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2020 – today
- 2024
[j27]Diego Díaz-Domínguez
, Miika Leinonen, Leena Salmela:
Space-efficient computation of k-mer dictionaries for large values of k. Algorithms Mol. Biol. 19(1): 14 (2024)- 2023
- [j26]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) - [j25]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): 1550-1562 (2023) - [c22]Diego Díaz-Domínguez, Leena Salmela:
Computing All-vs-All MEMs in Grammar-Compressed Text. SPIRE 2023: 157-170 - [c21]Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, Leena Salmela:
Simple Runs-Bounded FM-Index Designs Are Fast. SEA 2023: 7:1-7:16 - [i4]Diego Díaz-Domínguez, Leena Salmela:
Computing all-vs-all MEMs in grammar-compressed text. CoRR abs/2306.16815 (2023) - 2022
- [j24]Riku Walve, Leena Salmela:
HGGA: hierarchical guided genome assembler. BMC Bioinform. 23(1): 167 (2022) - [j23]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): 2454-2462 (2022) - [j22]Miika Leinonen, Leena Salmela:
Extraction of Long k-mers Using Spaced Seeds. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3444-3455 (2022) - [c20]Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela:
Computing All-vs-All MEMs in Run-Length-Encoded Collections of HiFi Reads. SPIRE 2022: 198-213 - [c19]Leena Salmela:
Efficient Solutions to Biological Problems Using de Bruijn Graphs (Invited Talk). WABI 2022: 1:1-1:2 - [i3]Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela:
Computing all-vs-all MEMs in run-length encoded collections of HiFi reads. CoRR abs/2208.14787 (2022) - 2021
- [j21]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): 6 (2021) - [j20]Borja Freire, Susana Ladra, José R. Paramá, Leena Salmela:
Inference of viral quasispecies with a paired de Bruijn graph. Bioinform. 37(4): 473-481 (2021) - [j19]Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher:
Succinct dynamic de Bruijn graphs. Bioinform. 37(14): 1946-1952 (2021) - [i2]Borja Freire, Susana Ladra, José R. Paramá, Leena Salmela:
ViQUF: de novo Viral Quasispecies reconstruction using Unitig-based Flow networks. CoRR abs/2112.06590 (2021) - 2020
- [j18]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): 682-689 (2020) - [j17]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): 2974 (2020) - [j16]Miika Leinonen, Leena Salmela:
Optical map guided genome assembly. BMC Bioinform. 21(1): 285 (2020) - [c18]Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher:
Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph. WABI 2020: 9:1-9:16
2010 – 2019
- 2019
- [j15]Riku Walve, Pasi Rastas, Leena Salmela:
Kermit: linkage map guided long read assembly. Algorithms Mol. Biol. 14(1): 8:1-8:10 (2019) - [j14]Kingshuk Mukherjee, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, Christina Boucher:
Aligning optical maps to de Bruijn graphs. Bioinform. 35(18): 3250-3256 (2019) - [j13]Leena Salmela, Alexandru I. Tomescu:
Safely Filling Gaps with Partial Solutions Common to All Solutions. IEEE ACM Trans. Comput. Biol. Bioinform. 16(2): 617-626 (2019) - [c17]Niko Kiirala, Leena Salmela, Alexandru I. Tomescu:
Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding. CPM 2019: 8:1-8:16 - 2018
- [c16]Riku Walve, Pasi Rastas, Leena Salmela:
Kermit: Guided Long Read Assembly using Coloured Overlap Graphs. WABI 2018: 11:1-11:11 - 2017
- [j12]Leena Salmela, Riku Walve, Eric Rivals, Esko Ukkonen:
Accurate self-correction of errors in long reads using de Bruijn graphs. Bioinform. 33(6): 799-806 (2017) - [c15]Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin D. Muggli, Christina Boucher:
Disentangled Long-Read De Bruijn Graphs via Optical Maps. WABI 2017: 1:1-1:14 - 2016
- [j11]Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu:
Gap Filling as Exact Path Length Problem. J. Comput. Biol. 23(5): 347-361 (2016) - [c14]Mikko Rautiainen, Leena Salmela, Veli Mäkinen:
