Leena Salmela

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 30

Top Topics

Compressed Text

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Diego Díaz-Domínguez, Miika Leinonen, Leena Salmela
Space-efficient computation of k-mer dictionaries for large values of k. Algorithms Mol. Biol. 19 (1) (2024)
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)
Borja Freire, Susana Ladra, José R. Paramá, Leena Salmela
ViQUF: De Novo Viral Quasispecies Reconstruction Using Unitig-Based Flow Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (2) (2023)
Diego Díaz-Domínguez, Leena Salmela
Computing All-vs-All MEMs in Grammar-Compressed Text. SPIRE (2023)
Diego Díaz-Domínguez, Leena Salmela
Computing all-vs-all MEMs in grammar-compressed text. CoRR (2023)
Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, Leena Salmela
Simple Runs-Bounded FM-Index Designs Are Fast. SEA (2023)
Leena Salmela
Efficient Solutions to Biological Problems Using de Bruijn Graphs (Invited Talk). WABI (2022)
Miika Leinonen, Leena Salmela
Extraction of Long k-mers Using Spaced Seeds. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela
Computing all-vs-all MEMs in run-length encoded collections of HiFi reads. CoRR (2022)
Riku Walve, Leena Salmela
HGGA: hierarchical guided genome assembler. BMC Bioinform. 23 (1) (2022)
Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela
Computing All-vs-All MEMs in Run-Length-Encoded Collections of HiFi Reads. SPIRE (2022)
Riku Walve, Simon J. Puglisi, Leena Salmela
Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (4) (2022)
Borja Freire, Susana Ladra, José R. Paramá, Leena Salmela
ViQUF: de novo Viral Quasispecies reconstruction using Unitig-based Flow networks. CoRR (2021)
Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher
Succinct dynamic de Bruijn graphs. Bioinform. 37 (14) (2021)
Borja Freire, Susana Ladra, José R. Paramá, Leena Salmela
Inference of viral quasispecies with a paired de Bruijn graph. Bioinform. 37 (4) (2021)
Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher
Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph. Algorithms Mol. Biol. 16 (1) (2021)
Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher
Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph. WABI (2020)
Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. 36 (9) (2020)
Miika Leinonen, Leena Salmela
Optical map guided genome assembly. BMC Bioinform. 21 (1) (2020)
Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. 36 (3) (2020)
Kingshuk Mukherjee, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, Christina Boucher
Aligning optical maps to de Bruijn graphs. Bioinform. 35 (18) (2019)
Leena Salmela, Alexandru I. Tomescu
Safely Filling Gaps with Partial Solutions Common to All Solutions. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (2) (2019)
Riku Walve, Pasi Rastas, Leena Salmela
Kermit: linkage map guided long read assembly. Algorithms Mol. Biol. 14 (1) (2019)
Niko Kiirala, Leena Salmela, Alexandru I. Tomescu
Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding. CPM (2019)
Riku Walve, Pasi Rastas, Leena Salmela
Kermit: Guided Long Read Assembly using Coloured Overlap Graphs. WABI (2018)
Leena Salmela, Riku Walve, Eric Rivals, Esko Ukkonen
Accurate self-correction of errors in long reads using de Bruijn graphs. Bioinform. 33 (6) (2017)
Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
Disentangled Long-Read De Bruijn Graphs via Optical Maps. WABI (2017)
Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu
Gap Filling as Exact Path Length Problem. J. Comput. Biol. 23 (5) (2016)
Mikko Rautiainen, Leena Salmela, Veli Mäkinen
Identification of Variant Compositions in Related Strains Without Reference. AlCoB (2016)
Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu
Gap Filling as Exact Path Length Problem. RECOMB (2015)
Leena Salmela, Eric Rivals
LoRDEC: accurate and efficient long read error correction. Bioinform. 30 (24) (2014)
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)
Francisco Claude, Gonzalo Navarro, Hannu Peltola, Leena Salmela, Jorma Tarhio
String matching with alphabet sampling. J. Discrete Algorithms 11 (2012)
Leena Salmela
Average complexity of backward q-gram string matching algorithms. Inf. Process. Lett. 112 (11) (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)
Leena Salmela, Jan Schröder
Correcting errors in short reads by multiple alignments. Bioinform. 27 (11) (2011)
Branislav Durian, Hannu Peltola, Leena Salmela, Jorma Tarhio
Bit-Parallel Search Algorithms for Long Patterns. SEA (2010)
Leena Salmela, Jorma Tarhio
Approximate String Matching with Reduced Alphabet. Algorithms and Applications (2010)
Leena Salmela, Jorma Tarhio, Petri Kalsi
Approximate Boyer-Moore String Matching for Small Alphabets. Algorithmica 58 (3) (2010)
Travis Gagie, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Leena Salmela
Pattern Kits CoRR (2010)
Leena Salmela
Correction of sequencing errors in a mixed set of reads. Bioinform. 26 (10) (2010)
Leena Salmela, Jorma Tarhio, Timo Montonen
Towards Automated Management of Compiler Assignments. CSEDU (2) (2009)
Gonzalo Navarro, Leena Salmela
Indexing Variable Length Substrings for Exact and Approximate Matching. SPIRE (2009)
Eric Rivals, Leena Salmela, Petteri Kiiskinen, Petri Kalsi, Jorma Tarhio
mpscan: Fast Localisation of Multiple Reads in Genomes. WABI (2009)
Leena Salmela, Jorma Tarhio
Fast parameterized matching with q-grams. J. Discrete Algorithms 6 (3) (2008)
Francisco Claude, Gonzalo Navarro, Hannu Peltola, Leena Salmela, Jorma Tarhio
Speeding Up Pattern Matching by Text Sampling. SPIRE (2008)
Leena Salmela, Jorma Tarhio
Algorithms for Weighted Matching. SPIRE (2007)
Petri Kalsi, Leena Salmela, Jorma Tarhio
Tuning Approximate Boyer-Moore for Gene Sequences. SPIRE (2007)
Leena Salmela, Jorma Tarhio, Jari Kytöjoki
-grams. ACM J. Exp. Algorithmics 11 (2006)
Leena Salmela, Jorma Tarhio
Sublinear Algorithms for Parameterized Matching. CPM (2006)
Jari Kytöjoki, Leena Salmela, Jorma Tarhio
Tuning String Matching for Huge Pattern Sets. CPM (2003)