Systems Biology and Bioinformatics Laboratory (SYBILA)

Contact: doc. RNDr. David Šafránek, Ph.D.

Systems biology refers to multidisciplinary approaches designed to uncover emergent properties of complex biological systems. The aim of systems biology is to obtain a system-level understanding of such systems, by examining the structure and dynamics of cellular and organismal functions, rather than the characteristics of isolated parts of a cell or an organism.

Digital systems biology uses computational models together with the methodology of computer systems engineering supported by formal methods to study biological systems. It is an emerging field that dramatically enhances current analysis capabilities to increase our understanding of complex living systems. The technological impact of merging computer science and systems biology will be the design and implementation of digital biology laboratories capable of performing many more experiments than what is currently feasible in real labs and at lower cost (in terms both of human and financial resources) and in less time. These labs will allow biologists to design, execute, and analyze experiments to generate new hypotheses and develop novel high-throughput tools, resulting in advances in experimental design, documentation, and interpretation as well as a deeper integration between “wet” (lab-based) and “dry” research. Moreover, the digital biology laboratories will be a main vehicle for moving from single-gene diseases to multifactorial diseases, which account for more than 90% of the illnesses affecting our society.

In the field of bioinformatics, we carry out applied research centered primarily on genome analysis in humans, selected plant species, and other model organisms. In genomics, we employ state-of-the-art sequencing technologies to decode complete DNA sequences—including highly complex and repetitive regions such as centromeres, telomeres, ribosomal DNA, and acrocentric chromosomes.

We develop innovative bioinformatics tools and algorithms that facilitate the analysis of repetitive DNA and enable the identification of secondary DNA structures (such as quadruplexes). These efforts contribute to a deeper understanding of genome organization and function.

Main research priorities

Our long-term research goal is to develop and apply computational science and technology to enhance our understanding of the molecular mechanisms underlying the behavior of living systems and develop scalable methods and tools for modeling and computerized analysis of large and complex living systems. The focus is on scalable methods and tools for modeling complex systems, parameter synthesis in biological models, digital bifurcation analysis. Our further goal is to develop a tool integration framework which is targeted towards modeling, simulation, visualisation, and analysis of complex biological systems. The framework will allow the instantiation of different tool chains supporting various process flows for which different tools and combination of tools are required.Our long-term research goal is to develop and apply computational science and technology to enhance our understanding of the molecular mechanisms underlying the behavior of living systems and develop scalable methods and tools for modeling and computerized analysis of large and complex living systems. The focus is on scalable methods and tools for modeling complex systems, parameter synthesis in biological models, digital bifurcation analysis. Our further goal is to develop a tool integration framework which is targeted towards modeling, simulation, visualisation, and analysis of complex biological systems. The framework will allow the instantiation of different tool chains supporting various process flows for which different tools and combination of tools are required.

The applied branch of the laboratory focuses on:

Developing advanced algorithms for biological sequence analysis
Annotation and functional understanding of repetitive DNA
Improving applications in nanopore sequencing
Designing methods for complete genome assembly and personalized medicine

Research team

The research is performed in the Systems Biology Laboratory (SYBILA). The web pages of the laboratory give more detailed and complete picture about our research related activities, including publications, seminars, research projects etc.The research is performed in the Systems Biology Laboratory (SYBILA). Prospective students joining SYBILA will become part of a dynamic, interdisciplinary environment at the interface of biology, informatics, and computational science—contributing to research that pushes the boundaries of our understanding of life at the systems level.

All research groups