Doctoral studies
Terms of admission to study
Only students with completed or soon-to-be completed MSc. are admitted to the Doctoral Study Program (DSP). Admission is subject to passing an entrance interview hold in English. The admission committee consists of at least three members; the chairperson is usually the head of the department, the supervisor is one of the committee members. During the interview, the applicant briefly familiarizes the committee not only with his/her diploma thesis, but also with main aims of his/her dissertation work.
Study plan
The study in DSP follows the individual study plan (ISP) compiled jointly by the student and the supervisor. The ISP must include at least 4 courses selected according to the following rules:
- 3 courses mus be selected from the Module A that consists of "core" bio- and chemoinformatics subjects.
- 1 course must be selected from the Module B that contains subjects from areas complementary to the studied DSP.
- None or more courses are selected from the optional Module C that contains subjects focused on the so-called "soft skills". It is highly recommended that students attend a two-semester course Effective Scientific Writing.
Furthemore, the part of the Ph.D. sudy is the foreign study stay long at least 1 month.
It is assumed that the student passes all ISP courses by the end of the 2nd year at the latest. Each student is also obliged, usually by the end of the 2nd year, to attend student scientific conference at the UCT Prague, where he/she will present results of his/her work. At the end of the 2nd year at the latest, the student selects 3 areas that constitute his/her final exam. The final exam is taken by the end of 3rd year.
Subjects of Ph.D. study
Module A
Code | Course name |
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AP500002 | Computational genomics algorithms
AnnotationThe course deals with efficient algorithms for various tasks in bioinformatics. One fo such task is an alingment of two or more sequences. Other topic covers algorithms for individual phases of genome aseembly. The course also presents compressed data structures for storing and indexing genomes and very fast pattern matching in them. Algorithms for efficient analysis and comparison of genomes. Syllabus
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AP143001 | Advanced chemoinformatics
AnnotationThe class covers advanced chemoinformatics and computational drug design techniques, such as lead optimization, biological information in models or the generation and exploration of chemical space. Syllabus
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AP143005 | Advanced structural bioinformatics
AnnotationThe course covers selected advanced topics in structural bioinformatics. We first focus on protein-protein and protein-DNA interactions. We introduce methods to calculate Gibbs free energy associated with these interactions, as well as docking algorithms, software tools and web interfaces. We then explain computational proteomics, protein interaction networks, induced fit, and ab initio methods for protein and peptide design. The section devoted to nucleic acids deals with sequence-dependent structural features of DNA, as well as RNA secondary and tertiary structure modelling. Finally, integrative structural bioinformatics combining experimental and theoretical approaches is exposed. Case studies will present selected problems based on current journal literature. Syllabus
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AP143003 | Advanced biomolecular modelling
AnnotationProcesses in molecular biology and genetics take place at different length and time scales. The course deals with modelling at the mesoscopic scale, where the atoms of the biomolecules are united in larger entities. Students will first deepen their knowledge of nucleic acid structure and dynamics, an important application field of the course. Mesoscopic models of biomolecules and the solvent, including the necessary mathematical tools, are then exposed. Biomolecules often behave as stochastic systems, exhibiting transitions between different conformational states. The course therefore also includes an introduction to Markov processes and their algorithmic realization. Case studies will present selected problems based on current journal literature. Syllabus
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AP143004 | Semantic web in chemistry and biology
AnnotationA course introduces theoretical and practical aspects of Semantic Web technologies used in areas of chemical and biological databases. The Semantic Web was meant to address data interoperability. The interoperability is achieved by the conceptualization of data and storing them according to standardized rules. The key is the creation of ontologies that describe data organizations in various scientific domains. The theoretical part of the lecture is focused on Semantic Web technologies allowing storing, accessing, querying and processing of data. Whereas the practical part of the lecture is focused on ontologies used in chemical and biological databases build on these technologies. Syllabus
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AP143002 | Systems Biology
AnnotationThis is an introductory course of systems biology. We will focus on the structure of regulatory networks, their global properties and enrichment of regulatory motifs. We will study commonly repeating motifs, and will explain their function and reason for their evolutionary conservation. Syllabus
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AP500001 | Text mining
Important noteThe necessary prerequisite is the completion of the Information retrieval course from the module B. AnnotationA number of electronic documents grows much faster than a human is able to deal with. Though inormation retrieval methods help to identify documents likely containing a given information based on keywords, text mining approaches deal with the interpretation of information hidden in the documents. This difficult task is related to the semantics of a natural language that is difficult to interpret unequivocally even for trained experts. Text mining adopts various statistical and information retrieval methods, approaches of a computational linguistics and artificial intelligence classification methods. In text mining, following tasks are solved: Informatin extraction - the identification of key text components and of relationships between them, Topic tracking - an intelligent text filtering based on the user profile, Summarization - the summariozation of text content, Sentence extraction - the identification of sentences that are important for text understanding, Categorization, classification, clustering - text categorization based on content similarity, Concept linkage - the identification of relationships between texts with common concepts. Syllabus
