Veli Mäkinen

ORCID

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 61

Top Venues

Publications

Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Finding maximal exact matches in graphs. Algorithms Mol. Biol. 19 (1) (2024)
Nicola Rizzo, Massimo Equi, Tuukka Norri, Veli Mäkinen
Elastic founder graphs improved and enhanced. Theor. Comput. Sci. 982 (2024)
Nicola Rizzo, Massimo Equi, Tuukka Norri, Veli Mäkinen
Elastic Founder Graphs Improved and Enhanced. CoRR (2023)
Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Finding Maximal Exact Matches in Graphs. WABI (2023)
Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Chaining of Maximal Exact Matches in Graphs. SPIRE (2023)
Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
Algorithms and Complexity on Indexing Founder Graphs. Algorithmica 85 (6) (2023)
Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Finding Maximal Exact Matches in Graphs. CoRR (2023)
Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu
Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. Bioinform. 39 (8) (2023)
Massimo Equi, Arianne Meijer-van de Griend, Veli Mäkinen
From Bit-Parallelism to Quantum String Matching for Labelled Graphs. CPM (2023)
Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu, Roberto Grossi
On the Complexity of String Matching for Graphs. ACM Trans. Algorithms 19 (3) (2023)
Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Chaining of Maximal Exact Matches in Graphs. CoRR (2023)
Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
Graphs cannot be indexed in polynomial time for sub-quadratic time string matching, unless SETH fails. Theor. Comput. Sci. 975 (2023)
Nicola Rizzo, Veli Mäkinen
Indexable Elastic Founder Graphs of Minimum Height. CPM (2022)
Nicola Rizzo, Veli Mäkinen
Linear Time Construction of Indexable Elastic Founder Graphs. IWOCA (2022)
Nicola Rizzo, Veli Mäkinen
Linear Time Construction of Indexable Elastic Founder Graphs. CoRR (2022)
Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
Algorithms and Complexity on Indexing Founder Graphs. CoRR (2021)
Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
Graphs Cannot Be Indexed in Polynomial Time for Sub-quadratic Time String Matching, Unless SETH Fails. SOFSEM (2021)
Tuukka Norri, Bastien Cazaux, Saska Dönges, Daniel Valenzuela, Veli Mäkinen
Founder reconstruction enables scalable and seamless pangenomic analysis. Bioinform. 37 (24) (2021)
Kristoffer Sahlin, Veli Mäkinen
Accurate spliced alignment of long RNA sequencing reads. Bioinform. 37 (24) (2021)
Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
Algorithms and Complexity on Indexing Elastic Founder Graphs. ISAAC (2021)
Massimo Equi, Arianne Meijer-van de Griend, Veli Mäkinen
From Bit-Parallelism to Quantum: Breaking the Quadratic Barrier. CoRR (2021)
Veli Mäkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri, Alexandru I. Tomescu
Linear Time Construction of Indexable Founder Block Graphs. WABI (2020)
Dustin Cobas, Veli Mäkinen, Massimiliano Rossi
Tailoring r-index for Document Listing Towards Metagenomics Applications. SPIRE (2020)
Veli Mäkinen, Kristoffer Sahlin
Chaining with overlaps revisited. CoRR (2020)
Dustin Cobas, Veli Mäkinen, Massimiliano Rossi
Tailoring r-index for metagenomics. CoRR (2020)
Veli Mäkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri, Alexandru I. Tomescu
Linear Time Construction of Indexable Founder Block Graphs. CoRR (2020)
Altti Ilari Maarala, Ossi Arasalo, Daniel Valenzuela, Keijo Heljanko, Veli Mäkinen
Scalable Reference Genome Assembly from Compressed Pan-Genome Index with Spark. BigData Congress (2020)
Veli Mäkinen, Kristoffer Sahlin
Chaining with Overlaps Revisited. CPM (2020)
Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen, Veli Mäkinen
Linear-time String Indexing and Analysis in Small Space. ACM Trans. Algorithms 16 (2) (2020)
Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
Conditional Indexing Lower Bounds Through Self-Reducibility. CoRR (2020)
Massimo Equi, Roberto Grossi, Veli Mäkinen
On the Complexity of Exact Pattern Matching in Graphs: Binary Strings and Bounded Degree. CoRR (2019)
Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov, Veli Mäkinen
Linear time minimum segmentation enables scalable founder reconstruction. Algorithms Mol. Biol. 14 (1) (2019)
Mikko Rautiainen, Veli Mäkinen, Tobias Marschall
Bit-parallel sequence-to-graph alignment. Bioinform. 35 (19) (2019)
Edin Husic, Xinyue Li, Ademir Hujdurovic, Miika Mehine, Romeo Rizzi, Veli Mäkinen, Martin Milanic, Alexandru I. Tomescu
MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP. Bioinform. 35 (5) (2019)
