithmica, 2003)

Compact Suffix Array - A Space-Efficient Full-Text Index. - Veli Mäkinen (Fundam. Informaticae, 2003)

Compressed Compact Suffix Arrays. - Veli Mäkinen; Gonzalo Navarro 001 (CPM, 2004)

Advantages of Backward Searching - Efficient Secondary Memory and Distributed Implementation of Compressed Suffix Arrays. - Veli Mäkinen; Gonzalo Navarro 001; Kunihiko Sadakane (ISAAC, 2004)

An Alphabet-Friendly FM-Index. - Paolo Ferragina; Giovanni Manzini; Veli Mäkinen; Gonzalo Navarro 001 (SPIRE, 2004)

First Huffman, Then Burrows-Wheeler: A Simple Alphabet-Independent FM-Index. - Szymon Grabowski; Veli Mäkinen; Gonzalo Navarro 001 (SPIRE, 2004)

Finding Missing Patterns. - Shunsuke Inenaga; Teemu Kivioja; Veli Mäkinen (WABI, 2004)

Maximum line-pair stabbing problem and its variations. - Sebastian Böcker; Veli Mäkinen (EuroCG, 2005)

A simple alphabet-independent FM-index. - Szymon Grabowski; Veli Mäkinen; Gonzalo Navarro 001; Alejandro Salinger (Stringology, 2005)

Transposition invariant string matching. - Veli Mäkinen; Gonzalo Navarro 001; Esko Ukkonen (J. Algorithms, 2005)

On minimizing pattern splitting in multi-track string matching. - Kjell Lemström; Veli Mäkinen (J. Discrete Algorithms, 2005)

Succinct Suffix Arrays based on Run-Length Encoding. - Veli Mäkinen; Gonzalo Navarro 001 (Nord. J. Comput., 2005)

Position-Restricted Substring Searching. - Veli Mäkinen; Gonzalo Navarro 001 (LATIN, 2006)

Flexible Music Retrieval in Sublinear Time. - Kimmo Fredriksson; Veli Mäkinen; Gonzalo Navarro 001 (Int. J. Found. Comput. Sci., 2006)

A Simple Alphabet-independent Fm-index. - Szymon Grabowski; Gonzalo Navarro 001; Rafal Przywarski; Alejandro Salinger; Veli Mäkinen (Int. J. Found. Comput. Sci., 2006)

Space-Efficient Algorithms for Document Retrieval. - Niko Välimäki; Veli Mäkinen (CPM, 2007)

Implicit Compression Boosting with Applications to Self-indexing. - Veli Mäkinen; Gonzalo Navarro 001 (SPIRE, 2007)

Compressed suffix tree - a basis for genome-scale sequence analysis. - Niko Välimäki; Wolfgang Gerlach; Kashyap Dixit; Veli Mäkinen (Bioinform., 2007)

Compressed full-text indexes. - Gonzalo Navarro 001; Veli Mäkinen (ACM Comput. Surv., 2007)

Rotation and lighting invariant template matching. - Kimmo Fredriksson; Veli Mäkinen; Gonzalo Navarro 001 (Inf. Comput., 2007)

Compressed representations of sequences and full-text indexes. - Paolo Ferragina; Giovanni Manzini; Veli Mäkinen; Gonzalo Navarro 001 (ACM Trans. Algorithms, 2007)

Rank and select revisited and extended. - Veli Mäkinen; Gonzalo Navarro 001 (Theor. Comput. Sci., 2007)

An(other) Entropy-Bounded Compressed Suffix Tree. - Johannes Fischer 001; Veli Mäkinen; Gonzalo Navarro 001 (CPM, 2008)

An In-Memory XQuery/XPath Engine over a Compressed Structured Text Representation. - Angela Bonifati; Gregory Leighton; Veli Mäkinen; Sebastian Maneth; Gonzalo Navarro 001; Andrea Pugliese 001 (Structure-Based Compression of Complex Massive Data, 2008)

On Self-Indexing Images - Image Compression with Added Value. - Veli Mäkinen; Gonzalo Navarro 001 (DCC, 2008)

Space Efficient String Mining under Frequency Constraints. - Johannes Fischer 001; Veli Mäkinen; Niko Välimäki (ICDM, 2008)

Fast Index Based Filters for Music Retrieval. - Kjell Lemström; Niko Mikkilä; Veli Mäkinen (ISMIR, 2008)

Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections. - Jouni Sirén; Niko Välimäki; Veli Mäkinen; Gonzalo Navarro 001 (SPIRE, 2008)

Dynamic entropy-compressed sequences and full-text indexes. - Veli Mäkinen; Gonzalo Navarro 001 (ACM Trans. Algorithms, 2008)

Combinatorial Approaches for Mass Spectra Recalibration. - Sebastian Böcker; Veli Mäkinen (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Compressed Suffix Array. - Veli Mäkinen (Encyclopedia of Algorithms, 2008)

Compressed Text Indexing. - Veli Mäkinen; Gonzalo Navarro 001 (Encyclopedia of Algorithms, 2008)

Point Pattern Matching. - Veli Mäkinen; Esko Ukkonen (Encyclopedia of Algorithms, 2008)

Storage and Retrieval of Individual Genomes. - Veli Mäkinen; Gonzalo Navarro 001; Jouni Sirén; Niko Välimäki (RECOMB, 2009)

Fast In-Memory XPath Search over Compressed Text and Tree Indexes - Diego Arroyuelo; Francisco Claude; Sebastian Maneth; Veli Mäkinen; Gonzalo Navarro 001; Kim Nguyen 001; Jouni Sirén; Niko Välimäki (CoRR, 2009)

Engineering a compressed suffix tree implementation. - Niko Välimäki; Veli Mäkinen; Wolfgang Gerlach; Kashyap Dixit (ACM J. Exp. Algorithmics, 2009)

Faster entropy-bounded compressed suffix trees. - Johannes Fischer 001; Veli Mäkinen; Gonzalo Navarro 001 (Theor. Comput. Sci., 2009)

Efficient construction of maximal and minimal representations of motifs of a string. - François Nicolas; Veli Mäkinen; Esko Ukkonen (Theor. Comput. Sci., 2009)

Unified View of Backward Backtracking in Short Read Mapping. - Veli Mäkinen; Niko Välimäki; Antti Laaksonen; Riku Katainen (Algorithms and Applications, 2010)

Pattern Kits - Travis Gagie; Kalle Karhu; Juha Kärkkäinen; Veli Mäkinen; Leena Salmela (CoRR, 2010)

Filtering methods for content-based retrieval on indexed symbolic music databases. - Kjell Lemström; Niko Mikkilä; Veli Mäkinen (Inf. Retr., 2010)

Storage and Retrieval of Highly Repetitive Sequence Collections. - Veli Mäkinen; Gonzalo Navarro 001; Jouni Sirén; Niko Välimäki (J. Comput. Biol., 2010)

Indexing Finite Language Representation of Population Genotypes. - Jouni Sirén; Niko Välimäki; Veli Mäkinen (WABI, 2011)

Fast scaffolding with small independent mixed integer programs. - Leena Salmela; Veli Mäkinen; Niko Välimäki; Johannes Ylinen; Esko Ukkonen (Bioinform., 2011)

The Cycle Switching Graph of the Steiner Triple Systems of Order 19 is Connected. - Petteri Kaski; Veli Mäkinen; Patric R. J. Östergård (Graphs Comb., 2011)

Missing pattern discovery. - Stanislav Angelov; Shunsuke Inenaga; Teemu Kivioja; Veli Mäkinen (J. Discrete Algorithms, 2011)

Efficient Path Kernels for Reaction Function Prediction. - Markus Heinonen; Niko Välimäki; Veli Mäkinen; Juho Rousu (BIOINFORMATICS, 2012)

Forbidden Patterns. - Johannes Fischer 001; Travis Gagie; Tsvi Kopelowitz; Moshe Lewenstein; Veli Mäkinen; Leena Salmela; Niko Välimäki (LATIN, 2012)

Indexed Multi-pattern Matching. - Travis Gagie; Kalle Karhu; Juha Kärkkäinen; Veli Mäkinen; Leena Salmela; Jorma Tarhio (LATIN, 2012)

Normalized N50 assembly metric using gap-restricted co-linear chaining. - Veli Mäkinen; Leena Salmela; Johannes Ylinen (BMC Bioinform., 2012)

Approximate all-pairs suffix/prefix overlaps. - Niko Välimäki; Susana Ladra; Veli Mäkinen (Inf. Comput., 2012)

Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform. - Djamal Belazzougui; Fabio Cunial; Juha Kärkkäinen; Veli Mäkinen (ESA, 2013)

