I work on computational analysis of biological data and the development of analysis methods for such purposes. My applied research has focused on population genetics of marine organisms and mutational mechanisms in DNA replication. My best-known analysis methods are PRANK and PAGAN, programs for phylogeny-aware alignment of multiple sequences, and the publications related to them have been cited over 3,000 times.

Alignment algorithms

PRANK is a probabilistic multiple alignment program for DNA, codon, and amino acid sequences. It’s based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. Instructions for its download and usage are available at the program’s homepage. PAGAN is a general-purpose method for the alignment of sequence graphs. It is based on the phylogeny-aware progressive alignment algorithm and uses graphs to describe the uncertainty in the presence of characters at certain sequence positions.Instructions for its download and usage are available at the program’s homepage.

More information about my software and analysis methods can be found in software publications.

Applied research

Short-range template switching in DNA replication is a mutational mechanism that creates clusters of differences in genomic sequences. I implemented a computational tool for detection of mutation cluster created by template switching and reconstruction of the mutation process (GitHub), and have studied their role in the evolution of human genomes (GitHub). An intriguing property of template-switch mutations (TSMs) is their ability to create perfect reverse-complement repeats with one mutation event. These repeats can form hairpin structures, which are then the basis of all RNA gene secondary structures. We showed that TSMs can explain the evolution of RNA secondary structures through compensatory mutations and create entirely novel microRNA genes. We are currently developing analysis software to identify TSMs in clinical genetics and medical research data. More information about template switching and RNA gene evolution can be found in TSM publications.

I have created analysis pipelines for whole-genome sequencing data and led bioinformatic analyses in various population genetic and comparative genomics projects. The two main study systems have been pinnipeds and stickleback fishes. In pinnipeds, I have been involved, e.g, in population genetic and comparative genomic studies of Saimaa ringed seals, an endangered population landlocked in a lake (GitHub), and the Kangia fjord ringed seals in the Arctic. Our studies on Saimaa ringed seals led them to be recognised as a species of their own (GitHub). In sticklebacks, I have been especially interested in population genomic processes involved in adaptation and the interplay of genetic divergence through drift and intra- and interspecific gene flow. More information about these topics can be found in pinniped publications and stickleback publications.