Journal Articles
- D. Díaz-Domínguez, M. Leinonen, and L. Salmela: Space-efficient computation of k-mer dictionaries for large values of k. Algorithms for Molecular Biology, Volume 19, Article number 14, 2024.
[Article online] [Implementation]
- M. Leinonen and L. Salmela: SAKE: Strobemer-assisted k-mer extraction. PLoS ONE, Volume 18, Issue 11, e0294415, 2023.
[Article online] [Implementation]
- J. Ma, M. Cáceres, L. Salmela, V. Mäkinen, A.I. Tomescu: Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. Bioinformatics, Volume 39, Issue 8, btad460, 2023.
[Article online]
- B. Freire, S. Ladra, J.R. Paramá, and L. Salmela: ViQUF: De novo viral quasispecies reconstruction using unitig-based flow networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 20, 2023, 1550-1562.
[Article online] [Implementation]
- M. Leinonen and L. Salmela: Extraction of long k-mers using spaced seeds. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 19, 2022, 3444–3455.
[Article online] [Implementation]
- R. Walve, S.J. Puglisi, and L. Salmela: Space-efficient indexing of spaced seeds for accurate overlap computation of raw optical mapping data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 19, 2022, 2454–2462.
[Article online] [Implementation]
- R. Walve and L. Salmela: HGGA: hierarchical guided genome assembler. BMC Bioinformatics, Volume 23, Article number 167, 2022.
[Article online] [Implementation]
- B. Alipanahi, A. Kuhnle, S.J. Puglisi, L. Salmela, and C. Boucher: Succinct dynamic de Bruijn graphs. Bioinformatics, Volume 37, Issue 14, 2021, 1946–1952.
[Article online] [Implementation]
- K. Mukherjee, M. Rossi, L. Salmela, and C. Boucher: Fast and efficient Rmap assembly using the bi-labelled de Bruijn graph. Algorithms for Molecular Biology, Volume 16, Article number 6, 2021.
[Article online] [Implementation]
- B. Freire, S. Ladra, J. Paramá, and L. Salmela: Inference of viral quasispecies with a paired de Bruijn graph. Bioinformatics, Volume 37, Issue 4, 2021, 473–481.
[Article online] [Implementation]
- M. Leinonen and L. Salmela: Optical map guided genome assembly. BMC Bioinformatics, Volume 21, Article number 285, 2020.
[Article online] [Implementation]
- L. Salmela, K. Mukherjee, S.J. Puglisi, M.D. Muggli, and C. Boucher: Fast and accurate correction of optical mapping data via spaced seeds. Bioinformatics, Volume 36, Issue 3, 2020, 682–689.
[Article online] [Implementation]
- K. Mukherjee, B. Alipanahi, T. Kahveci, L. Salmela, and C. Boucher: Aligning optical maps to de Bruijn graphs. Bioinformatics, Volume 35, Issue 18, 2019, 3250–3256.
[Article online] [Implementation]
- R. Walve, P. Rastas, and L. Salmela: Kermit: Linkage map guided long read assembly. Algorithms for Molecular Biology, Volume 14, Article 8, 2019.
[Article online] [Implementation]
- L. Salmela and A.I. Tomescu: Safely filling gaps with partial solutions common to all solutions. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 16, Issue 2, 2019, 617–626.
[Article online] [Implementation]
- K. Mukherjee, D. Washimkar, M.D. Muggli, L. Salmela, and C. Boucher: Error correcting optical mapping data. GigaScience, Volume 7, Issue 6, 2018, giy061.
[Article online] [Implementation]
- R. Walve, L. Salmela, and V. Mäkinen: Variant genotyping with gap filling. PLoS ONE, Volume 12, Issue 9, 2017, e0184608.
[Article online] [Implementation]
- L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Bioinformatics, Volume 33, Issue 6, 2017, 799–806. (Also in RECOMB-seq 2016).
[Article online] [Implementation]
- L. Salmela, K. Sahlin, V. Mäkinen, and A.I. Tomescu: Gap filling
as exact path length problem. Journal of Computational Biology, Volume 23, Issue 5, 2016, 347–361.