A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. - Alexandru I. Tomescu; Anna Kuosmanen; Romeo Rizzi; Veli Mäkinen (WABI, 2013)

Haploid to diploid alignment for variation calling assessment. - Veli Mäkinen; Jani Rahkola (BMC Bioinform., 2013)

A novel min-cost flow method for estimating transcript expression with RNA-Seq. - Alexandru I. Tomescu; Anna Kuosmanen; Romeo Rizzi; Veli Mäkinen (BMC Bioinform., 2013)

Editorial: Special Issue on Algorithms for Sequence Analysis and Storage. - Veli Mäkinen (Algorithms, 2014)

On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly. - Romeo Rizzi; Alexandru I. Tomescu; Veli Mäkinen (BMC Bioinform., 2014)

Multi-pattern matching with bidirectional indexes. - Simon Gog; Kalle Karhu; Juha Kärkkäinen; Veli Mäkinen; Niko Välimäki (J. Discrete Algorithms, 2014)

Towards the ground truth: Exact algorithms for bioinformatics research (NII Shonan Meeting 2014-2). - Sebastian Böcker; Gunnar W. Klau; Veli Mäkinen; Hon Wai Leong (NII Shonan Meet. Rep., 2014)

Indexing Graphs for Path Queries with Applications in Genome Research. - Veli Mäkinen; Niko Välimäki; Jouni Sirén (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing. - Veli Mäkinen; Djamal Belazzougui; Fabio Cunial; Alexandru I. Tomescu (Cambridge University Press, 2015)

Diploid Alignments and Haplotyping. - Veli Mäkinen; Daniel Valenzuela 001 (ISBRA, 2015)

SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP. - Karen E. van Rens; Veli Mäkinen; Alexandru I. Tomescu (Bioinform., 2015)

Repeat- and error-aware comparison of deletions. - Roland Wittler; Tobias Marschall; Alexander Schönhuth; Veli Mäkinen (Bioinform., 2015)

Interval scheduling maximizing minimum coverage. - Veli Mäkinen; Valeria Staneva; Alexandru I. Tomescu; Daniel Valenzuela 001 (CoRR, 2015)

Fast in-memory XPath search using compressed indexes. - Diego Arroyuelo; Francisco Claude; Sebastian Maneth; Veli Mäkinen; Gonzalo Navarro 001; Kim Nguyen 001; Jouni Sirén; Niko Välimäki (Softw. Pract. Exp., 2015)

Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly. - Alexandru I. Tomescu; Travis Gagie; Alexandru Popa 001; Romeo Rizzi; Anna Kuosmanen; Veli Mäkinen (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Identification of Variant Compositions in Related Strains Without Reference. - Mikko Rautiainen; Leena Salmela; Veli Mäkinen (AlCoB, 2016)

On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy. - Anna Kuosmanen; Ahmed Sobih; Romeo Rizzi; Veli Mäkinen; Alexandru I. Tomescu (BIOINFORMATICS, 2016)

MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows. - Ahmed Sobih; Alexandru I. Tomescu; Veli Mäkinen (RECOMB, 2016)

Fully Dynamic de Bruijn Graphs. - Djamal Belazzougui; Travis Gagie; Veli Mäkinen; Marco Previtali (SPIRE, 2016)

Diploid Alignment is NP-hard. - Romeo Rizzi; Massimo Cairo; Veli Mäkinen; Daniel Valenzuela 001 (CoRR, 2016)

Gap Filling as Exact Path Length Problem. - Leena Salmela; Kristoffer Sahlin; Veli Mäkinen; Alexandru I. Tomescu (J. Comput. Biol., 2016)

Compressed Suffix Array. - Djamal Belazzougui; Veli Mäkinen; Daniel Valenzuela 001 (Encyclopedia of Algorithms, 2016)

Compressed Text Indexing. - Veli Mäkinen; Gonzalo Navarro 001 (Encyclopedia of Algorithms, 2016)

Point Pattern Matching. - Veli Mäkinen; Esko Ukkonen (Encyclopedia of Algorithms, 2016)

A framework for space-efficient read clustering in metagenomic samples. - Jarno Alanko; Fabio Cunial; Djamal Belazzougui; Veli Mäkinen (BMC Bioinform., 2017)

