Hidden Markov Modelling Techniques for Haplotype Analysis. - Mikko Koivisto; Teemu Kivioja; Heikki Mannila; Pasi Rastas; Esko Ukkonen (ALT, 2004)

Recombination Systems. - Mikko Koivisto; Pasi Rastas; Esko Ukkonen (Theory Is Forever, 2004)

A Hidden Markov Technique for Haplotype Reconstruction. - Pasi Rastas; Mikko Koivisto; Heikki Mannila; Esko Ukkonen (WABI, 2005)

Fast Search Algorithms for Position Specific Scoring Matrices. - Cinzia Pizzi; Pasi Rastas; Esko Ukkonen (BIRD, 2007)

Haplotype Inference Via Hierarchical Genotype Parsing. - Pasi Rastas; Esko Ukkonen (WABI, 2007)

Fast Bayesian Haplotype Inference Via Context Tree Weighting. - Pasi Rastas; Jussi Kollin; Mikko Koivisto (WABI, 2008)

A General Framework for Local Pairwise Alignment Statistics with Gaps. - Pasi Rastas (WABI, 2009)

MOODS: fast search for position weight matrix matches in DNA sequences. - Janne H. Korhonen; Petri Martinmäki; Cinzia Pizzi; Pasi Rastas; Esko Ukkonen (Bioinform., 2009)

Computational Techniques for Haplotype Inference and for Local Alignment Significance. - Pasi Rastas (2009)

Finding Significant Matches of Position Weight Matrices in Linear Time. - Cinzia Pizzi; Pasi Rastas; Esko Ukkonen (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Lep-MAP: fast and accurate linkage map construction for large SNP datasets. - Pasi Rastas; Lars Paulin; Ilkka Hanski; Rainer Lehtonen; Petri Auvinen (Bioinform., 2013)

Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data. - Pasi Rastas (Bioinform., 2017)

Kermit: Guided Long Read Assembly using Coloured Overlap Graphs. - Riku Walve; Pasi Rastas; Leena Salmela (WABI, 2018)

Kermit: linkage map guided long read assembly. - Riku Walve; Pasi Rastas; Leena Salmela (Algorithms Mol. Biol., 2019)

Lep-Anchor: automated construction of linkage map anchored haploid genomes. - Pasi Rastas (Bioinform., 2020)