Full-time study

4 years

prof. Ing. Valentine Provazník, Ph.D.

Chairman :
prof. Ing. Valentine Provazník, Ph.D.
Councillor internal :
doc. Ing. Radim Kolář, Ph.D.
doc. Ing. Jana Kolářová, Ph.D.
doc. Ing. Daniel Schwarz, Ph.D.
Councillor external :
Prof. José Millet Roig
prof. Mgr. Jiří Damborský, Dr.
prof. MUDr. Marie Nováková, Ph.D.
prof. Ewaryst Tkacz, Ph.D.,D.Sc.
prof. Pharm.Dr. Petr Babula, Ph.D.
prof. Dr. Marcin Grzegorzek

The doctoral studies of a student follow the Individual Study Plan (ISP), which is defined by the supervisor and the student at the beginning of the study period. The ISP is obligatory for the student, and specifies all duties being consistent with the Study and Examination Rules of BUT, which the student must successfully fulfill by the end of the study period. The duties are distributed throughout the whole study period, scored by credits/points and checked in defined dates. The current point evaluation of all activities of the student is summarized in the “Total point rating of doctoral student” document and is part of the ISP. At the beginning of the next study year the supervisor highlights eventual changes in ISP. By October, 15 of each study year the student submits the printed and signed ISP to Science Department of the faculty to check and archive.
Within mainly the first four semesters the student passes the exams of compulsory, optional-specialized and/or optional-general courses to fulfill the score limit in Study area, and concurrently the student significantly deals with the study and analysis of the knowledge specific for the field defined by the dissertation thesis theme and also continuously deals with publishing these observations and own results. In the follow-up semesters the student focuses already more to the research and development that is linked to the dissertation thesis topic and to publishing the reached results and compilation of the dissertation thesis.
By the end of the second year of studies the student passes the Doctor State Exam, where the student proves the wide overview and deep knowledge in the field linked to the dissertation thesis topic. The student must apply for this exam by April, 30 in the second year of studies. Before the Doctor State Exam the student must successfully pass the exam from English language course.
In the third and fourth year of studies the student deals with the required research activities, publishes the reached results and compiles the dissertation thesis. As part of the study duties is also completing a study period at an abroad institution or participation on an international research project with results being published or presented in abroad or another form of direct participation of the student on an international cooperation activity, which must be proved by the date of submitting the dissertation thesis.
By the end of the winter term in the fourth year of study the full-time students submit the elaborated dissertation thesis to the supervisor, who scores this elaborate. The combined students submit the elaborated dissertation thesis by the end of winter term in the fifth year of study. The final dissertation thesis is expected to be submitted by the student by the end of the fourth or fifth year of the full-time or combined study form, respectively.
In full-time study form, during the study period the student is obliged to pass a pedagogical practice, i.e. participate in the education process. The participation of the student in the pedagogical activities is part of his/her research preparations. By the pedagogical practice the student gains experience in passing the knowledge and improves the presentation skills. The pedagogical practice load (exercises, laboratories, project supervision etc.) of the student is specified by the head of the department based on the agreement with the student’s supervisor. The duty of pedagogical practice does not apply to students-payers and combined study program students. The involvement of the student in the education process within the pedagogical practice is confirmed by the supervisor in the Information System of the university.

1. Advanced algorithms for monitoring human health and activity using a smartphone

   The theme of this dissertation is focused on monitoring of human health and activity using a smartphone and its integrated sensors (especially accelerometer, gyroscope, magnetometer, GPS, microphone, camera). The main motivation is the availability and great potential of smartphones, which is far from being used in health monitoring. The thesis has two main objectives. The first objective is to explore the potential of a smartphone and how to use it for human health and activity monitoring and to critically evaluate its real usability. The second objective of the thesis is to design advanced algorithms for processing of data captured by a smartphone (e.g. for the purpose of human activity classification or blood pressure determination) and to evaluate the performance and applicability of these algorithms in practice. It is possible to use smartphones available at the department to record own data. Applicants are expected to have knowledge of programming in Matlab or Python and base knowledge of processing and analysis of 1D signals. PhD students will complete a six-month internships at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

   Tutor: Vítek Martin, Ing., Ph.D.

