We develop laboratory and bioinformatics methods that help understand genetic variation, identify biomarkers and analyse microorganisms. We connect research with our partners’ practical needs and the development of reusable analytical tools.

Human genomics

We investigate genetic variation and its relevance to medicine. We connect human and population genomics with research into non-invasive biomarkers and circulating DNA.

Our main topics include:

●  population genetic variation and DNA copy number changes;

● hereditary cancer predispositions, including Lynch syndrome;

●  fragment characteristics, somatic mutations and other properties of cfDNA for the development of less invasive screening tests.

We combine sequencing data with computational models in collaboration with clinical institutions.

Selected publications:

Genetic variation and hereditary predispositions

●  Whole genome sequencing completes the molecular genetic testing workflow of patients with Lynch syndrome (2025) — A collaborative study on the contribution of whole-genome sequencing to resolving Lynch syndrome cases.

●  Understanding genetic variability: exploring large-scale copy number variants through non-invasive prenatal testing in European populations (2024) — Research into large-scale DNA copy number changes in European populations using NIPT data.

●  DNA copy number variation: Main characteristics, evolutionary significance, and pathological aspects (2021) — A review of the characteristics, evolutionary significance and pathological aspects of DNA copy number variation.

Liquid biopsy and non-invasive biomarkers

●  Breath biopsy biomarkers: cell-free nucleic acids in exhaled breath condensate (2025) — A review of cell-free nucleic acids in exhaled breath condensate as a potential source of non-invasive biomarkers.

●  Telomere length as a biomarker for fetal fraction prediction in non-invasive prenatal testing (2025) — Research into telomeric content as a complementary indicator for estimating fetal fraction in prenatal testing.

●  Novel liquid biopsy CNV biomarkers in malignant melanoma (2024) — A collaborative study of potential melanoma biomarkers based on DNA copy number changes in plasma.

●  Current Challenges of Methylation-Based Liquid Biopsies in Cancer Diagnostics (2024) — A review of the opportunities and limitations of circulating DNA methylation in cancer diagnostics.

●  Mitochondrial DNA copy number changes, heteroplasmy, and mutations in plasma-derived exosomes and brain tissue of glioblastoma patients (2022) — A study of mitochondrial DNA copy number changes, heteroplasmy and mutations in patients with glioblastoma.

●  Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes (2020) — A review of the technical and methodological aspects of cell-free nucleic acid analyses.

Microbial genomics and the microbiome

We analyse microbial genomes and the composition of microbial communities. Our experience includes microbiome research, bacteriophages and genomic surveillance of pathogens. During the pandemic, we contributed to national SARS-CoV-2 surveillance, connecting sequencing, bioinformatics and epidemiological interpretation.

Selected works:

●  Characterization of bacteriophages infecting multidrug-resistant uropathogenic Escherichia coli strains (2024) — Characterisation of bacteriophages infecting multidrug-resistant uropathogenic E. coli strains.

●  Systematic Genomic Surveillance of SARS-CoV-2 Virus on Illumina Sequencing Platforms in the Slovak Republic—One Year Experience (2022) — Experience with national SARS-CoV-2 genomic surveillance and the integration of sequencing with bioinformatics analysis.

Innovation and technology transfer

Team members are co-inventors of patented methods and published patent applications in prenatal testing, circulating DNA analysis and microbial genomics. We collaborate with technology partners on technology transfer.

●  Method and system for identifying tissue of origin of a tumor from sequenced cell-free circulating DNA (2025) — A Slovak patent application (SK802023A3) focused on computational identification of the tissue of origin of a tumour from circulating DNA.

●  Method for estimation of cell-free DNA mixture proportions based on telomere-derived fragments (2024) — An international patent application (WO2024253600A1) focused on estimating component proportions in cfDNA mixtures using telomeric fragments.

●  Methods and system for detecting microsatellite instability from sequenced cell-free circulating DNA (2025) — A Slovak patent application (SK882023A3) focused on detecting microsatellite instability (MSI) from cfDNA.