Bastien Cazaux, Dmitry Kosolobov, Veli Mäkinen, Tuukka Norri
Linear Time Maximum Segmentation Problems in Column Stream Model. SPIRE (2019)
Veli Mäkinen, Alexandru I. Tomescu, Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi
Sparse Dynamic Programming on DAGs with Small Width. ACM Trans. Algorithms 15 (2) (2019)
Massimo Equi, Roberto Grossi, Veli Mäkinen, Alexandru I. Tomescu
On the Complexity of String Matching for Graphs. ICALP (2019)
Romeo Rizzi, Massimo Cairo, Veli Mäkinen, Alexandru I. Tomescu, Daniel Valenzuela
Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (1) (2019)
Veli Mäkinen, Tuukka Norri
Applying the Positional Burrows-Wheeler Transform to all-pairs Hamming distance. Inf. Process. Lett. 146 (2019)
Massimo Equi, Roberto Grossi, Alexandru I. Tomescu, Veli Mäkinen
On the Complexity of Exact Pattern Matching in Graphs: Determinism and Zig-Zag Matching. CoRR (2019)
Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi
Bidirectional Variable-Order de Bruijn Graphs. Int. J. Found. Comput. Sci. 29 (8) (2018)
Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. RECOMB (2018)
Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen, Veli Mäkinen
Towards pan-genome read alignment to improve variation calling. BMC Genom. 19 (S2) (2018)
Veli Mäkinen, Simon J. Puglisi
Editorial: Special Issue on "Combinatorial Algorithms" (IWOCA 2016). Theory Comput. Syst. 62 (6) (2018)
Diego Díaz-Domínguez, Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Gonzalo Navarro, Simon J. Puglisi
Assembling Omnitigs using Hidden-Order de Bruijn Graphs. CoRR (2018)
Nidia Obscura Acosta, Veli Mäkinen, Alexandru I. Tomescu
A safe and complete algorithm for metagenomic assembly. Algorithms Mol. Biol. 13 (1) (2018)
Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov, Veli Mäkinen
Minimum Segmentation for Pan-genomic Founder Reconstruction in Optimal Time. CoRR (2018)
Anna Kuosmanen, Tuukka Norri, Veli Mäkinen
Evaluating approaches to find exon chains based on long reads. Briefings Bioinform. 19 (3) (2018)
Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov, Veli Mäkinen
Minimum Segmentation for Pan-genomic Founder Reconstruction in Linear Time. WABI (2018)
Veli Mäkinen, Valeria Staneva, Alexandru I. Tomescu, Daniel Valenzuela, Sebastian Wilzbach
Interval scheduling maximizing minimum coverage. Discret. Appl. Math. 225 (2017)
Jarno Alanko, Fabio Cunial, Djamal Belazzougui, Veli Mäkinen
A framework for space-efficient read clustering in metagenomic samples. BMC Bioinform. 18 (S-3) (2017)
Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
Speeding up Dynamic Programming on DAGs through a Fast Approximation of Path Cover. CoRR (2017)
Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu
Gap Filling as Exact Path Length Problem. J. Comput. Biol. 23 (5) (2016)
Romeo Rizzi, Massimo Cairo, Veli Mäkinen, Daniel Valenzuela
Diploid Alignment is NP-hard. CoRR (2016)
Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali
Fully Dynamic de Bruijn Graphs. SPIRE (2016)
Anna Kuosmanen, Ahmed Sobih, Romeo Rizzi, Veli Mäkinen, Alexandru I. Tomescu
On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy. BIOINFORMATICS (2016)
Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen, Veli Mäkinen
Linear-time string indexing and analysis in small space. CoRR (2016)
Mikko Rautiainen, Leena Salmela, Veli Mäkinen
Identification of Variant Compositions in Related Strains Without Reference. AlCoB (2016)
Ahmed Sobih, Alexandru I. Tomescu, Veli Mäkinen
MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows. RECOMB (2016)
Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi
Bidirectional Variable-Order de Bruijn Graphs. LATIN (2016)
Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali
Fully Dynamic de Bruijn Graphs. CoRR (2016)
Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu
Gap Filling as Exact Path Length Problem. RECOMB (2015)
Roland Wittler, Tobias Marschall, Alexander Schönhuth, Veli Mäkinen
Repeat- and error-aware comparison of deletions. Bioinform. 31 (18) (2015)
Veli Mäkinen, Valeria Staneva, Alexandru I. Tomescu, Daniel Valenzuela
Interval scheduling maximizing minimum coverage. CoRR (2015)
Karen E. van Rens, Veli Mäkinen, Alexandru I. Tomescu
SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP. Bioinform. 31 (7) (2015)
Veli Mäkinen, Daniel Valenzuela
Diploid Alignments and Haplotyping. ISBRA (2015)
Alexandru I. Tomescu, Travis Gagie, Alexandru Popa, Romeo Rizzi, Anna Kuosmanen, Veli Mäkinen
Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (6) (2015)
Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