2. Advanced detection of ECG significant points during pathological events

   The theme of this dissertation is focused on reliable and accurate detection of ECG significant points during pathological events. The thesis has two main objectives. The first objective is to map the potential of nowadays algorithms for QRS complex detection and ECG records delineation during various pathological events and to define their deficiencies. The second goal of the thesis is to design an advanced delineation algorithm that will work reliably during most common pathological events and verify its robustness on standard ECG databases. Applicants are expected to have knowledge of programming in Matlab or Python and base knowledge of processing and analysis of 1D signals. PhD students will complete a six-month internships at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

   Tutor: Vítek Martin, Ing., Ph.D.

3. Advanced methods for analysis of bacterial methylomes on a genome-wide scale using nanopore sequencing

   Changes in the expression of genetic information that are not caused by changes in the primary structure of DNA are referred to as epigenetic changes. A typical example can be found in DNA methylation, which was discovered in bacteria more than a half century ago. Despite that, a majority of studies aims on 5-methylcytosine (5mC) methylations in eukaryotic genomes by utilizing bisulfite sequencing with the next generation sequencing platforms. Unfortunately, bacterial methylomes are formed not only by 5mC, but also by N6-methyladenine (6mA) and N4-methylcytosine (4mC) methylations, which are undetectable (6mA) or difficult to detect (4mC) by this approach. Luckily, the solution exists in the utilization of the third generation sequencing (TGS) platforms. Although the nanopore TGS sequencing allows theoretically the detection of all above-mentioned types of methylations, this potential remains currently unused due to the lack of bioinformatics tools for the detection of methylated nucleotides in the current signal that is produced during data acquisition. The aim of this dissertation is to create a methodology for the detection of methylations using advanced bioinformatics and digital signal processing techniques for filtering and analyzing this noisy current signal. The whole methodology will be designed using data produced by Oxford Nanopore Technologies MinION and MinION/Flongle sequencing devices that UBMI owns. Suitable bacterial strains will be provided by cooperating institutions, mainly University Hospital Brno (pathogenic bacteria), UCT Prague, and the Faculty of Chemistry BUT (industrially utilizable bacteria). As a part of their studies, PhD students will complete six-month internships at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

   Tutor: Sedlář Karel, doc. Mgr. Ing., Ph.D.

4. Advanced methods for biological signals quality estimation

   The topic of dissertation thesis is focused on biological signals quality monitoring by wearable devices (e.g. PPG, ECG). Other concurrently sensed signals such as accelerometer data can be also used for this purpose. The thesis has two main objectives. The first objective is to propose signal quality classes with respect to possible sources of interference as well as the subsequent utilization of the signal. The second objective is to design advanced algorithms for real-time signal quality estimation and to verify the usability of the signal class for its intended purpose. Applicants are expected to have knowledge of programming in Matlab or Python and base knowledge of processing and analysis of 1D signals. It is possible to use wearable devices available at the department to record own data. PhD students will complete a six-month internships at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

   Tutor: Smital Lukáš, Ing., Ph.D.

5. Advanced methods for study of mitochondrial function and activity with application in regenerative medicine

   In most cells, mitochondria are the main producers of cellular energy with oxygen consumption and are also involved in apoptotic and other intracellular regulatory processes. They also play an important role in the field of regenerative medicine, where studies demonstrating mitochondrial transfer as one of the emerging mechanisms by which mesenchymal stem cells can regenerate and repair damaged cells or tissues. Microscopic fluorescence techniques are often used to real-time monitoring of mitochondrial function, particularly using fluorescent dyes based on mitochondrial membrane potential measurements. However, the reproducibility of the results across laboratories strongly depends upon following well validated and reliable protocols along with the appropriate controls. The dissertation thesis will deal with the research and development of new methods for studying cell function and activity using advanced fluorescent techniques, using fluorescent and fluorescent confocal microscopy and optical spectroscopy. The aim of this work is to create a methodology for evaluation of mitochondrial function and activity using in regenerative medicine in order to evaluate efficiency and rate of regeneration. Part of this work will be the creation of methodology for controlled simulation of mitochondrial function and activity in controlled environment. PhD students will complete a six-month internship at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

   Tutor: Čmiel Vratislav, Ing., Ph.D.