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Module B
Code | Course name |
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AP445003 | Analysis of Multidimensional Biomedical Signals
AnnotationThe subject deals with modern methods and tool in biomedisal and medical field (CT, NMR,...). Students will solve several case studies including real applications. For the exam it is necessary to propose a draft of publication form the field of disertation thesis. Syllabus
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AP320005 | Biophysical chemistry
AnnotationThe primary focus of the lectures is on the description of biological and biochemical systems using principles of physical chemistry. This interdisciplinary approach allows to apply the methodology of physical chemistry on biological and biochemical systems and to use the mathematical background of physico-chemical methods for the description of the behavior of living matter on the molecular and structural level. Syllabus
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AP320006 | Imunochemistry
AnnotationThe course focuses on antibody-antigen interaction aspects especially in terms of in vitro characterization, resulting in a wide variety of immunoassays. After understanding the functions of the immune system and the characteristics of the structure and properties of antigens and antibodies, including their interaction, methods of targeted antibody preparation for analyzes and the characteristics of immunochemical techniques will be described. In individual projects the students will study a selected type of immunochemical technique, principles and possibilities of use. The choice of topics will either be in line with the topic of the doctoral project, or with regard to the current state of research in this area. The results will be presented in the form of short presentation during the course. Syllabus
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AP500003 | Information retrieval
AnnotationA number of electronic documents grows much faster than a human is able to deal with. The information retrieval methods help to identify documents likely containing a given information. The selection of documents is based on keywords, that are assigned to characterize document content and used to specify the aims of user search. To achieve this aim, information retrieval utilizes the methods of linear algebra that work with the vector model, statistical and probability methods, methods of computational linguistics or classification and clustering methods of artificial intelligence. Syllabus
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AP320003 | Microbial Ecology
AnnotationThe aim of the classes is to introduce to students the major topics of microbial ecology. Apart from origins of life, students will get familiar with extensive interactions in the microbial world, interactions among microorganisms and higher organisms or interactions among microorganisms and their abiotic surroundings. Information will be provided on how these interactions determine stability of microbial communities, ecosystem functioning and equilibrium maintaining. Furthermore, the relation of phylogenetics and taxonomic and functional diversity will be given. The classes are composed in a way that students will obtain key theoretical knowledge as well as overview of state of the art microbiological-ecological techniques. Syllabus
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AP403001 | Molecular Modelling and Simulation
AnnotationBasics of modeling of molecules (and other many-particle systems) by means of classical statistical mechanics, from force field construction to molecular dynamics and Monte Carlo simulations. Emphasis is on the methodology of a computer experiment (pseudoexperiment). A simulation project is required, either developing a code for a simple system or using a simulation package. Edu-software is available. Syllabus
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AP320002 | Molecular Mechanisms of Bacteria-Host Interactions
AnnotationThe subject deals with cellular and molecular biology of host-pathogen interactions, placing a particular emphasis on mechanisms by which bacteria manipulate the immunity of the host. Specific attention is paid to regulation of gene expression and to genes involved in virulence of bacterial pathogens. The mechanisms of evasion from host immunity and action of adhesins, toxins and other virulence factors are analyzed in detail using prototypic examples of human and animal pathogens. Syllabus
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AP445001 | Numerical Analysis and Computer Graphics
AnnotationThe subject presents computational and visualization tools of the MATLAB / SIMULINK environment and its use for numeric and symbolic solution of selected computational problems. A special attention is paid to problems of data analysis, solution of linear algebraic equations, linear and nonlinear approximation, solution of nonlinear equations, to methods of numeric interpolation, derivation and integration and to the solution of difference equations. Further topis will include fundamentals of modelling and data visualization. Selected case studies will be devoted to applications of computational methods for processing of engineering and biomedical signals and images. Syllabus
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AP413002 | Numerical Linear Algebra
AnnotationThe lectures aim to extend the student's view to the field of numerical linear algebra. All of the most important topics in the field are covered, including iterative methods for systems of equations and eigenvalue problems and the underlying principles of conditioning and stability. Syllabus
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AP320001 | General Microbiology
AnnotationThe course requires the ability of application of basic characteristics of microorganisms arising from cytology, morfology, taxonomy, genetics, growth conditions, reproduction and metabolism on solving of concrete task conected with microorganisms. Syllabus
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AP445004 | Computational Intelligence