[Article
online] [Implementation]
- Y. Le Bras, O. Collin, C. Monjeaud, V. Lacroix, E. Rivals, C. Lemaitre, V. Miele, G. Sacomoto, C. Marchet, B. Cazaux, A. Zine El Aabidine, L. Salmela, S. Alves-Carvalho, A. Andrieux, R. Uricaru, P. Peterlongo: Colib'read on Galaxy: A tools suite dedicated to biological information extraction from raw NGS reads. GigaScience, Volume 5, Issue 9, 2016.
[Article online]
- J. Kvist, et al. Flight-induced changes in gene expression in
the Glanville fritillary butterfly. Molecular Ecology, Volume 24,
Issue 19, 2015, 4886–4900.
[Article online]
- L. Salmela, and E. Rivals. LoRDEC: accurate and efficient long
read error correction. Bioinformatics, Volume 30, Issue 24, 2014, 3506–3514.
[Article
online] [Implementation]
- V. Ahola, R. Lehtonen, P. Somervuo, et al. The Glanville
fritillary genome retains an ancient karyotype and reveals selective
chromosomal fusions in Lepidoptera. Nature Communications, Volume 5,
Article 4737, 2014.
[Article
online] [Genome]
- V. Mäkinen, L. Salmela, and J. Ylinen. Normalized N50 assembly
metric using gap-restricted co-linear chaining. BMC
Bioinformatics, Volume 13, 2012,
255.
[Article
online] [Implementation]
- L. Salmela: Average complexity of backward q-gram string
matching algorithms. Information Processing Letters, Volume 112,
Issue 11, 2012, 433–437.
[Article online]
- F. Claude, G. Navarro, H. Peltola, L. Salmela and J. Tarhio:
String matching with alphabet sampling. Journal of Discrete
Algorithms, Volume 11, 2012, 37–50.
[Article online]
- L. Salmela, V. Mäkinen, N. Välimäki, J. Ylinen, and E. Ukkonen: Fast
scaffolding with small independent mixed integer programs.
Bioinformatics, Volume 27, Issue 23, 2011,
3259–3265.
[Article
online] [Implementation]
- L. Salmela and J. Schröder: Correcting errors in short reads by
multiple alignments. Bioinformatics, Volume 27, Issue 11, 2011,
1455–1461. (Also in HiTSeq
2011).
[Article
online] [Implementation]
- L. Salmela: Correction of sequencing errors in a mixed set of
reads. Bioinformatics, Volume 26, Issue 10, 2010, 1284–1290.
(Award for best paper submitted to HiTSeq
2010).
[Article
online] [Implementation]
- L. Salmela, J. Tarhio and P. Kalsi: Approximate Boyer-Moore
string matching for small alphabets. Algorithmica, Volume 58, Issue
3, 2010, 591–609.
[Article online]
- L. Salmela and J. Tarhio: Fast parameterized matching with
q-grams. Journal of Discrete Algorithms, Volume 6, Issue 3, 2008,
408–419.
[Article online]
- L. Salmela, J. Tarhio, and J. Kytöjoki: Multi-pattern string
matching with q-grams. ACM Journal of Experimental Algorithmics,
Volume 11, 2006.
[Article online]
Conference Articles
- D. Díaz-Domínguez and L. Salmela: Computing all-vs-all MEMs in grammar-compressed text. In Proc. SPIRE 2023, International symposium on String Processing and Information Retrieval (ed. F.M. Nardini, N. Pisanti, and R. Venturini), Lecture Notes in Computer Science 14240, Springer, 2023, 157-170.
[Article online]
- D. Díaz-Domínguez, S. Dönges, S. Puglisi, and L. Salmela: Simple runs-bounded FM-index designs are fast. In Proc. SEA 2023, International Symposium on Experimental Algorithms (ed. L. Georgiadis), Leibniz International Proceedings in Informatics (LIPIcs) 265, Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, 2023, 7:1-7:16..
[Article online]
- D. Díaz-Domínguez, S.J. Puglisi, and L. Salmela: Computing all-vs-all MEMs in run-length encoded collections of HiFi reads. In Proc. SPIRE 2022, International symposium on String Processing and Information Retrieval (ed. D. Arroyuelo and B. Poblete), Lecture Notes in Computer Science 13617, Springer, 2022, 198-213.
