Mgr. Miloslava Kollarčíková
Consultant
e‑mail: |
---|
Doctoral degree in full-time or combined form. The language of instruction is Czech.
The programme can be studied only as a single subject.
The aim of the study is to educate students in the field of life sciences and to prepare them as highly qualified specialists for scientific activities. The introductory part of the study concentrates on deepening theoretical and practical knowledge. At the same time, separate literary research on the assigned topic of the doctoral dissertation is being prepared. The core of students’ activities lies in their own scientific work. Students are guided by the supervisor to be able to independently implement all phases of a scientific project. They are also encouraged to the processing of the obtained experimental data methodologically relevant, as well as to their interpretation and subsequent presentation in various forms. The programme is highly multidisciplinary and, compared to the traditional study of biology, is more methodologically and analytically focused. Thanks to access to state-of-the-art infrastructure, students can better combine various biochemical, bioanalytical and visualization instrumental techniques with solving biological problems, which increases the impact of their scientific activities and their flexibility in the labor market, including positions in academia, e.g. within existing biotechnology companies or in newly emerging spin-offs.
The concept of the programme reflects the current level of scientific knowledge, the needs of the labor market, and overall trends in the field. At the same time, it benefits from the support system within the so-called CEITEC PhD School, which presents the concept of care for doctoral students involved in research teams at CEITEC and at the same time emphasizes expanding the competencies of the future graduates in socio-managerial, technological and soft skills. That will enable them to conduct their follow-up research in an efficient and modern way and provide them with a very good overview of the ethical aspects of research necessary for life sciences research and research and development in general.Life for Science. Science for Life.
The programme aims at the international employment of graduates. It is prepared in Czech and English versions, most subjects are taught, all seminars and, to a large extent, research is conducted in English. The environment at CEITEC MU is significantly international, so students are exposed to communication in English not only during official teaching but practically everywhere within CEITEC.
An important contribution to the acquisition of practical skills of DSP students of Life Sciences is their natural involvement in research teams at CEITEC MU. In this way, students can immediately acquire the necessary practical skills for team management and research projects, acquire networking skills and directly engage in research projects and grants (including H2020 projects and ERC grants) to understand the issues of research funding. Students can also routinely use eleven uniquely equipped shared laboratories and gain significant practical experience in this form within the so-called internal internship, or in another institution in the Czech Republic as part of an external internship (recommended volume is 10 working days (80 working hours).
A compulsory part of the study obligations in the doctoral study program is completing part of the study at a foreign institution for at least one month, or participating in an international creative project with results published or presented abroad or another form of student direct participation in international cooperation.
The program supports Collaborative PhD, i.e. completing a doctoral project in cooperation with a commercial entity. That allows students to expose themselves to a more non-academic environment. Also, within the TAC system, students cooperate more often with experts from practice.
The Office for Doctoral Studies, Quality, Academic Affairs and Internationalization takes care of doctoral students SCI MU
https://www.sci.muni.cz/en/students/phd
On the department's website, you can find the following information:
but also office hours, contacts, news, information on skills development and scholarships.
Detailed information on stays abroad can be found on this website:
https://www.sci.muni.cz/en/students/phd/develop-your-skills/stay-abroad
In the doctoral programme, great emphasis is placed on internationalization, there are also conditions for interdisciplinary solutions to the assigned topics of the dissertation, and the emphasis is placed on strengthening socio-managerial and soft-skills. This increases the real chances of graduates to apply in top scientific and technological, academic and commercial teams around the world, such as in:
Data from the previous admission procedure (1 Dec 2024 – 28 Feb 2025)
Requirements are specified in detail here. The admission procedure is carried out in two rounds. The first round is based on the application and background information - only complete applications with all mandatory parts will be accepted and reviewed. The applicants selected for the next round will be invited for the admission interview with the committee. Please check your e-mails, including spam folders.
