Leena Salmela - RankMe

56 papers B 8C 12Journal 32Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Sama: a contig assembler with correctness guarantee. Algorithms Mol. Biol. Leena Salmela
2024	J	`jnl`	Space-efficient computation of k-mer dictionaries for large values of k. Algorithms Mol. Biol. Diego Díaz-Domínguez, Miika Leinonen, Leena Salmela
2023	J	`jnl`	Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. Bioinform. Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu
2023	C	`conf`	Computing All-vs-All MEMs in Grammar-Compressed Text. SPIRE Diego Díaz-Domínguez, Leena Salmela
2023	J	`jnl`	Computing all-vs-all MEMs in grammar-compressed text. CoRR Diego Díaz-Domínguez, Leena Salmela
2023	B	`conf`	Simple Runs-Bounded FM-Index Designs Are Fast. SEA Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, Leena Salmela
2023	J	`jnl`	ViQUF: De Novo Viral Quasispecies Reconstruction Using Unitig-Based Flow Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Borja Freire, Susana Ladra, José R. Paramá, Leena Salmela
2022	C	`conf`	Computing All-vs-All MEMs in Run-Length-Encoded Collections of HiFi Reads. SPIRE Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela
2022	J	`jnl`	Computing all-vs-all MEMs in run-length encoded collections of HiFi reads. CoRR Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela
2022	C	`conf`	Efficient Solutions to Biological Problems Using de Bruijn Graphs (Invited Talk). WABI Leena Salmela
2022	J	`jnl`	Extraction of Long k-mers Using Spaced Seeds. IEEE ACM Trans. Comput. Biol. Bioinform. Miika Leinonen, Leena Salmela
2022	J	`jnl`	HGGA: hierarchical guided genome assembler. BMC Bioinform. Riku Walve, Leena Salmela
2022	J	`jnl`	Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data. IEEE ACM Trans. Comput. Biol. Bioinform. Riku Walve, Simon J. Puglisi, Leena Salmela
2021	J	`jnl`	Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph. Algorithms Mol. Biol. Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher
2021	J	`jnl`	Inference of viral quasispecies with a paired de Bruijn graph. Bioinform. Borja Freire, Susana Ladra, José R. Paramá, Leena Salmela
2021	J	`jnl`	Succinct dynamic de Bruijn graphs. Bioinform. Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher
2021	J	`jnl`	ViQUF: de novo Viral Quasispecies reconstruction using Unitig-based Flow networks. CoRR Borja Freire, Susana Ladra, José R. Paramá, Leena Salmela
2020	C	`conf`	Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph. WABI Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher
2020	J	`jnl`	Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
2020	J	`jnl`	Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
2020	J	`jnl`	Optical map guided genome assembly. BMC Bioinform. Miika Leinonen, Leena Salmela
2019	J	`jnl`	Aligning optical maps to de Bruijn graphs. Bioinform. Kingshuk Mukherjee, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, Christina Boucher
2019	J	`jnl`	Kermit: linkage map guided long read assembly. Algorithms Mol. Biol. Riku Walve, Pasi Rastas, Leena Salmela
2019	B	`conf`	Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding. CPM Niko Kiirala, Leena Salmela, Alexandru I. Tomescu
2019	J	`jnl`	Safely Filling Gaps with Partial Solutions Common to All Solutions. IEEE ACM Trans. Comput. Biol. Bioinform. Leena Salmela, Alexandru I. Tomescu
2018	C	`conf`	Kermit: Guided Long Read Assembly using Coloured Overlap Graphs. WABI Riku Walve, Pasi Rastas, Leena Salmela
2017	J	`jnl`	Accurate self-correction of errors in long reads using de Bruijn graphs. Bioinform. Leena Salmela, Riku Walve, Eric Rivals, Esko Ukkonen