Speeding up Dynamic Programming on DAGs through a Fast Approximation of Path Cover. - Anna Kuosmanen; Topi Paavilainen; Travis Gagie; Rayan Chikhi; Alexandru I. Tomescu; Veli Mäkinen (CoRR, 2017)

Interval scheduling maximizing minimum coverage. - Veli Mäkinen; Valeria Staneva; Alexandru I. Tomescu; Daniel Valenzuela 001; Sebastian Wilzbach (Discret. Appl. Math., 2017)

Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. - Anna Kuosmanen; Topi Paavilainen; Travis Gagie; Rayan Chikhi; Alexandru I. Tomescu; Veli Mäkinen (RECOMB, 2018)

Minimum Segmentation for Pan-genomic Founder Reconstruction in Linear Time. - Tuukka Norri; Bastien Cazaux; Dmitry Kosolobov; Veli Mäkinen (WABI, 2018)

A safe and complete algorithm for metagenomic assembly. - Nidia Obscura Acosta; Veli Mäkinen; Alexandru I. Tomescu (Algorithms Mol. Biol., 2018)

Evaluating approaches to find exon chains based on long reads. - Anna Kuosmanen; Tuukka Norri; Veli Mäkinen (Briefings Bioinform., 2018)

Towards pan-genome read alignment to improve variation calling. - Daniel Valenzuela 001; Tuukka Norri; Niko Välimäki; Esa Pitkänen; Veli Mäkinen (BMC Genom., 2018)

Minimum Segmentation for Pan-genomic Founder Reconstruction in Optimal Time. - Tuukka Norri; Bastien Cazaux; Dmitry Kosolobov; Veli Mäkinen (CoRR, 2018)

Assembling Omnitigs using Hidden-Order de Bruijn Graphs. - Diego Díaz-Domínguez; Djamal Belazzougui; Travis Gagie; Veli Mäkinen; Gonzalo Navarro 001; Simon J. Puglisi (CoRR, 2018)

Bidirectional Variable-Order de Bruijn Graphs. - Djamal Belazzougui; Travis Gagie; Veli Mäkinen; Marco Previtali; Simon J. Puglisi (Int. J. Found. Comput. Sci., 2018)

Editorial: Special Issue on "Combinatorial Algorithms" (IWOCA 2016). - Veli Mäkinen; Simon J. Puglisi (Theory Comput. Syst., 2018)

Linear Time Maximum Segmentation Problems in Column Stream Model. - Bastien Cazaux; Dmitry Kosolobov; Veli Mäkinen; Tuukka Norri (SPIRE, 2019)

Linear time minimum segmentation enables scalable founder reconstruction. - Tuukka Norri; Bastien Cazaux; Dmitry Kosolobov; Veli Mäkinen (Algorithms Mol. Biol., 2019)

MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP. - Edin Husic; Xinyue Li; Ademir Hujdurovic; Miika Mehine; Romeo Rizzi; Veli Mäkinen; Martin Milanic; Alexandru I. Tomescu (Bioinform., 2019)

Bit-parallel sequence-to-graph alignment. - Mikko Rautiainen; Veli Mäkinen; Tobias Marschall (Bioinform., 2019)

On the Complexity of Exact Pattern Matching in Graphs: Binary Strings and Bounded Degree. - Massimo Equi; Roberto Grossi; Veli Mäkinen (CoRR, 2019)

On the Complexity of Exact Pattern Matching in Graphs: Determinism and Zig-Zag Matching. - Massimo Equi; Roberto Grossi; Alexandru I. Tomescu; Veli Mäkinen (CoRR, 2019)

Applying the Positional Burrows-Wheeler Transform to all-pairs Hamming distance. - Veli Mäkinen; Tuukka Norri (Inf. Process. Lett., 2019)

Sparse Dynamic Programming on DAGs with Small Width. - Veli Mäkinen; Alexandru I. Tomescu; Anna Kuosmanen; Topi Paavilainen; Travis Gagie; Rayan Chikhi (ACM Trans. Algorithms, 2019)

Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics. - Romeo Rizzi; Massimo Cairo; Veli Mäkinen; Alexandru I. Tomescu; Daniel Valenzuela 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Scalable Reference Genome Assembly from Compressed Pan-Genome Index with Spark. - Altti Ilari Maarala; Ossi Arasalo; Daniel Valenzuela 001; Keijo Heljanko; Veli Mäkinen (BigData, 2020)