AnnotationThe subject is devoted to selected problems of computational intelligence and machine learning including architecture of artificial neural networks, their optimization for signal and image processing and their use for adaptive noise rejection. A special attention is paid to signal and image features extraction, pattern recognition and to the use of neural networks for their classification into given number of classes. Selected case studies presented in the MATLAB computational environment are devoted to biomedical and engineering data processing. Syllabus
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AP402001 | Computer Simulation of Molecular Properties
AnnotationThe lecture gives theoretical foundations to modern methods of computational chemistry and applications to molecular properties-IR, NMR spectra, etc. The lecture is altered with practical exercises on computers. Syllabus
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AP403005 | Advanced methods of molecular dynamics
AnnotationThe course covers advanced methods of molecular and coarse-grained computer simulations with applications in biology, thermodynamics of solutions, and theory of phase transitions. Syllabus
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AP320007 | Advanced imaging techniques
AnnotationMicroscopy techniques provide an efficient and unique approach to the study of fixed tissues and living cells with high specificity and sensitivity. Course aims to acquaint students with modern microscopy techniques for biology object imaging. Part of the workshop will be the introduction to automated wide-field, confocal and superresolution fluorescent microscopy. First, a brief introduction to the physical mechanisms underlying these imaging techniques will be given. Then we introduce the theoretical and/or practical basis of particular advanced imaging techniques. The basics of image analysis will be covered as well. Syllabus
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AP320004 | Special Enzymology
AnnotationThis course focuses on kinetics and mechanisms of enzymatic reactions, thermodynamics of enzyme-inhibitor (or enzyme-cofactor, enzyme-activator etc) interactions, analytical applications and biophysical methods for enzyme assays, 3D structure and mechanisms of their action. The course also focuses on enzyme engineering approaches and enzyme prospection by gene technologies. Properties of selected industrial enzymes will be presented. Enzymes used in molecular biology will be also discussed. In individual projects the students will study a selected type of enzymes, their structure, mechanism, function and application. The choice will follow the topic of the doctoral project or the current state of research in enzymology. The results will be presented in the form of short presentation. Syllabus
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AP413001 | Graph Theory and Applications
AnnotationThe basic concepts of graph theory are introduced. Algorithmic solutions of engineering problems are discussed. Syllabus
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AP320008 | Research Trends in Biochemistry and Microbiology
AnnotationAn interactive course focused on current research trends in the areas of biochemical and microbiological research with emphasis on topical and fundamental discoveries and new, state-of-the-art experimental strategies. The course consists of independent lectures on subjects inspired by recent publications in top journals, followed by facilitated discussions. Specific topics of lectures are not usually repeated year-round, teachers select them based on the progress in relevant scientific fields. Lectures are prepared and delivered by students under the guidance of teachers; the lectures on selected topics will be delivered by invited experts. In the introductory lecture, the students are acquainted with the lecture topics plan, which may be a subject to modification based on the discussions of the proposals from the students. The sessions can be organized in semester weeks or as a block "miniconference". Syllabus
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AP445002 | Image Processing
AnnotationThe subject presents principles of image processing and functional transforms usage in image analysis. Special attention is paid to colour processing, image segmentation, noise components rejection, image enhancement, data compression, pattern recognition and feature classification including estimation of accuracy and cross-validation errors. Applications include processing of images related to chemistry, material engineering, biochemistry, and biomedicine. Syllabus
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In addition, doctoral or, in exceptional cases, master's courses from other universities may also be chosen for Module B. |
Module C
Code | Course name |
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P834001 | Effective Scientific Writing I
AnnotationHowever good your science is, if it is not communicated effectively, its value is lessened. Whether you like it or not, the modern scientist is a professional writer. Yet despite the ‘publish or perish’ culture in scientific research, almost no investment is made into teaching researchers how to become better writers. Since 2006, Craig Riddell has helped edit hundreds of scientific papers to successful publication, many for high-impact factor journals. This experience led to the development of a bespoke scientific writing course, Effective Scientific Writing (ESW), for researchers working in educational institutions and commercial research institutes. Writing is a fundamental professional development skill that can and should be learned. ESW uses real-life examples to change your way of thinking about writing and your approach to it. Syllabus
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Other Module C courses are currently in preparation and will be added later. |
Final exam
The final exam consists of two mandatory and one optional areas. The optional area is selected based on the topic of the student thesis. Every area is coupled with one subject from the Module A.
- Bioinformatics and system biology (coupled with the course Systems biology)
- Bioinformatics algorithms (coupled with the course Computational genomics algorithms)
- Biomolecular modeling (coupled with the course Advanced biomolecular modelling)
- Chemoinformatics (coupled with the course Advanced chemoinformatics)
- Computer text processing (coupled with the course Text mining)
- Structural bioinformatics (coupled with the course Advanced structural bioinformatics)