Supervisors and Their Subject Areas

This page lists the supervisors available at the Faculty of Informatics together with a brief description of their subject specialism. Ph.D. study applicants will find this information useful when specifying their subject of study interest.

It is recommended that all applicants consult with an appropriate supervisor on the intended subject of their work. It is possible to agree on a theme that is not included in the list below.

Applicants may contact the Vice-Dean for doctoral studies should there be any doubt on the most appropriate supervisor to consult with.

prof. RNDr. Jiří Barnat, Ph.D.
Software tools for automated formal analysis and verification of large-scale systems.

Dr. rer. nat. Achim Blumensath
Logic, Algorithmic Model Theory, Automata Theory, Formal Language Theory.

doc. RNDr. Jan Bouda, Ph.D.
Randomness, Cryptography, Information theory, Quantum Information Processing.

doc. Ing. Michal Brandejs, CSc.
Information systems.

doc. RNDr. Tomáš Brázdil, Ph.D.
Explainable artificial intelligence in biomedicine.

prof. RNDr. Luboš Brim, CSc.
Formal methods in molecular and systems biology (analysis of genetic regulatory networks and signaling pathways).

doc. Ing. RNDr. Barbora Bühnová, Ph.D.
Software architecture design of complex ecosystems with the focus on trust management, security, safety, and reliability. Trustworthiness of autonomous systems.

doc. Ing. Pavel Čeleda, Ph.D.
Cybersecurity operations, computer and network security, network situational awareness, simulation and emulation environments, interactive learning environments, learning technologies, cybersecurity education, learning analytics, and educational data mining.

prof. RNDr. Ivana Černá, CSc.
Formal methods for verification of computer systems. Algorithms and tools for efficient analysis, design, and verification of properties of large-scale (concurrent) systems. Application of formal verification in component-based design. Application of formal methods in systems biology. Design and analysis of algorithm.

doc. RNDr. Vlastislav Dohnal, Ph.D.
Similarity data management. Organizing and searching in databases of complex data. Design of traditional indexing techniques and search algorithms. Applications of artificial intelligence methods for data management and indexing.

prof. RNDr. Ladislav Dušek, Ph.D.

prof. RNDr. Jozef Gruska, DrSc.
Methods of quantum information processing. Basic concepts and techniques; quantum automata, algorithms and protocols. Quantum computation and communication complexity. Methods and techniques of broadly understood quantum cryptography.
Classical cryptography. Cryptographic protocols and their security. Randomized algorithms.
Foundations and history of informatics as of fundamental science with similar goals as that of physics. Basics and history of informatics as basis of a new, third, methodology of science (next to theoretical and experimental methodology).
Relations between informatics, physics and mathematics.

doc. RNDr. Eva Hladká, Ph.D.

prof. RNDr. Petr Hliněný, Ph.D.
Combinatorial and parameterized algorithmics: parameterized complexity, combinatorial optimization, FO and MSO model checking, metatheorems.
Topological and structural graph theories: graph minors, width and depth parameters, sparsity, graph crossing number, drawings and representations of graphs.

doc. RNDr. Petr Holub, Ph.D.
Explainable AI methods in biomedicine. Traceability and reproducibility of biomedical data and analyses, provenance of sensitive data. Processing and compression of multimedia. Processing sensitive biomedical data and privacy risk analyses.

doc. RNDr. Aleš Horák, Ph.D.
Natural language processing (syntactic analysis, semantic analysis, knowledge extraction), knowledge representation and reasoning, artificial intelligence, multiagent systems.

doc. RNDr. Barbora Kozlíková, Ph.D.
Visualization and visual analysis for the purpose of data exploration, analysis, and presentation.

prof. RNDr. Michal Kozubek, Ph.D.
Digital image acquisition and analysis, automation of these processes and biomedical applications using optical microscopy. Optimization of critical algorithms with respect to output quality and/or quantity. Simulation of image formation in optical systems: blur, noise, artifacts and their correction using hardware and/or software means. Analysis of multi-dimensional image data. Segmentation of cells and their components. Tracking of moving objects in live cell imaging.

prof. RNDr. Daniel Kráľ, Ph.D., DSc.
Structural graph theory (graph coloring in particular), analytic methods in combinatorics (graph limits and their applications in extremal graph theory), extremal combinatorics, and algorithmic graph theory (algorithmic metatheorems, width parameters, applications of logic methods) with its applications in discrete optimization.