Fast in-memory XPath search using compressed indexes. Softw. Pract. Exp. 45 (3) (2015)
Veli Mäkinen, Niko Välimäki, Jouni Sirén
Indexing Graphs for Path Queries with Applications in Genome Research. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (2) (2014)
Veli Mäkinen
Editorial: Special Issue on Algorithms for Sequence Analysis and Storage. Algorithms 7 (1) (2014)
Romeo Rizzi, Alexandru I. Tomescu, Veli Mäkinen
On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly. BMC Bioinform. 15 (S-9) (2014)
Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Niko Välimäki
Multi-pattern matching with bidirectional indexes. J. Discrete Algorithms 24 (2014)
Sebastian Böcker, Gunnar W. Klau, Veli Mäkinen, Hon Wai Leong
Towards the ground truth: Exact algorithms for bioinformatics research (NII Shonan Meeting 2014-2). NII Shonan Meet. Rep. 2014 (2014)
Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen
A novel min-cost flow method for estimating transcript expression with RNA-Seq. BMC Bioinform. 14 (S-5) (2013)
Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen
A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. WABI (2013)
Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen, Veli Mäkinen
Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform. ESA (2013)
Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen
A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. CoRR (2013)
Veli Mäkinen, Jani Rahkola
Haploid to diploid alignment for variation calling assessment. BMC Bioinform. 14 (S-15) (2013)
Markus Heinonen, Niko Välimäki, Veli Mäkinen, Juho Rousu
Efficient Path Kernels for Reaction Function Prediction. BIOINFORMATICS (2012)
Travis Gagie, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Leena Salmela, Jorma Tarhio
Indexed Multi-pattern Matching. LATIN (2012)
Johannes Fischer, Travis Gagie, Tsvi Kopelowitz, Moshe Lewenstein, Veli Mäkinen, Leena Salmela, Niko Välimäki
Forbidden Patterns. LATIN (2012)
Niko Välimäki, Susana Ladra, Veli Mäkinen
Approximate all-pairs suffix/prefix overlaps. Inf. Comput. 213 (2012)
Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Niko Välimäki
Multi-pattern Matching with Bidirectional Indexes. COCOON (2012)
Veli Mäkinen, Leena Salmela, Johannes Ylinen
Normalized N50 assembly metric using gap-restricted co-linear chaining. BMC Bioinform. 13 (2012)
Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen
Fast scaffolding with small independent mixed integer programs. Bioinform. 27 (23) (2011)
Petteri Kaski, Veli Mäkinen, Patric R. J. Östergård
The Cycle Switching Graph of the Steiner Triple Systems of Order 19 is Connected. Graphs Comb. 27 (4) (2011)
Jouni Sirén, Niko Välimäki, Veli Mäkinen
Indexing Finite Language Representation of Population Genotypes. WABI (2011)
Stanislav Angelov, Shunsuke Inenaga, Teemu Kivioja, Veli Mäkinen
Missing pattern discovery. J. Discrete Algorithms 9 (2) (2011)
Niko Välimäki, Susana Ladra, Veli Mäkinen
Approximate All-Pairs Suffix/Prefix Overlaps. CPM (2010)
Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
Fast in-memory XPath search using compressed indexes. ICDE (2010)
Travis Gagie, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Leena Salmela
Pattern Kits CoRR (2010)
Kjell Lemström, Niko Mikkilä, Veli Mäkinen
Filtering methods for content-based retrieval on indexed symbolic music databases. Inf. Retr. 13 (1) (2010)
Veli Mäkinen, Niko Välimäki, Antti Laaksonen, Riku Katainen
Unified View of Backward Backtracking in Short Read Mapping. Algorithms and Applications (2010)
Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki
Storage and Retrieval of Highly Repetitive Sequence Collections. J. Comput. Biol. 17 (3) (2010)
Jouni Sirén, Niko Välimäki, Veli Mäkinen
Indexing Finite Language Representation of Population Genotypes CoRR (2010)
Niko Välimäki, Veli Mäkinen, Wolfgang Gerlach, Kashyap Dixit
Engineering a compressed suffix tree implementation. ACM J. Exp. Algorithmics 14 (2009)
Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
Fast In-Memory XPath Search over Compressed Text and Tree Indexes CoRR (2009)
François Nicolas, Veli Mäkinen, Esko Ukkonen
Efficient construction of maximal and minimal representations of motifs of a string. Theor. Comput. Sci. 410 (30-32) (2009)
Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki
Storage and Retrieval of Individual Genomes. RECOMB (2009)
Johannes Fischer, Veli Mäkinen, Gonzalo Navarro
Faster entropy-bounded compressed suffix trees. Theor. Comput. Sci. 410 (51) (2009)

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Publication Activity (10 Years)

Top Topics

Top Venues

Veli Mäkinen