Research

Gemonics, bioinformatics, next-generation sequencing, cancer transcriptomics

Activity of our laboratory is based on advanced applications of genomics, transcriptomics and bioinformatics, the most vigorously developing disciplines of contemporary life sciences. Since 2017, we have been equipped with the Illumina NextSeq 500 next-generation sequencer, which replaced outdated microarray technology. Since 2019, we have been using single cell transcriptomics and epigenomics technology (10x Genomics). As a part of our know-how, we develop sophisticated bioinformatical tools and pipelines to analyse produced data sets as well as those available in public databases. We use all these high-throughput and bioinformatic tools to conduct our own scientific projects, for long term collaborations with our colleagues and clinicians, and to support other scientific groups at the Institute.

Cancer transcriptomics
We have been involved in a long term-project focused on head and neck squamous cell carcinoma and skin cancers. We focus on tumour microenvironment and on interactions between cancer associated fibroblasts and malignant cells. We have collected a large data sets of patient samples (>100 patients) and cancer associated fibroblasts that are being analysed in the recently awarded project Center for Tumor Ecology supported by the Operational Programme Research, Development and Education.

Bioinformatics and databases, genomics
The laboratory forms the local node of the Pan-European ELIXIR bioinformatics research infrastructure. We curate and maintain the database of mitochondrial sequences coming from the ancient DNA samples AmtDB and the database of human endogenous retroviruses HERVd. In collaboration with the Laboratory of Viral and Cellular Genetics, we study endogenous retroviruses also in other species. In collaboration with other groups of the Institute, members of the laboratory became involved in functional genomics research of several models of malignant and immune diseases.

An integral part of our laboratory is the Core Facility of Genomics and Bioinformatics.

 

Last change: July 23, 2020