Priv.-Doz. Dipl.-Ing. Dr. Simone Kriglstein
Human Computer Interaction, User Interface and Interaction Design, Human Centered Design, Game Design, Games User Research, Games Experience, Game Analytics, Gameplay Visualization, and Esports.

prof. Dr. rer. nat. RNDr. Mgr. Bc. Jan Křetínský, Ph.D.
Formal verification and synthesis, probabilistic model checking, applications of machine learning in verification, verification of learnt systems (e.g. neural networks), explainable AI (e.g. explainable controllers of cyber-physical systems), temporal logics, automata theory.

prof. RNDr. Mojmír Křetínský, CSc.
Concurrent and distributed systems; concurrency theory; modeling; analysis and verification of infinite state systems, semantics, process algebras/process rewrite systems, (un)decidability; concurrent constraint systems

prof. RNDr. Antonín Kučera, Ph.D.
Formal modeling and verification of computer systems (model checking, equivalence checking). Modal and temporal logics and their probabilistic extensions. Game theory and its applications in computer science (Markov decision processes, stochastic games). Effective analysis of stochastic systems with infinitely many states. Methods, algorithms and tools for analysis and verification of programs written in imperative languages.

doc. Ing. Matej Lexa, Ph.D.
Bioinformatics, computational DNA sequence and genome analysis, sequence repeats.
Examples of possible topics include:
- tools and algorithms for working with the pan-genomes and/or pan-repeatomes,
- simulation models of repeat dynamics in eukaryotic genomes,
- 3D organization of chromatin in the nucleus,
- detection and quantification of recombination events in and outside the repeatome,
- genotype-phenotype relationships in biobanks and other publicly available data.

doc. RNDr. Martin Maška, Ph.D.
Object tracking and cell fate profiling in large-scale bioimage data; analysis of multidimensional bioimage data using deep learning and well-founded methods; analysis and synthesis of multidimensional image data of cells with complex shapes.

doc. RNDr. Zdeněk Matěj, Ph.D.
Digital data analysis in the field of ionizing radiation detectors; HW architecture design for data analysis using real-time machine learning methods; acceleration of simulation tools (e.g. Monte-Carlo methods).

doc. RNDr. Pavel Matula, Ph.D.
Digital image analysis and biomedical applications using optical microscopy. Analysis of higher-dimensional image data. Image segmentation using mathematically well founded methods (active contours, graph-cut minimalization, etc.). Object tracking in live cell imaging.

doc. RNDr. Petr Matula, Ph.D.
Analysis of multi-dimensional biomedical image data mostly acquired using optical microscopes. Mathematical morphology.

prof. RNDr. Václav Matyáš, M.Sc., Ph.D.
Applied cryptography, computer and communications security, privacy.

prof. RNDr. Luděk Matyska, CSc.
Parallel and distributed systems (Grids, metacomputers), infrastructure, monitoring and management, including implications for robustness and fault tolerance; parallel and distributed applications.
High performance networks and their transport protocols, multimedia transports, including use-in (e-)learning support.
Scheduling in distributed systems, primary based on constrain (logic) programming.

doc. Mgr. Bc. Vít Nováček, PhD
Health informatics, Discovery informatics, Biomedical AI/ML applications, Knowledge graphs, Ontologies, Knowledge representation, Representation (graph) learning, Explainable AI, Interpretable ML, Text mining.

doc. RNDr. Petr Novotný, Ph.D.
Risk-aware and safe reinforcement learning. Formal methods for analysis of probabilistic programs. Controller synthesis for probabilistic agents, stochastic games on graphs.