Chaining with Overlaps Revisited. - Veli Mäkinen; Kristoffer Sahlin (CPM, 2020)

Tailoring r-index for Document Listing Towards Metagenomics Applications. - Dustin Cobas; Veli Mäkinen; Massimiliano Rossi 001 (SPIRE, 2020)

Linear Time Construction of Indexable Founder Block Graphs. - Veli Mäkinen; Bastien Cazaux; Massimo Equi; Tuukka Norri; Alexandru I. Tomescu (WABI, 2020)

Conditional Indexing Lower Bounds Through Self-Reducibility. - Massimo Equi; Veli Mäkinen; Alexandru I. Tomescu (CoRR, 2020)

Tailoring r-index for metagenomics. - Dustin Cobas; Veli Mäkinen; Massimiliano Rossi 001 (CoRR, 2020)

Linear-time String Indexing and Analysis in Small Space. - Djamal Belazzougui; Fabio Cunial; Juha Kärkkäinen; Veli Mäkinen (ACM Trans. Algorithms, 2020)

Algorithms and Complexity on Indexing Elastic Founder Graphs. - Massimo Equi; Tuukka Norri; Jarno Alanko; Bastien Cazaux; Alexandru I. Tomescu; Veli Mäkinen (ISAAC, 2021)

Founder reconstruction enables scalable and seamless pangenomic analysis. - Tuukka Norri; Bastien Cazaux; Saska Dönges; Daniel Valenzuela 001; Veli Mäkinen (Bioinform., 2021)

Accurate spliced alignment of long RNA sequencing reads. - Kristoffer Sahlin; Veli Mäkinen (Bioinform., 2021)

Indexable Elastic Founder Graphs of Minimum Height. - Nicola Rizzo 001; Veli Mäkinen (CPM, 2022)

Linear Time Construction of Indexable Elastic Founder Graphs. - Nicola Rizzo 001; Veli Mäkinen (IWOCA, 2022)

Genome-Scale Algorithm Design: Bioinformatics in the Era of High-Throughput Sequencing (2nd edition). - Veli Mäkinen; Djamal Belazzougui; Fabio Cunial; Alexandru I. Tomescu (Cambridge University Press, 2023)

From Bit-Parallelism to Quantum String Matching for Labelled Graphs. - Massimo Equi; Arianne Meijer-van de Griend; Veli Mäkinen (CPM, 2023)

Chaining of Maximal Exact Matches in Graphs. - Nicola Rizzo 001; Manuel Cáceres; Veli Mäkinen (SPIRE, 2023)

Algorithms and Complexity on Indexing Founder Graphs. - Massimo Equi; Tuukka Norri; Jarno Alanko; Bastien Cazaux; Alexandru I. Tomescu; Veli Mäkinen (Algorithmica, 2023)

On the Complexity of String Matching for Graphs. - Massimo Equi; Veli Mäkinen; Alexandru I. Tomescu; Roberto Grossi (ACM Trans. Algorithms, 2023)

Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. - Jun Ma; Manuel Cáceres; Leena Salmela; Veli Mäkinen; Alexandru I. Tomescu (Bioinform., 2023)

Graphs cannot be indexed in polynomial time for sub-quadratic time string matching, unless SETH fails. - Massimo Equi; Veli Mäkinen; Alexandru I. Tomescu (Theor. Comput. Sci., 2023)

Elastic founder graphs improved and enhanced. - Nicola Rizzo 001; Massimo Equi; Tuukka Norri; Veli Mäkinen (Theor. Comput. Sci., 2024)

Finding maximal exact matches in graphs. - Nicola Rizzo 001; Manuel Cáceres; Veli Mäkinen (Algorithms Mol. Biol., 2024)

On the Construction of Elastic Degenerate Strings. - Nicola Rizzo 001; Veli Mäkinen; Nadia Pisanti (From Strings to Graphs, and Back Again, 2025)

Graph Indexing Beyond Wheeler Graphs. - Jarno N. Alanko; Elena Biagi 002; Massimo Equi; Veli Mäkinen; Simon J. Puglisi; Nicola Rizzo 001; Kunihiko Sadakane; Jouni Sirén (The Expanding World of Compressed Data, 2025)

Practical Colinear Chaining on Sequences Revisited. - Nicola Rizzo 001; Manuel Cáceres; Veli Mäkinen (ISBRA (2), 2025)