1. MODELLING DNA-DNA HYBRIDIZATION AND DEVELOPMENT OF PRIMER DESIGN SOFTWARE
For more than 10 years we have been studying how DNA molecules hybridize to their specific and non-specific targets. This is important for designing highly specific PCR primers or microarray probes. We have written several software packages facilitating genomic PCR primer design. Our workgroup has participated in development of widely used Primer3 software and we host official webpage for Primer3.
We have implemented our theoretical knowledge in practice in form of various DNA-based molecular tests. For example, we have developed diagnostic tests for respiratory disease pathogen detection for Estonian company Quattromed HTI, blood sepsis related pathogen tests for Dutch start-up company Microbiome Ltd and food allergen detection test for Estonian biotech company Icosagen Ltd.
2. ASSEMBLY AND ANNOTATION OF GENOMES
Also, we work on sequencing and assembly of bacterial genomes. Knowing the sequence variation in microbial genomes is important for developing new, more specific diagnostic tests for pathogen detection. For example, we participated in assembly of new phenol-degrading species of Limnobacter genome.
3. COMPUTATIONAL METHODS FOR STUDYING VARIATIONS IN PERSONAL GENOMES
We study large-scale structural variations in human genome. The examples of large-scale variations are copy-number variations (CNVs), Alu-element insertions and insertions of viral genomes. All these structural variations are polymorphic (different between different individuals) and thus might affect our health and behaviour. We develop computational methods for detection of novel Alu-elements from 2nd generation sequencing data.
We also work on improving computational methods for 2nd generation sequencing read mapping and variant calling.