Main R&D areas

In addition to developing new computational tools for annotation and functional description of non-model organisms, our research team also focuses on advanced analysis of molecular biology data. Emphasis is placed primarily on the research of bacterial organisms utilizable in bio-based engineering and industrial biotechnology. The aim is to obtain a systems description of organisms with maximum use of lab data, besides genomic, transcriptomic, and epigenomic sequencing tools also high pressure liquid chromatography, quantitative polymerase chain reaction and many other techniques.

The research group is focused on the development of microscopy image processing methods and their application to various image data acquired during specific experiments. Typical applications cover cell segmentation, cell tracking during long-term experiments, cell classification, etc. The most commonly processed modalities include (quantitative) phase microscopy, widefield and confocal fluorescence microscopy.

Our team develops new methods for digital signal processing of large-scale genomic data, focusing on de novo genome assembly, new bacterial strains genotyping, or metataxonomic and metagenomic studies. In contrast to conventional text-based DNA processing, our methods allow systematic approach and more computationally efficient analysis of often periodic and redundant genomic data.

The research group works mainly in the areas of cell and tissue engineering with the aim of applying the results in regenerative medicine. In research on living cells and tissue samples, technologically demanding measurement and imaging methods are applied to monitor and measure electrical, mechanical and fluorescence phenomena, together with the use of nanoparticles and bioprinting. Research is supported by the use of fluorescence, confocal and holographic microscopy or advanced microfluidic and incubation techniques. Typical applications include monitoring the migration of cells in the extracellular matrix in 2D and 3D space using confocal fluorescence microscopy, monitoring changes in their motility due to mechanical/electrical or chemical stimuli, as well as monitoring mitochondrial function and activity. Another area of activity is the electrophysiology of excitable cells and tissue, where microelectrode arrays or fast fluorescence cameras are applied to map the electrical activity of cardiac cells or neurons. Bioprinting and optogenetic facilities allow to follow current trends in cell engineering.

The research group is focused on the theory and application of advanced methods for medical image data analysis and processing. Our main topic is to develop complex algorithms for application especially (but not only) to data acquired by tomographic imaging systems such as X-ray computed tomography (CT) and magnetic resonance imaging (MRI) to support medical diagnosis in various medical fields. Our activities include theoretical research, development of new algorithms, their implementation and functional validation, including clinical testing at collaborating clinical sites. Our research group actively collaborates with a number of distinguished international  and national  institutions such as King's College London (KCL) – UK; German Cancer Research Center (DKFZ) – Heidelberg, Germany; Philips HealthCare; General University Hospital (VFN) in Prague, Czech Republic; University Hospital Brno (FN Brno), Czech Republic; University Hospital at St. Anne's University Hospital Brno, Czech Republic).

Our team was founded in 2015. We publish exclusively in impacted journals, which in most cases are included in the Q1 category. The group focuses primarily on filtering, analysis and compression of ECG recordings. We also focus on the processing and analysis of data from wearable devices (smartphones, watches and bracelets) in order to assess the health and activity of individuals. For this purpose, we also use professional wearable devices (Faros, Shimmer). As part of our activities, we have created several publicly available databases of signals and their annotations, which are freely available on the Physionet.org website. We are currently a solver of a prestigious grant for the US Navy ("Health and activity monitoring by wearables in extreme conditions") focused on the analysis of health and activity of individuals in extreme conditions in real time (soldiers, firefighters, police).

This research group is focused on the development of new diagnostic approaches in ophthalmology with a focus on retinal diseases. This mainly involves the application of advanced image processing and machine or deep learning methods. The activity also includes the experimental development of new devices for ophthalmology such as the video-ophthalmoscope or the camera for pupillometry.

Chemoinformatics research in our group involves the application of computer and information systems related techniques to understand the relationship between biological activity and the structure of an organic compound. We work in interdisciplinary field combining chemistry, statistics, informatics and molecular biology.