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 12.04.2013 (Separate exam)

Algoritmit bioinformatiikassa
Algoritmer för bioinformatik
Algorithms for Bioinformatics

  • Register 16.04.2013 (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

Forbidden Patterns

Fischer, J. , Gagie, T. , Kopelowitz, T. , Lewenstein, M. , Mäkinen, V. , Salmela, L. & Välimäki, N. 2012 p. 327-337.

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

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)

Normalized N50 Assembly Metric using Gap-Restricted Co-Linear Chaining

Mäkinen, V. , Salmela, L. & Ylinen, J. 03.10.2012 In : BMC Bioinformatics. 13, p. 255. 5 p.

Publication: Contribution to journal › A1 Refereed journal article

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. 13 p.

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

Exact search algorithms for biological sequences

Rivals, E. , Salmela, L. & Tarhio, J. 2011 In: Algorithms in computational molecular biology: Techniques, approaches and applications. 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. & 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 string matching with reduced alphabet

Salmela, L. & Tarhio, J. 2010 In: Algorithms and applications: Essays dedicated to Esko Ukkonen on the occasion of his 60th birthday. Elomaa, T., Mannila, H. & Orponen, P. (eds.). 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

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

2009

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)

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 vocational 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)