Research is done in three areas of bioinformatics:
- sequencing data analysis;
- expression data analysis;
- integrating different types of biological data.
In sequencing data analysis we work on developing mathematical models and algorithms for genome assembly. It is a very important task because assembled genomes are used in a variety of bioinformatical pipelines (e.g. variant calling). We also study the problem of genome assembly from theoretical point of view. For instance, we have prooved NP-hardness of the genome assembly problem.
Expression data analysis includes designing methods of extracting biologicaly relevant information from gene expression profiles. It could be, for example, finding a set of genes characteristic for a particular type of cells. Another problem we are working on is gene expression deconvolution: determining what type of cells in what
quantities are present in samples.
Advance in biological profiling technologies also allows to use not only one technology (for exampla, RNA-sequencing) but mutltiple of them. This poses a problem of integrating these multiple types of data to view on the biological problem simulthaneously from multiple perspectives. Currently, in a collaboration with Washington University in St. Louis we work on integrating transcriptional and metabolic profiling data in a context of biochemical reactions.