Leena Salmela

Postdoctoral Researcher

Contact Information

Leena.Salmela[at]cs.helsinki.fi
http://www.cs.helsinki.fi/u/lmsalmel/
B230
(09) 191 51376

Examiner for exams

(to registration)

Computational Methods of Systems Biology
Computational Methods of Systems Biology
Computational Methods of Systems Biology

  • Register 12.06.2012 (Separate exam)

Teaching

2013 spring
Seminar: High-throughput Sequencing Data Analysis
Seminar: High-throughput Sequencing Data Analysis
Seminar: High-throughput Sequencing Data Analysis

  • In charge

2013 spring
MSc Thesis Seminar on Bioinformatics
MSc Thesis Seminar on Bioinformatics
MSc Thesis Seminar on Bioinformatics

  • In charge

2012 autumn
Project in Biodatabases
Projekt i Biodatabaser
Biotietokantojen harjoitustyö

  • Lecturer , in charge

2012 autumn
Algorithms for Bioinformatics
Algoritmer för bioinformatik
Algoritmit bioinformatiikassa

  • Lecturer , in charge

2012 autumn
MSc Thesis Seminar on Bioinformatics
MSc Thesis Seminar on Bioinformatics
MSc Thesis Seminar on Bioinformatics

  • In charge

2012 spring
Computational Methods of Systems Biology
Computational Methods of Systems Biology
Computational Methods of Systems Biology

  • Lecturer , in charge

2011 spring
Computational Methods of Systems Biology
Computational Methods of Systems Biology
Computational Methods of Systems Biology

  • Assistant

2009 autumn
Computational Methods of Systems Biology
Computational Methods of Systems Biology
Computational Methods of Systems Biology

  • Assistant
  • Assistant

Publications

Publications gathered from the TUHAT database profile.

2012

Average complexity of backward q-gram string matching algorithms

Salmela, L. 2012 In : Information Processing Letters. 112, 11, p. 433-437. 5 p.

Publication: Contribution to journal › A1 Refereed journal article

Indexed Multi-Pattern Matching

Gagie, T., Karhu, K., Kärkkäinen, J., Mäkinen, V., Salmela, L. & Tarhio, J. 2012 p. 399-407. 10 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

String matching with alphabet sampling

Claude, F., Navarro, G., Peltola, H., Salmela, L. & Tarhio, J. 2012 In : Journal of Discrete Algorithms. 11, p. 37-50.

Publication: Contribution to journal › A1 Refereed journal article

2011

Coral

Salmela, L. 2011

Publication: Sound and image media › I2 ICT programs or applications

Correcting errors in short reads by multiple alignments

Salmela, L. & Schröder, J. 2011 In : Bioinformatics. 27, 11, p. 1455-1461. 7 p.

Publication: Contribution to journal › A1 Refereed journal article

Correcting errors in short reads by multiple alignments

Salmela, L. & Schröder, J. 2011 In : Bioinformatics. 27, 11, p. 1455-1461. 7 p.

Publication: Contribution to journal › A1 Refereed journal article

Exact search algorithms for biological sequences

Rivals, E., Salmela, L. & Tarhio, J. 2011 Algorithms in computational molecular biology. Elloumi, M. & Zomaya, A. Y. (eds.). John Wiley & Sons p. 91-111. 21 p. (Bioinformatics: Computational Techniques and Engineering).

Publication: Contribution to book/anthology › A3 Contribution to book/other compilations (refereed)

Fast scaffolding with small independent mixed integer programs

Salmela, L., Mäkinen, V., Välimäki, N., Ylinen, J. E. & Ukkonen, E. 2011 In : Bioinformatics. 27, 23, p. 3259-3265. 7 p.

Publication: Contribution to journal › A1 Refereed journal article

Fast scaffolding with small independent mixed integer programs

Salmela, L., Mäkinen, V., Välimäki, N., Ylinen, J. E. & Ukkonen, E. 2011 In : Bioinformatics. 27, 23, p. 3259-3265. 7 p.

Publication: Contribution to journal › A1 Refereed journal article

MIP Scaffolder

Salmela, L. 2011

Publication: Sound and image media › I2 ICT programs or applications

2010

Approximate Boyer-Moore string matching for small alphabets

Salmela, L., Tarhio, J. & Kalsi, P. 2010 In : Algorithmica. 58, 3, p. 591-609. 19 p.

Publication: Contribution to journal › A1 Refereed journal article

Approximate Boyer-Moore string matching for small alphabets

Salmela, L., Tarhio, J. & Kalsi, P. 2010 In : Algorithmica. 58, 3, p. 591-609. 19 p.