2017	C	`conf`	Disentangled Long-Read De Bruijn Graphs via Optical Maps. WABI Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
2016	C	`ed.`	Combinatorial Algorithms - 27th International Workshop, IWOCA 2016, Helsinki, Finland, August 17-19, 2016, Proceedings IWOCA Veli Mäkinen, Simon J. Puglisi, Leena Salmela
2016	J	`jnl`	Gap Filling as Exact Path Length Problem. J. Comput. Biol. Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu
2016	—	`conf`	Identification of Variant Compositions in Related Strains Without Reference. AlCoB Mikko Rautiainen, Leena Salmela, Veli Mäkinen
2015	B	`conf`	Gap Filling as Exact Path Length Problem. RECOMB Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu
2014	J	`jnl`	LoRDEC: accurate and efficient long read error correction. Bioinform. Leena Salmela, Eric Rivals
2012	J	`jnl`	Average complexity of backward q-gram string matching algorithms. Inf. Process. Lett. Leena Salmela
2012	B	`conf`	Forbidden Patterns. LATIN Johannes Fischer, Travis Gagie, Tsvi Kopelowitz, Moshe Lewenstein, Veli Mäkinen, Leena Salmela, Niko Välimäki
2012	B	`conf`	Indexed Multi-pattern Matching. LATIN Travis Gagie, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Leena Salmela, Jorma Tarhio
2012	J	`jnl`	Normalized N50 assembly metric using gap-restricted co-linear chaining. BMC Bioinform. Veli Mäkinen, Leena Salmela, Johannes Ylinen
2012	J	`jnl`	String matching with alphabet sampling. J. Discrete Algorithms Francisco Claude, Gonzalo Navarro, Hannu Peltola, Leena Salmela, Jorma Tarhio
2011	J	`jnl`	Correcting errors in short reads by multiple alignments. Bioinform. Leena Salmela, Jan Schröder
2011	J	`jnl`	Fast scaffolding with small independent mixed integer programs. Bioinform. Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen
2010	J	`jnl`	Approximate Boyer-Moore String Matching for Small Alphabets. Algorithmica Leena Salmela, Jorma Tarhio, Petri Kalsi
2010	—	`conf`	Approximate String Matching with Reduced Alphabet. Algorithms and Applications Leena Salmela, Jorma Tarhio
2010	B	`conf`	Bit-Parallel Search Algorithms for Long Patterns. SEA Branislav Durian, Hannu Peltola, Leena Salmela, Jorma Tarhio
2010	J	`jnl`	Correction of sequencing errors in a mixed set of reads. Bioinform. Leena Salmela
2010	J	`jnl`	Pattern Kits CoRR Travis Gagie, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Leena Salmela
2009	—	`—`	Improved algorithms for string searching problems. Leena Salmela
2009	C	`conf`	Indexing Variable Length Substrings for Exact and Approximate Matching. SPIRE Gonzalo Navarro, Leena Salmela
2009	—	`conf`	Towards Automated Management of Compiler Assignments. CSEDU (2) Leena Salmela, Jorma Tarhio, Timo Montonen
2009	C	`conf`	mpscan: Fast Localisation of Multiple Reads in Genomes. WABI Eric Rivals, Leena Salmela, Petteri Kiiskinen, Petri Kalsi, Jorma Tarhio
2008	J	`jnl`	Fast parameterized matching with q-grams. J. Discrete Algorithms Leena Salmela, Jorma Tarhio
2008	C	`conf`	Speeding Up Pattern Matching by Text Sampling. SPIRE Francisco Claude, Gonzalo Navarro, Hannu Peltola, Leena Salmela, Jorma Tarhio
2007	C	`conf`	Algorithms for Weighted Matching. SPIRE Leena Salmela, Jorma Tarhio
2007	C	`conf`	Tuning Approximate Boyer-Moore for Gene Sequences. SPIRE Petri Kalsi, Leena Salmela, Jorma Tarhio
2006	J	`jnl`	Multipattern string matching with ACM J. Exp. Algorithmics Leena Salmela, Jorma Tarhio, Jari Kytöjoki
2006	B	`conf`	Sublinear Algorithms for Parameterized Matching. CPM Leena Salmela, Jorma Tarhio
2003	B	`conf`	Tuning String Matching for Huge Pattern Sets. CPM Jari Kytöjoki, Leena Salmela, Jorma Tarhio