doc. Mgr. Jan Obdržálek, PhD.
Logics and algorithms for verification. Program verification and analysis. Graph width/depth parameters and related algorithmic topics (incl. model checking and parameterized complexity).

doc. RNDr. Radek Ošlejšek, Ph.D.
Data semantics and its interactive visual analytics. Software architectures for data analysis and visualizations.

doc. Ing. Václav Oujezský, Ph.D.
Cutting-edge networking technologies, Internet of Things (IoT), Software-defined Networking (SDN), wireless and mobile communication systems, programmable networks, artificial intelligence applications in networking technologies, network traffic analysis, and network security.

doc. Mgr. Radek Pelánek, Ph.D.
Intelligent tutoring systems, computerized adaptive practice, recommendation systems with applications in education, automated methods for programming education.

prof. RNDr. Tomáš Pitner, Ph.D.
Monitoring systems, Intelligent buildings and Smart-grids, Large software architectures, Person-Centered Approach in Technology-enhanced Learning.

doc. RNDr. Lubomír Popelínský, Ph.D.
Machine learning, ensemble methods, anomaly analysis, multirelational learning with a domain knowledge, AutoML, neuro-symbolic learning.

doc. Ing. Vlad Popovici, PhD

prof. Ing. Václav Přenosil, CSc.
Design and architecture of the digital systems. Dependability and diagnostics of the digital systems. Fault tolerant systems. Embedded systems. Training systems.

doc. Mgr. Hana Rudová, Ph.D.
Scheduling, timetabling, planning. Educational timetabling. Job scheduling in parallel and distributed environments. Data transfer planning. Solution approaches: constraint programming, meta-heuristics, search algorithms, integer programming.

doc. Mgr. Pavel Rychlý, Ph.D.
Processing of text, natural language processing, information extraction, big data, machine translation, language modeling.

doc. RNDr. Vojtěch Řehák, Ph.D.
Formal models of stochastic systems and their algortihmic analysis. Agent systems with randomized behavior. Game theory and its applications in computer science (Markov decision processes, stochastic games).

doc. RNDr. Jan Sedmidubský, Ph.D.
Similarity modeling using deep neural networks with the main emphasis on the domain of spatio-temporal human motion data (so-called motion-capture data). Action recognition, event detection, and explainability in the domain of spatio-temporal human motion data. General-purpose indexing algorithms for similarity searching in various application domains.

doc. RNDr. Petr Sojka, Ph.D.
Machine learning [of text and word representation]. Natural language processing. Classification of [mathematical] texts.
Information retrieval, text corpora. Digital libraries, digitisation, recognition (OCR) and indexing.
Digital typography, electronic publishing, visualization.

prof. RNDr. Jan Strejček, Ph.D.
Automated analysis and verification of software. Automata over infinite and finite words. SMT solcing (focused on bit-vector logic).

doc. RNDr. David Svoboda, Ph.D.
Image processing in biomedicine: image augmentation, image synthesis, generative modeling, simulation of time-lapse image sequences of living cells, checking the plausibility of synthetic image data, manipulation of higher-dimensional data.

doc. RNDr. David Šafránek, Ph.D.
Development of computational methods for specification and analysis of models of complex systems. Modelling of signalling, metabolic, and gene regulatory networks. Algorithms for monitoring and control of complex dynamical processes.

prof. PhDr. David Šmahel, Ph.D.
Human Computer Interaction (HCI), Usable Security, Social Informatics, User Experience (UX), Risks of the Technology Usage (online addictions, online aggression), Digital Technology and Well-being

doc. RNDr. Petr Švenda, Ph.D.
Applied cryptography. Security analysis of cryptographic smartcards. Protocols for secure multiparty computation in limited environments. Security of cryptocurrency hardware wallets.

doc. RNDr. Jan Vykopal, Ph.D.
Cybersecurity education, interactive learning environments, learning analytics, and educational data mining.

prof. Ing. Pavel Zezula, CSc.
Database systems, storage and search structures, multimedia and XML data, distibuted index structures, similarity search, performance evaluation.

prof. RNDr. Jiří Zlatuška, CSc.
Electronic publishing. Information society.