Functional Genomics Lab research is focused on genomes analysis and gene discovery, comparative and evolutionary genomics, and mechanisms of evolution. We also work on biological databases development and bioinformatics tools.


Overlapping genes: expression and evolution

Genes from the same genomic locus are often called overllaping genes as they share fragments of DNA. The presence of such genes has been predicted for prokaryotes as well as eukaryotes. However, the high number of overlapping genes in eukaryotic genomes, including human, was quite surprising. Despite a number of overlapping genes studies their origin and evolution are not known. Similarily, quite misterious is the functional role of such organisation of genes. We study overlapping genes in animal and plant genomes in three main aspects: conservation, evolution, and expression.



Retrogenes are processed copies of genes that originate through reverse-transcription of a parental mRNA and cDNA insertion into an organism's genome. Retroposed gene copies are often believed to be pseudogenes because they lack regulatory regions and, as a consequence, they will often degenerate. However, many of them are known to produce functional proteins and give rise to lineage-specific new functional genes. They can also lead to regulatory RNAs or retroposed regulatory sequences. We are interested in the evolution of retrogenes and their contribution to the inter-species differences. We are working on effective methods of functional retrogenes indetification in various animal genomes. We are considering a few aspects during this process, like identification of retrogenes in the genome, across genomes or utilization of next generation sequencing data to obtain candidates for functional retrogenes. In this field of our research we are using not only bioinformatics tools but also some experimental techniques based on molecular biology to look for evidences for retrogenes functionality and expression.


Introns evolution

Despite the progress in genome sequencing and analysis some questions in regard to genome evolution remain unanswered. One of these unsolved misteries is the history of introns. Supporters of 'intron-early' and 'intron-late' hypotheses have been arguing for decades about the time and mechanisms of intron origination. We are studing intron evolution in animal genomes. Our main focus is on the intron gain in mammals.



microRNAs (miRNAs) are key players in regulation of gene expression in Eukaryotes. In plants miRNAs regulate for instance the expression of transcription factors that activate genes responsible for morphogenesis and development. They also actively participate in stress response (as drought or salinity) and therefore hope is reposed in using miRNAs in plant biotechnology. In animals, where it is estimated that miRNAs regulate up to 60% of protein-coding genes, the cellular processes that are under miRNA control include apoptosis and signal transduction. miRNAs have also been associated with a number of diseases and tests are being conducted to improve the treatment and diagnosis, using miRNAs. For the above reasons, we are developing new methods for miRNA identification. We are also interested in some aspects of microRNA biology, as polymorphisms in human genome, evolution or  so called miRNA sponges.