6. Advanced methods of fetal ECG signal processing measured transabdominally

   The theme of this dissertation thesis is measurement and processing of fetal ECG signals recorded by non-invasive way (transabdominally). The thesis has two main objectives. The first objective is to explore the area of monitoring and diagnosis of the fetus during pregnancy and delivery aimed at identifying and suppressing additive interference, especially suppression of the mother ECG. The second objective is to design methods for heart rate detection and fetal electrocardiogram extraction. Applicants are expected to have knowledge of programming in Matlab or Python and base knowledge of processing and analysis of 1D signals. PhD students will complete a six-month internships at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

   Tutor: Smital Lukáš, Ing., Ph.D.

7. Computational analysis and prediction of gene flow between bacteria

   The microbiome is the collection of microorganisms and their genetic material within an environment. It is a dynamic system which is also shaped by bacterial ability to horizontally transfer blocks of DNA between species. Horizontal gene transfer (HGT) by mobile elements plays a central role in the evolution and functions of well studied intestinal bacteria. However, most of microbiota has never been cultured and characterized so the composition of mobile elements remains poorly defined. Recently, hundreds of novel anaerobic bacteria of gut origin have been isolated, characterized and sequenced in a collaborative laboratory. The PhD topic will be focused on identification and characterization of mobile genetic material (e.g. transposons, plasmids, antibiotic resistance genes, hypothetical proteins) from individually sequenced gut microbiota members of human, chicken and porcine origin. To examine to which extent closely related species share horizontally acquired genes and to distinguish those from phylogenetically shared genes, new computational methods are of necessity. The database of identified mobile elements will be used as a reference for the computational isolation of HGT in metagenome sequencing data. Predicted behaviour of gene flow in human and animal gut, as well as between members of the sewage environment will serve as foundation for risk assessment of resistome evolution, and the potential spread of resistant genes in other environments. PhD students will complete a six-month internship at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

   Tutor: Čejková Darina, Mgr. Bc., Ph.D.

8. Genetic variation in cardiomyopathy and coronary artery disease

   Patients suffering cardiovascular diseases such as cardiomyopathy and coronary artery disease tend to cluster in families due to underlying monogenic or polygenic genetic architectures. The main aim of the project is search for genetic variation in these diseases in order to find causative genes and susceptibility loci. Distribution of the allele frequencies of the selected set of loci in a sample population will be analyzed and modelled. The study will be extended to identify loci that implicate pathways in blood vessel morphogenesis and inflammation related to the diseases. Data from 1000 Genomes Project and from CARDIoGRAMplusC4D Consortium project will be used to conduct large genome-wide bioinformatics analysis. There will opportunities to develop and apply research methodologies in statistical genetics and bioinformatics, develop skills in programming in high-level analysis packages, and develop skills in high-performance computing. PhD students will complete a six-month internship at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

   Tutor: Provazník Valentine, prof. Ing., Ph.D.

9. High resolution retinal image analysis

   The topic is based on the cooperation with University of Leipzig and will focus on the image sequences from retinal cameras with adaptive optics. The image data from this camera has very high spatial resolution and enables to analyze the retina at the level of individual photoreceptors. To enable this, a sequence of low-resolution images and appropriate processing into high resolution images is needed. The development of these methods is one of the topics of this thesis. Another part is the analysis of high resolution retinal images. In addition to the detection of photoreceptors, the wall thickness of the retinal arteries can be analyzed and evaluated. Because, automatic segmentation of the arterial wall is not solved yet, the development of automatic and robust methods for assessment of arterial wall thickness is highly needed. The topic is based on cooperation with the University of Leipzig, Institute for Medical Informatics, Statistics and Epidemiology. During the PhD study, regular scientific visits are expected and approximately six months' internship at this (or similarly oriented) institution. The study also includes presentation of scientific results at conferences abroad and publication in scientific journals. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

   Tutor: Kolář Radim, doc. Ing., Ph.D.

10. Medical image segmentation using deep learning techniques

    The theme of this thesis is aimed on medical image segmentation and classification using deep learning methods. The first aim of this thesis is to improve on actual methods for segmentation of 2D medical images. In next step these methods will be adapted for segmentation of 3D volume images, especially images from microCT system. The classification of images using deep learning methods will be also part of this thesis. Machine learning methods, especially neural networks, which represents new and perspective algorithms of image processing, will be used for the solution of this thesis. The main aim of this thesis is extend possibilities of automatic processing and classification of large volume of data like images from CT scanners. PhD students will complete a six-month internship at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

    Tutor: Harabiš Vratislav, Ing., Ph.D.