[Article online]
- K. Mukherjee, M. Rossi, L. Salmela, and C. Boucher: Fast and efficient Rmap assembly using bi-labelled de Bruijn graph. In Proc. WABI 2020, Workshop on Algorithms in Bioinformatics (ed. C. Kingsford and N. Pisanti), Leibniz International Proceedings in Informatics (LIPIcs) 172, Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, 2020, 9:1-9:16.
[Article online] [Implementation]
- N. Kiirala, L. Salmela, and A.I. Tomescu: Safe and complete algorithms for dynamic programming problems, with an application to RNA folding. In Proc. of CPM 2019, Annual Symposium on Combinatorial Pattern Matching (ed. N. Pisanti and S.P. Pissis), Leibniz International Proceedings in Informatics (LIPIcs) 128, Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, 2019, 8:1-8:16.
[Article online] [Implementation]
- R. Walve, P. Rastas, and L. Salmela: Kermit: Guided long read assembly using coloured overlap graphs. In Proc. WABI 2018, Workshop on Algorithms in Bioinformatics (ed. L. Parida and E. Ukkonen), Leibniz International Proceedings in Informatics (LIPIcs) 113, Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, 2018, 11:1-11:11.
[Article online] [Implementation]
- B. Alipanahi, L. Salmela, S. Puglisi, M. Muggli, and C. Boucher: Disentangled long-read de Bruijn graphs via optical maps. In Proc. WABI 2017, Workshop on Algorithms in Bioinformatics (ed. R. Schwartz and K. Reinert), Leibniz International Proceedings in Informatics (LIPIcs) 88, Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, 2017, 1:1-1:14.
[Article online]
- L. Salmela and A.I. Tomescu: Safely filling gaps with partial solutions common to all solutions. In Proc. WABI '16, Workshop on Algorithms in Bioinformatics (ed. M. Frith and C.N.S. Pedersen), Lecture Notes in Bioinformatics 9838, Springer, 2016, xiv, short abstract.
[Article online] [Implementation]
- M. Rautiainen, L. Salmela, and V. Mäkinen: Identification of variant compositions in related strains without reference. In Proc. AlCoB 2016, Algorithms for Computational Biology (ed. M. Botón-Fernández et al.), Lecture Notes in Bioinformatics 9702, Springer 2016, 158–170.
[Article online]
- L. Salmela, K. Sahlin, V. Mäkinen, and A.I. Tomescu: Gap filling
as exact path length problem. In Proc. RECOMB 2015, Research in
Computational Molecular Biology (ed. T. M. Przytycka), Lecture Notes
in Bioinformatics 9029, Springer 2015,
281–292.
[Article online] [Implementation]
- T. Gagie, K. Karhu, J. Kärkkäinen, V. Mäkinen, L. Salmela, and
J. Tarhio: Indexed multi-pattern matching. In Proc. LATIN 2012,
Latin American Theoretical Informatics Symposium (ed. D.
Fernández-Baca), Lecture Notes in Computer Science 7256, Springer
2012, 399–407.
[Article online]
- J. Fischer, T. Gagie, T. Kopelowitz, M. Lewenstein, V. Mäkinen,
L. Salmela, and N. Välimäki: Forbidden patterns. In Proc. LATIN
2012, Latin American Theoretical Informatics Symposium (ed. D.
Fernández-Baca), Lecture Notes in Computer Science 7256, Springer
2012, 327–337.
[Article online]
- B. Ďurian, H. Peltola, L. Salmela, and J. Tarhio:
Bit-parallel search algorithms for long patterns. In
Proc. SEA 2010, Symposium on Experimental Algorithms (ed. Paola
Festa), Lecture Notes in Computer Science 6049, Springer 2010,
129–140.
[Article online]
- E. Rivals, L. Salmela, P. Kiiskinen, P. Kalsi, and J. Tarhio:
MPSCAN: fast localisation of multiple reads in genomes. In
Proc. WABI '09, Workshop on Algorithms in Bioinformatics (ed. S.L.
Salzberg and T. Warnow), Lecture Notes in Bioinformatics 5724,
Springer, 2009,
246–260.