Publication: Contribution to journal › A1 Refereed journal article

Approximate string matching with reduced alphabet

Salmela, L. & Tarhio, J. 2010 Algorithms and applications. Elomaa, T., Mannila, H. & Orponen, P. (eds.). Heidelberg, Berlin, Springer Verlag, 11 p. (Lecture Notes in Computer Science; 6060).

Publication: Contribution to book/anthology › A3 Contribution to book/other compilations (refereed)

Bit-parallel search algorithms for long patterns

Durian, B., Peltola, H., Salmela, L. & Tarhio, J. 2010 p. 129-140. 12 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

Correction of sequencing errors in a mixed set of reads

Salmela, L. 2010 In : Bioinformatics. 26, 10, p. 1284-1290. 7 p.

Publication: Contribution to journal › A1 Refereed journal article

Correction of sequencing errors in a mixed set of reads

Salmela, L. 2010 In : Bioinformatics. 26, 10, p. 1284-1290. 7 p.

Publication: Contribution to journal › A1 Refereed journal article

Hybrid SHREC

Salmela, L. 2010

Publication: Sound and image media › I2 ICT programs or applications

Merkkijonoalgoritmeja monen hahmon hakuun

Salmela, L. 2010 In : Tietojenkäsittelytiede. 2010, 31, p. 70-83. 14 p.

Publication: Contribution to journal › B1 Unrefereed journal article

Merkkijonoalgoritmeja monen hahmon hakuun

Salmela, L. 2010 In : Tietojenkäsittelytiede. 2010, 31, p. 70-83. 14 p.

Publication: Contribution to journal › B1 Unrefereed journal article

2009

Improved algorithms for string searching problems

Salmela, L. 2009 Espoo. 141 p. (TKK Research Reports in Computer Science and Engineering A; TKK-CSE-A1/09).

Publication: Book/anthology › G4 Doctoral Thesis, monography

Improved algorithms for string searching problems

Salmela, L. 2009 Espoo : Helsinki University of Technology. 141 p. (TKK Research Reports in Computer Science and Engineering A; TKK-CSE-A1/09).

Publication: Book/anthology › G4 Doctoral Thesis, monography

Improved algorithms for string searching problems

Salmela, L. 2009 Espoo : Helsinki University of Technology. 141 p. (TKK Research Reports in Computer Science and Engineering A; TKK-CSE-A1/09).

Publication: Book/anthology › G4 Doctoral Thesis, monography

Indexing variable length substrings for exact and approximate matching

Navarro, G. & Salmela, L. 2009 p. 214-221. 8 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

Indexing variable length substrings for exact and approximate matching

Navarro, G. & Salmela, L. 2009 p. 214-221. 8 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

Indexing variable length substrings for exact and approximate matching

Navarro, G. & Salmela, L. 2009 p. 214-221. 8 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

MPSCAN: fast localisation of multiple reads in genomes

Rivals, E., Salmela, L., Kiiskinen, P., Kalsi, P. & Tarhio, J. 2009 p. 246-260. 15 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

Towards automated management of compiler assignments

Salmela, L., Tarhio, J. & Montonen, T. 2009 p. 243-249. 7 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

2008

Fast parameterized matching with q-grams

Salmela, L. & Tarhio, J. 2008 In : Journal of Discrete Algorithms. 6, 3, p. 408-419. 12 p.

Publication: Contribution to journal › A1 Refereed journal article

Speeding up pattern matching by text sampling

Claude, F., Navarro, G., Salmela, L., Peltola, H. & Tarhio, J. 2008 p. 87-98. 12 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

2007

Algorithms for Weighted Matching

Salmela, L. & Tarhio, J. 2007 p. 276-286. 11 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

Tuning approximate Boyer-Moore for gene sequences

Kalsi, P., Salmela, L. & Tarhio, J. 2007 p. 173-183. 11 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

2006

Multi-pattern string matching with q-grams

Salmela, L., Tarhio, J. & Kytöjoki, J. 2006 In : Journal of Experimental Algorithmics. 11, 19 p.

Publication: Contribution to journal › A1 Refereed journal article

Sublinear algorithms for parameterized matching

Salmela, L. & Tarhio, J. 2006 p. 354-364. 11 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

2005

Automaattiset kääntäjänlaatimistehtävät

Salmela, L. 2005 Helsinki University of Technology. 78 p.

Publication: Book/anthology › G2 Master's thesis, diploma work, upper higher voational diploma

2004

ACE: Automated Compiler Exercises

Salmela, L. & Tarhio, J. 2004 p. 131-135. 5 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)

2003

Tuning string matching for huge pattern sets

Kytöjoki, J., Salmela, L. & Tarhio, J. 2003 p. 211-224. 14 p.

Publication: Conference contribution › A4 Article in conference publication (refereed)