Pasi Rastas
University of Helsinki, Department of Computer Science
P.O. Box 68 (Gustaf Hällströmin katu 2 b)
FIN-00014 UNIVERSITY OF HELSINKI
Office: B216
Phone: +358 9 191 51271
Email: Pasi.Rastas@cs.helsinki.fi
Publications
- J. Korhonen, P. Martinmäki, C. Pizzi, P. Rastas and E. Ukkonen: MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics 2009 (to appear).
- Cinzia Pizzi, Pasi Rastas, Esko Ukkonen: Finding Significant Matches of Position Weight Matrices in Linear Time. IEEE/ACM Transactions on Computational Biology and Bioinformatics (to appear).
- Pasi Rastas: A General Framework for Local Pairwise Alignment Statistics with Gaps, In: S. Salzberg, T. Warnow (Eds.) Algorithms in Bioinformatics: 9th International Workshop (WABI 2009), LNCS 5724, pp. 233-245, Springer 2009.
- Pasi Rastas, Jussi Kollin, Mikko Koivisto: Fast Bayesian Haplotype Inference via Context Tree Weighting, In: K. Crandall, J. Lagergren (Eds.), Algorithms in Bioinformatics: 8th International Workshop (WABI 2008), LNCS 5251, pp. 259-270, Springer 2008. software
- Pasi Rastas, Mikko Koivisto, Heikki Mannila, and Esko Ukkonen: Phasing genotypes using a hidden Markov model. In: I. Mandoiu and A. Zelikovsky (eds.), Bioinformatics Algorithms: Techniques and Applications, pp. 373-391, Wiley 2008.
- Pasi Rastas and Esko Ukkonen: Haplotype Inference via Hierarchical Genotype Parsing. In: R. Giancarlo, S. Hannenhalli (Eds.): Algorithms in Bioinformatics, 7th International Workshop (WABI 2007), LNCS 4645, pp. 85-97, Springer 2007. (software available here)
- Cinzia Pizzi, Pasi Rastas and Esko Ukkonen: Fast search algorithms for position specific scoring matrices. In: S. Hochreiter, R. Wagner (Eds.): Bioinformatics Research and Development, First International Conference (BIRD 2007), LNCS 4414, pp. 239-250, Springer 2007. (a related software)
- Pasi Rastas, Mikko Koivisto, Heikki Mannila, and Esko Ukkonen: A hidden Markov technique for haplotype reconstruction. In: R. Casadio and G. Myers (eds.), Algorithms in Bioinformatics: 5th International Workshop (WABI 2005), LNCS 3692, pp. 140-151, Springer, 2005. (software HIT is here)
- Mikko Koivisto, Teemu Kivioja, Pasi Rastas, Heikki Mannila, and Esko Ukkonen: Hidden Markov modelling techniques for haplotype analysis. In: S. Ben-David, J. Case, and A. Maruoka (eds.), Algorithmic Learning Theory: 15th International Conference (ALT 2004), LNCS 3244, pp. 37-52, Springer, 2004.
- Mikko Koivisto, Pasi Rastas, and Esko Ukkonen: Recombination systems. In: J. Karhumaki, H. Maurer, G. Paun, G. Rozenberg (eds.), Theory is Forever (Salomaa Festschrift), LNCS 3113, pp. 159-169, Springer-Verlag, Berlin, Heidelberg, 2004.
Software
- LASWG - Local Alignment Statistics with Gaps
- MOODS - MOtif Occurrence Detection Suite
- BACH - BAyesian context-based Haplotype inference
- HIT - Haplotype Inference Technique
- HaploVisual
- HaploParser - Haplotype inference using combinatoric Parsing
Teaching
- Biological sequence analysis (autumn 2008)
- Approximation Algorithms (spring 2008)
- Biological sequence analysis (spring 2007)
- Teacher tutoring 2005-2007
- Biological sequence analysis (autumn 2005)
- String Matching (spring 2005)
Links
Pasi Rastas Last modified: Thu Dec 4 15:16:32 EET 2008