[Article
online] [Implementation]
- G. Navarro and L. Salmela: Indexing variable length substrings
for exact and approximate matching. In Proc. SPIRE'09,
String Processing and Information Retrieval (ed. J. Karlgren, J.
Tarhio, and H. Hyyrö), Lecture Notes in Computer Science
5721, Springer, 2009, 214–221.
[Article online]
- L. Salmela, J. Tarhio, and T. Montonen: Towards automated
management of compiler assignments. In: Proc. CSEDU 2009, Int. Conf.
on Computer Supported Education (ed. J. Cordeiro, B.
Shishkov, A. Verbraeck, and M. Helfert), Vol. 2, INSTICC, 2009,
243–249.
- F. Claude, G. Navarro, H. Peltola, L. Salmela, and J. Tarhio:
Speeding up pattern matching by text sampling. In: Proc SPIRE'08,
String Processing and Information Retrieval (ed. A. Amir, A. Turpin,
and A. Moffat), Lecture Notes in Computer Science 5280, Springer,
2008, 87–98.
[Article online]
- L. Salmela and J. Tarhio: Algorithms for weighted matching. In:
Proc SPIRE '07, String Processing and Information Retrieval (ed. N.
Ziviani and R. Baeza-Yates), Lecture Notes in Computer Science 4726,
Springer, 2007, 276–286.
[Article online]
- P. Kalsi, L. Salmela, and J. Tarhio: Tuning approximate
Boyer-Moore for gene sequences. In: Proc SPIRE '07, String
Processing and Information Retrieval (ed. N. Ziviani and R.
Baeza-Yates), Lecture Notes in Computer Science 4726, Springer,
2007, 173–183.
[Article online]
- L. Salmela and J. Tarhio: Sublinear algorithms for parameterized
matching. In: Proc. CPM '06, Combinatorial Pattern Matching
(ed. M. Lewenstein et al.), Lecture Notes in Computer Science 4009,
Springer, 2006, 354–364.
[Article online]
- L. Salmela and J. Tarhio: ACE: Automated compiler exercises. In
Proceedings of the 4th Finnish/Baltic Sea Conference on Computer
Science Education, 2004, 131–135.
[Article online]
- J. Kytöjoki, L. Salmela, and J. Tarhio: Tuning string matching for
huge pattern sets. In: Proc. CPM '03, Combinatorial Pattern Matching
(ed. R. Baeza-Yates et al.), Lecture Notes in Computer Science 2676,
Springer, 2003, 211–224.
[Article online]
Books, Book Chapters and Other Publications
- R. Patro and L. Salmela: Algorithms meet sequencing technologies - 10th edition of the RECOMB-Seq workshop. iScience, Volume 24, Issue 1, 2021, 101956.
[Article online]
- V. Mäkinen, S.J. Puglisi, and L. Salmela (editors): Proceedings of the 27th International Workshop on Combinatorial Algorithms (IWOCA 2016), Springer, 2016.
[Book online]
- E. Rivals, L. Salmela, and J. Tarhio: Exact search algorithms for
biological sequences. In: M. Elloumi, A. Zomaya (eds.):
Algorithms in Computational Molecular Biology: Techniques,
Approaches and Applications. Wiley, 2011, 91–111.
- L. Salmela: Merkkijonoalgoritmeja monen hahmon hakuun.
Tietojenkäsittelytiede 31, 2010,
70–83.
[Artikkeli verkossa]
- L. Salmela and J. Tarhio: Approximate string matching with
reduced alphabet. In: Algorithms and Applications (Ukkonen
Festschrift 2010, ed. T. Elomaa, H. Mannila, and P. Orponen),
Lecture Notes in Computer Science 6060, Springer, 2010, 210–220.
[Article online]
Thesis
- L.
Salmela: Improved
algorithms for string searching problems. Doctoral dissertation,
TKK Research Reports in Computer Science and Engineering A,
TKK-CSE-A1/09, Department of Computer Science and Engineering,
Helsinki University of Technology, 2009.
- L. Salmela: Automatic compiler building exercises. Master's
Thesis, Laboratory of Information Processing Science, Helsinki
University of Technology, 2005 (In Finnish).