Identification of Variant Compositions in Related Strains Without Reference. AlCoB 2016: 158-170 - [e1]Veli Mäkinen, Simon J. Puglisi, Leena Salmela:
Combinatorial Algorithms - 27th International Workshop, IWOCA 2016, Helsinki, Finland, August 17-19, 2016, Proceedings. Lecture Notes in Computer Science 9843, Springer 2016, ISBN 978-3-319-44542-7 [contents] - 2015
- [c13]Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu:
Gap Filling as Exact Path Length Problem. RECOMB 2015: 281-292 - 2014
- [j10]Leena Salmela, Eric Rivals:
LoRDEC: accurate and efficient long read error correction. Bioinform. 30(24): 3506-3514 (2014) - 2012
- [j9]Veli Mäkinen, Leena Salmela, Johannes Ylinen:
Normalized N50 assembly metric using gap-restricted co-linear chaining. BMC Bioinform. 13: 255 (2012) - [j8]Leena Salmela:
Average complexity of backward q-gram string matching algorithms. Inf. Process. Lett. 112(11): 433-437 (2012) - [j7]Francisco Claude, Gonzalo Navarro, Hannu Peltola, Leena Salmela, Jorma Tarhio:
String matching with alphabet sampling. J. Discrete Algorithms 11: 37-50 (2012) - [c12]Johannes Fischer, Travis Gagie, Tsvi Kopelowitz, Moshe Lewenstein, Veli Mäkinen, Leena Salmela, Niko Välimäki:
Forbidden Patterns. LATIN 2012: 327-337 - [c11]Travis Gagie, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Leena Salmela, Jorma Tarhio:
Indexed Multi-pattern Matching. LATIN 2012: 399-407 - 2011
- [j6]Leena Salmela, Jan Schröder:
Correcting errors in short reads by multiple alignments. Bioinform. 27(11): 1455-1461 (2011) - [j5]Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen:
Fast scaffolding with small independent mixed integer programs. Bioinform. 27(23): 3259-3265 (2011) - 2010
- [j4]Leena Salmela, Jorma Tarhio, Petri Kalsi:
Approximate Boyer-Moore String Matching for Small Alphabets. Algorithmica 58(3): 591-609 (2010) - [j3]Leena Salmela:
Correction of sequencing errors in a mixed set of reads. Bioinform. 26(10): 1284-1290 (2010) - [c10]Leena Salmela, Jorma Tarhio:
Approximate String Matching with Reduced Alphabet. Algorithms and Applications 2010: 210-220 - [c9]Branislav Durian, Hannu Peltola, Leena Salmela, Jorma Tarhio:
Bit-Parallel Search Algorithms for Long Patterns. SEA 2010: 129-140 - [i1]Travis Gagie, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Leena Salmela:
Pattern Kits. CoRR abs/1011.3491 (2010)
2000 – 2009
- 2009
- [b1]Leena Salmela:
Improved algorithms for string searching problems. Aalto University, Espoo, Finland, 2009 - [c8]Leena Salmela, Jorma Tarhio, Timo Montonen:
Towards Automated Management of Compiler Assignments. CSEDU (2) 2009: 243-249 - [c7]Gonzalo Navarro, Leena Salmela:
Indexing Variable Length Substrings for Exact and Approximate Matching. SPIRE 2009: 214-221 - [c6]Eric Rivals, Leena Salmela, Petteri Kiiskinen, Petri Kalsi, Jorma Tarhio:
mpscan: Fast Localisation of Multiple Reads in Genomes. WABI 2009: 246-260 - 2008
- [j2]Leena Salmela, Jorma Tarhio:
Fast parameterized matching with q-grams. J. Discrete Algorithms 6(3): 408-419 (2008) - [c5]Francisco Claude, Gonzalo Navarro, Hannu Peltola, Leena Salmela, Jorma Tarhio:
Speeding Up Pattern Matching by Text Sampling. SPIRE 2008: 87-98 - 2007
- [c4]Petri Kalsi, Leena Salmela, Jorma Tarhio:
Tuning Approximate Boyer-Moore for Gene Sequences. SPIRE 2007: 173-183 - [c3]Leena Salmela, Jorma Tarhio:
Algorithms for Weighted Matching. SPIRE 2007: 276-286 - 2006
- [j1]Leena Salmela, Jorma Tarhio, Jari Kytöjoki:
Multipattern string matching with q-grams. ACM J. Exp. Algorithmics 11 (2006) - [c2]Leena Salmela, Jorma Tarhio:
Sublinear Algorithms for Parameterized Matching. CPM 2006: 354-364 - 2003
- [c1]Jari Kytöjoki, Leena Salmela, Jorma Tarhio:
Tuning String Matching for Huge Pattern Sets. CPM 2003: 211-224
Coauthor Index
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last updated on 2025-01-07 00:57 CET by the dblp team
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