Leena Salmela's Publications
Journal Articles
- L. Salmela: Average complexity of backward q-gram string
matching algorithms. Information Processing Letters, Volume 112,
Issue 11, 2012, 433–437.
- 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.
- 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.
- 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).
- 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).
- L. Salmela, J. Tarhio and P. Kalsi: Approximate Boyer-Moore
string matching for small alphabets. Algorithmica, Volume 58, Issue
3, 2010, 591–609.
- L. Salmela and J. Tarhio: Fast parameterized matching with
q-grams. Journal of Discrete Algorithms, Volume 6, Issue 3, 2008,
408–419.
- L. Salmela, J. Tarhio, and J. Kytöjoki: Multi-pattern string
matching with q-grams. ACM Journal of Experimental Algorithmics,
Volume 11, 2006.
Conference Articles
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
Book Chapters and Other Publications
- 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.
- 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.
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).