11. Methods and workflow for the analysis of host-pathogen interactions in the case of TBEV infection

    Tick-borne encephalitis virus (TBEV) is the causative agent of tick-borne encephalitis, a disease affecting annually over 10 000 people in Europe and Asia. TBEV circulates between ticks and their vertebrate hosts (e.g. mouse). The next generation sequencing (NGS) will be employed in order to identify host-pathogen interactions. The PhD topic will be aimed at the bioinformatic analysis of host responses involved in anti-TBEV response at the level of host cells, tissues and organs. Both, mRNA and miRNA expression profiles will be compared between infected and non-infected host cells/tissues/organs. Since TBEV elicits some kind of host immune reaction to promote viral replication, host candidate genes involved in TBEV replication will be determined (dry lab experiments) and silenced using RNA interference (wet lab experiments). The effect of silencing will be confirmed or rejected using NGS and subsequent analysis. PhD students will complete a six-month internship at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

    Tutor: Čejková Darina, Mgr. Bc., Ph.D.

12. New imaging approaches for retinal diagnosis

    This topic focuses on analysis of retinal video sequences. It covers several areas - from data acquisition, including hardware modification of an experimental video-ophthalmoscope to processing and analysis of acquired video-sequences. The focus will be mainly on multispectral ophthalmoscopy, which is a promising method for obtaining diagnostically valuable information, in addition to video-ophthalmoscopy. During this project, it is expected to modify the existing video-ophthalmoscope to a multispectral system, eventually another extension (e.g. adaptive optics). The processing of the measured sequences will then be focused on segmentation of vascular tree, evaluation of vascular pulsation and retinal tissue perfusion or pulse oximetry using multispectral sequences. PhD students will complete a six-month internship at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

    Tutor: Kolář Radim, doc. Ing., Ph.D.

13. Signal based genome assembly of nanopore sequencing raw data

    The aim of the dissertation is to develop method for direct genome assembly of signal reads from nanopore sequencing without the need of DNA symbols decoding. The decoding step (called “basecalling”) is the main source of errors in nanopore sequencing data processing. Although the nowadays basecalling methods for nanopore sequencing have significantly increased accuracy in the last years, it still can fall to 95 % and that is insufficient for clinical utilization. Each subsequent step of processing the genetic information following the decoding (as e.g. genome assembly) is influenced by finite accuracy. Therefore, the hybrid assembly requiring another sequencing technology in addition is used instead of true de novo assembly. Development of a new method for assembly genomes directly from raw signal reads (called “squiggles”) eliminates the need of other sequencing techniques, but will also allow real-time assembly during sequencing run. The applicant is expected being mastering basic methodology of processing and analysis of genomic data and should also have an overview in the field of processing and analysis of 1D signals. The programming in appropriate environment is commonplace. The topic will be solved in cooperation with the Children's Hospital - University Hospital Brno. PhD students will complete a six-month internship at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

    Tutor: Vítková Helena, Ing., Ph.D.

14. Utilization of signal processing techniques for refinement of nanopore sequencing data decoding

    The aim of the dissertation is to develop methodology for pre-processing of raw nanopore sequencing data consisting from signal reads called “squiggles”. The proposed procedure should precede DNA sequence decoding, where the neural networks are used exclusively nowadays. The decoding step called “basecalling” is the main source of errors in nanopore sequencing data processing. Although the nowadays basecalling methods for nanopore sequencing have significantly increased accuracy in the last years, it still can fall to 95 % and that is insufficient for clinical utilization. Appropriate combination of advance signal filtering of high level noise, signal segmentation into specific sections called “events” corresponding to DNA symbols and mutual adjustment of events durations by dynamic time warping can significantly improve accuracy of genetic information decoding. The applicant is expected being mastering basic methodology of processing and analysis of genomic data and should also have an overview in the field of processing and analysis of 1D signals. The programming in appropriate environment is commonplace. The topic will be solved in cooperation with the Children's Hospital - University Hospital Brno. PhD students will complete a six-month internship at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.

    Tutor: Vítková Helena, Ing., Ph.D.