Tuning String Matching for Huge Pattern Sets. - Jari Kytöjoki; Leena Salmela; Jorma Tarhio (CPM, 2003)

Sublinear Algorithms for Parameterized Matching. - Leena Salmela; Jorma Tarhio (CPM, 2006)

Multipattern string matching with q-grams. - Leena Salmela; Jorma Tarhio; Jari Kytöjoki (ACM J. Exp. Algorithmics, 2006)

Tuning Approximate Boyer-Moore for Gene Sequences. - Petri Kalsi; Leena Salmela; Jorma Tarhio (SPIRE, 2007)

Algorithms for Weighted Matching. - Leena Salmela; Jorma Tarhio (SPIRE, 2007)

Speeding Up Pattern Matching by Text Sampling. - Francisco Claude; Gonzalo Navarro 001; Hannu Peltola; Leena Salmela; Jorma Tarhio (SPIRE, 2008)

Fast parameterized matching with q-grams. - Leena Salmela; Jorma Tarhio (J. Discrete Algorithms, 2008)

Towards Automated Management of Compiler Assignments. - Leena Salmela; Jorma Tarhio; Timo Montonen (CSEDU (2), 2009)

Indexing Variable Length Substrings for Exact and Approximate Matching. - Gonzalo Navarro 001; Leena Salmela (SPIRE, 2009)

mpscan: Fast Localisation of Multiple Reads in Genomes. - Eric Rivals; Leena Salmela; Petteri Kiiskinen; Petri Kalsi; Jorma Tarhio (WABI, 2009)

Improved algorithms for string searching problems. - Leena Salmela (2009)

Approximate String Matching with Reduced Alphabet. - Leena Salmela; Jorma Tarhio (Algorithms and Applications, 2010)

Bit-Parallel Search Algorithms for Long Patterns. - Branislav Durian; Hannu Peltola; Leena Salmela; Jorma Tarhio (SEA, 2010)

Approximate Boyer-Moore String Matching for Small Alphabets. - Leena Salmela; Jorma Tarhio; Petri Kalsi (Algorithmica, 2010)

Correction of sequencing errors in a mixed set of reads. - Leena Salmela (Bioinform., 2010)

Pattern Kits - Travis Gagie; Kalle Karhu; Juha Kärkkäinen; Veli Mäkinen; Leena Salmela (CoRR, 2010)

Fast scaffolding with small independent mixed integer programs. - Leena Salmela; Veli Mäkinen; Niko Välimäki; Johannes Ylinen; Esko Ukkonen (Bioinform., 2011)

Correcting errors in short reads by multiple alignments. - Leena Salmela; Jan Schröder (Bioinform., 2011)

Forbidden Patterns. - Johannes Fischer 001; Travis Gagie; Tsvi Kopelowitz; Moshe Lewenstein; Veli Mäkinen; Leena Salmela; Niko Välimäki (LATIN, 2012)

Indexed Multi-pattern Matching. - Travis Gagie; Kalle Karhu; Juha Kärkkäinen; Veli Mäkinen; Leena Salmela; Jorma Tarhio (LATIN, 2012)

Normalized N50 assembly metric using gap-restricted co-linear chaining. - Veli Mäkinen; Leena Salmela; Johannes Ylinen (BMC Bioinform., 2012)

Average complexity of backward q-gram string matching algorithms. - Leena Salmela (Inf. Process. Lett., 2012)

String matching with alphabet sampling. - Francisco Claude; Gonzalo Navarro 001; Hannu Peltola; Leena Salmela; Jorma Tarhio (J. Discrete Algorithms, 2012)

LoRDEC: accurate and efficient long read error correction. - Leena Salmela; Eric Rivals (Bioinform., 2014)

Identification of Variant Compositions in Related Strains Without Reference. - Mikko Rautiainen; Leena Salmela; Veli Mäkinen (AlCoB, 2016)

Gap Filling as Exact Path Length Problem. - Leena Salmela; Kristoffer Sahlin; Veli Mäkinen; Alexandru I. Tomescu (J. Comput. Biol., 2016)

Disentangled Long-Read De Bruijn Graphs via Optical Maps. - Bahar Alipanahi; Leena Salmela; Simon J. Puglisi; Martin D. Muggli; Christina Boucher 001 (WABI, 2017)

Accurate self-correction of errors in long reads using de Bruijn graphs. - Leena Salmela; Riku Walve; Eric Rivals; Esko Ukkonen (Bioinform., 2017)

Kermit: Guided Long Read Assembly using Coloured Overlap Graphs. - Riku Walve; Pasi Rastas; Leena Salmela (WABI, 2018)

Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding. - Niko Kiirala; Leena Salmela; Alexandru I. Tomescu (CPM, 2019)

Kermit: linkage map guided long read assembly. - Riku Walve; Pasi Rastas; Leena Salmela (Algorithms Mol. Biol., 2019)

Aligning optical maps to de Bruijn graphs. - Kingshuk Mukherjee; Bahar Alipanahi; Tamer Kahveci; Leena Salmela; Christina Boucher 001 (Bioinform., 2019)

Safely Filling Gaps with Partial Solutions Common to All Solutions. - Leena Salmela; Alexandru I. Tomescu (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Fast and accurate correction of optical mapping data via spaced seeds. - Leena Salmela; Kingshuk Mukherjee; Simon J. Puglisi; Martin D. Muggli; Christina Boucher 001 (Bioinform., 2020)

Optical map guided genome assembly. - Miika Leinonen; Leena Salmela (BMC Bioinform., 2020)

Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph. - Kingshuk Mukherjee; Massimiliano Rossi 001; Leena Salmela; Christina Boucher 001 (Algorithms Mol. Biol., 2021)

Inference of viral quasispecies with a paired de Bruijn graph. - Borja Freire; Susana Ladra; José R. Paramá; Leena Salmela (Bioinform., 2021)

Succinct dynamic de Bruijn graphs. - Bahar Alipanahi; Alan Kuhnle; Simon J. Puglisi; Leena Salmela; Christina Boucher 001 (Bioinform., 2021)

Computing All-vs-All MEMs in Run-Length-Encoded Collections of HiFi Reads. - Diego Díaz-Domínguez; Simon J. Puglisi; Leena Salmela (SPIRE, 2022)

Efficient Solutions to Biological Problems Using de Bruijn Graphs (Invited Talk). - Leena Salmela (WABI, 2022)

HGGA: hierarchical guided genome assembler. - Riku Walve; Leena Salmela (BMC Bioinform., 2022)

Extraction of Long k-mers Using Spaced Seeds. - Miika Leinonen; Leena Salmela (IEEE ACM Trans. Comput. Biol. Bioinform., 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)

Computing All-vs-All MEMs in Grammar-Compressed Text. - Diego Díaz-Domínguez; Leena Salmela (SPIRE, 2023)

Simple Runs-Bounded FM-Index Designs Are Fast. - Diego Díaz-Domínguez; Saska Dönges; Simon J. Puglisi; Leena Salmela (SEA, 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)

Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. - Jun Ma; Manuel Cáceres; Leena Salmela; Veli Mäkinen; Alexandru I. Tomescu (Bioinform., 2023)

Space-efficient computation of k-mer dictionaries for large values of k. - Diego Díaz-Domínguez; Miika Leinonen; Leena Salmela (Algorithms Mol. Biol., 2024)

Sama: a contig assembler with correctness guarantee. - Leena Salmela (Algorithms Mol. Biol., 2025)