We provide expert analyses and consulting to support research activities in biomedicine. We develop and apply computational tools for the processing, analysis, and visualization of biological data, including genomic, transcriptomic, and metagenomic datasets. Our laboratory offers automated bioinformatics pipelines for the identification of genetic variants, gene expression analysis, and microbiome profiling, as well as the development of custom solutions tailored to specific research projects.
The laboratory provides services to researchers both within and outside the Biomedical Research Center of the Slovak Academy of Sciences (BMC SAS), primarily for data generated by Next Generation Sequencing (NGS) technologies. In addition to analytical services, we offer training, courses, and consultations in bioinformatics and experimental design.
Software Solutions and Technologies
The laboratory uses open-source platforms such as Toil (Python) and Chipster in combination with GATK and R scripts, enabling reproducible and scalable data analyses. Pipelines can be customized and new methods developed according to research needs. Parallel bioinformatics programs in C/C++ and MPI for supercomputers, as well as applications with interactive interfaces, are also being developed.
Technical Infrastructure
The laboratory is equipped with a high-performance server with 80 processors for primary and secondary sequence analysis of pilot projects, which can then be transferred to HPC supercomputers for large-scale processing.
Provided Services
• Gene expression studies (RNA-Seq, smallRNA-Seq, microarrays)
• Identification of SNV, InDel, and CNV variants
• Microbiome analysis (MICCA, DADA2, Microbiome-Analyst)
• Genome and transcriptome assembly
• Customized pipelines (Chipster, Toil)
• Support for GWAS and polygenic disease risk calculation
Additional Services
• Bioinformatics support, statistical analysis, and data visualization
• Training and consultations in bioinformatics and experimental design
• Access to specialized software and computational resources
Contact
Ing. Miloslav Karhánek, PhD.
| T: | 02 3229 5289 |
| @: | miloslav.karhanek@savba.sk |
Dr. Miloslav Karhánek specializes in genomic analysis of sequences and genotypes using open-source software (GATK, Chipster, SnpEff, Annovar, Toil). He has contributed to publications on the microbiome, miRNA discrimination in endometrial cancer, and statistical and genomic analyses in metabolomics and hearing research. In collaboration with NASA, he performed mutation analysis of mice from the International Space Station (ISS) and oversees bioinformatics for several national projects, including APVV, OBEZITA, and BIOFORD.