Leena Salmela

According to our database, Leena Salmela authored at least 48 papers between 2003 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Space-efficient computation of k-mer dictionaries for large values of k.

Diego Díaz-Domínguez, Miika Leinonen, Leena Salmela

Algorithms Mol. Biol., December, 2024

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., August, 2023

ViQUF: De Novo Viral Quasispecies Reconstruction Using Unitig-Based Flow Networks.

Borja Freire, Susana Ladra, José R. Paramá, Leena Salmela

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

Simple Runs-Bounded FM-Index Designs Are Fast.

Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, Leena Salmela

Proceedings of the 21st International Symposium on Experimental Algorithms, 2023

Computing All-vs-All MEMs in Grammar-Compressed Text.

Diego Díaz-Domínguez, Leena Salmela

Proceedings of the String Processing and Information Retrieval, 2023

2022

Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data.

Riku Walve, Simon J. Puglisi, Leena Salmela

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Extraction of Long k-mers Using Spaced Seeds.

Miika Leinonen, Leena Salmela

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

HGGA: hierarchical guided genome assembler.

Riku Walve, Leena Salmela

BMC Bioinform., 2022

Efficient Solutions to Biological Problems Using de Bruijn Graphs (Invited Talk).

Leena Salmela

Proceedings of the 22nd International Workshop on Algorithms in Bioinformatics, 2022

Computing All-vs-All MEMs in Run-Length-Encoded Collections of HiFi Reads.

Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela

Proceedings of the String Processing and Information Retrieval, 2022

2021

Succinct dynamic de Bruijn graphs.

Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher

Bioinform., August, 2021

Inference of viral quasispecies with a paired de Bruijn graph.

Borja Freire, Susana Ladra, José R. Paramá, Leena Salmela

Bioinform., 2021

Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph.

Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher

Algorithms Mol. Biol., 2021

2020

Optical map guided genome assembly.

Miika Leinonen, Leena Salmela

BMC Bioinform., 2020

Fast and accurate correction of optical mapping data via spaced seeds.

Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher

Bioinform., 2020

2019

Safely Filling Gaps with Partial Solutions Common to All Solutions.

Leena Salmela, Alexandru I. Tomescu

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Aligning optical maps to de Bruijn graphs.

Kingshuk Mukherjee, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, Christina Boucher

Bioinform., 2019

Kermit: linkage map guided long read assembly.

Riku Walve, Pasi Rastas, Leena Salmela

Algorithms Mol. Biol., 2019

Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding.

Niko Kiirala, Leena Salmela, Alexandru I. Tomescu

Proceedings of the 30th Annual Symposium on Combinatorial Pattern Matching, 2019

2018

Kermit: Guided Long Read Assembly using Coloured Overlap Graphs.

Riku Walve, Pasi Rastas, Leena Salmela

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

2017

Accurate self-correction of errors in long reads using de Bruijn graphs.

Leena Salmela, Riku Walve, Eric Rivals, Esko Ukkonen

Bioinform., 2017

Disentangled Long-Read De Bruijn Graphs via Optical Maps.

Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin D. Muggli, Christina Boucher

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

2016

Gap Filling as Exact Path Length Problem.

Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu

J. Comput. Biol., 2016

Identification of Variant Compositions in Related Strains Without Reference.

Mikko Rautiainen, Leena Salmela, Veli Mäkinen

Proceedings of the Algorithms for Computational Biology - Third International Conference, 2016

2014

LoRDEC: accurate and efficient long read error correction.

Leena Salmela, Eric Rivals

Bioinform., 2014

2012

String matching with alphabet sampling.

Francisco Claude, Gonzalo Navarro, Hannu Peltola, Leena Salmela, Jorma Tarhio

J. Discrete Algorithms, 2012

Average complexity of backward q-gram string matching algorithms.

Leena Salmela

Inf. Process. Lett., 2012

Normalized N50 assembly metric using gap-restricted co-linear chaining.

Veli Mäkinen, Leena Salmela, Johannes Ylinen

BMC Bioinform., 2012

Indexed Multi-pattern Matching.

Travis Gagie, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Leena Salmela, Jorma Tarhio

Proceedings of the LATIN 2012: Theoretical Informatics, 2012

Forbidden Patterns.

Johannes Fischer, Travis Gagie, Tsvi Kopelowitz, Moshe Lewenstein, Veli Mäkinen, Leena Salmela, Niko Välimäki

Proceedings of the LATIN 2012: Theoretical Informatics, 2012

2011

Correcting errors in short reads by multiple alignments.

Leena Salmela, Jan Schröder

Bioinform., 2011

Fast scaffolding with small independent mixed integer programs.

Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen

Bioinform., 2011

2010

Pattern Kits

Travis Gagie, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Leena Salmela

CoRR, 2010

Correction of sequencing errors in a mixed set of reads.

Leena Salmela

Bioinform., 2010

Approximate Boyer-Moore String Matching for Small Alphabets.

Leena Salmela, Jorma Tarhio, Petri Kalsi

Algorithmica, 2010

Bit-Parallel Search Algorithms for Long Patterns.

Branislav Durian, Hannu Peltola, Leena Salmela, Jorma Tarhio

Proceedings of the Experimental Algorithms, 9th International Symposium, 2010

Approximate String Matching with Reduced Alphabet.

Leena Salmela, Jorma Tarhio

Proceedings of the Algorithms and Applications, 2010

2009

Improved algorithms for string searching problems.

Leena Salmela

PhD thesis, 2009

mpscan: Fast Localisation of Multiple Reads in Genomes.

Eric Rivals, Leena Salmela, Petteri Kiiskinen, Petri Kalsi, Jorma Tarhio

Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

Indexing Variable Length Substrings for Exact and Approximate Matching.

Gonzalo Navarro, Leena Salmela

Proceedings of the String Processing and Information Retrieval, 2009

Towards Automated Management of Compiler Assignments.

Leena Salmela, Jorma Tarhio, Timo Montonen

Proceedings of the CSEDU 2009 - Proceedings of the First International Conference on Computer Supported Education, Lisboa, Portugal, March 23-26, 2009, 2009

2008

Fast parameterized matching with q-grams.

Leena Salmela, Jorma Tarhio

J. Discrete Algorithms, 2008

Speeding Up Pattern Matching by Text Sampling.

Francisco Claude, Gonzalo Navarro, Hannu Peltola, Leena Salmela, Jorma Tarhio

Proceedings of the String Processing and Information Retrieval, 2008

2007

Algorithms for Weighted Matching.

Leena Salmela, Jorma Tarhio

Proceedings of the String Processing and Information Retrieval, 2007

Tuning Approximate Boyer-Moore for Gene Sequences.

Petri Kalsi, Leena Salmela, Jorma Tarhio

Proceedings of the String Processing and Information Retrieval, 2007

2006

Multipattern string matching with <i>q</i>-grams.

Leena Salmela, Jorma Tarhio, Jari Kytöjoki

ACM J. Exp. Algorithmics, 2006

Sublinear Algorithms for Parameterized Matching.

Leena Salmela, Jorma Tarhio

Proceedings of the Combinatorial Pattern Matching, 17th Annual Symposium, 2006

2003

Tuning String Matching for Huge Pattern Sets.

Jari Kytöjoki, Leena Salmela, Jorma Tarhio

Proceedings of the Combinatorial Pattern Matching, 14th Annual Symposium, 2003