Annotation:
This Ph.D. project is part of a national initiative to build a cutting-edge platform for storing and analyzing omics data, spanning genomic, epigenomic, transcriptomic, and proteomic datasets. The platform will be integrated with European networks created through the Genomic Data Infrastructure (GDI) project, enabling the sharing and analysis of data across borders, granting access to vast amounts of multi-omics data. This level of collaboration requires a federated approach, where data remains at local nodes, while computation and model training happen across distributed systems, ensuring both data privacy and security.
The primary goal of this Ph.D. will be to develop and orchestrate bioinformatics tools that leverage federated learning. These tools will facilitate scalable, collaborative computation across multiple European institutions, allowing local nodes to train models independently and contribute to a global model without centralized data storage. The Ph.D. candidate will design and deploy these federated bioinformatics tools, focusing on integrating long-read sequencing technologies - emphasizing the detection of structural variants and modeling methylation patterns - along with short-read sequencing data for a comprehensive analysis.
Federated learning will be crucial for efficiently processing the distributed datasets, allowing the platform to securely compute over sensitive data while preserving its informative value. By developing novel algorithms and workflows that integrate federated computing with omics data, the Ph.D. candidate will push the boundaries of current bioinformatics approaches. The research will lead to first-author publications, making significant contributions to both national and European scientific advancements in genomics, epigenomics, and multi-omics data integration.
Requirements for candidate:
The ideal candidate should possess strong IT skills, particularly in coding, machine learning, and data science, with a solid understanding of bioinformatics. Experience with sequencing data analysis, especially long-read and short-read technologies, is highly advantageous. Familiarity with federated computing concepts is also a plus.
PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340
Recommended literature:
1.Zhao, Y., et al. “Federated Learning with Non-IID Data.” Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics (2018).
2. Li, T., et al. “Federated Optimization in Heterogeneous Networks.” arXiv preprint arXiv:1812.06127 (2018).
3.Celi, L. A., et al. “Federated Learning Applications in Medicine: A Systematic Review.” PLOS Digital Health (2022).
4.Rieke, N., et al. “The Future of Digital Health with Federated Learning.” Nature Medicine 26 (2020): 1691–1700.
5.Wang, S., et al. “Privacy-Preserving Federated Learning for Bioinformatics Data Integration.” IEEE Transactions on Big Data (2022).
Dishevelled (DVL) is the central hub of Wnt signal transduction that integrates and transduces upstream signals through distinct cytoplasmic cascades. Looking at the many DVL faces reported in literature, three salient features underlying its function in signaling can be highlighted: (1) it interacts with more than seventy binding partners, (2) it is heavily phosphorylated at multiple sites by at least eight different kinases, in particular by Ck1epsilon/sigma after Wnt stimulation, and (3) it consistently forms puncta in the cytosol, that are phase-separated self-assemblies also called liquid droplets.
Our working hypothesis is that DVL conformational plasticity mediated by the order-disorder interactions allows the combinatorial integration of phosphorylation input, partners binding, self assembly in droplets, and allosteric coupling, to exquisitely control signal routing. We integrate structural biology (NMR, SAXS, X-ray, MS-HDX) and biophysical techniques (FRET, ITC, BLI) with cellular readouts (TopFlash, BRET) to understand DVL structure, function, and regulation. Candidates can choose among three open questions, that if resolved, will have significant impact on Wnt research.
1) Does disorder provide new contexts to structured domain(s) and, hence, enhance the DVL functional space associated with them?
2) Is there a direction, order or hierarchy in the phosphorylation of individual S/T sites and clusters in DVL?
3) What are the physical behaviors associated with intrinsic disorder and their connection to DVL liquid-liquid phase separation?
Requirements on candidates:
Biomolecular NMR, Biochemistry, Molecular Cell Biology
More information: RG Protein-DNA Interactions
PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340
Recommended literature:
Kravec M. et al. A new mechanism of posttranslational polyglutamylation regulates phase separation and signaling of the Wnt pathway protein Dishevelled. Embo J., 2024 (accepted)
Hanáková K. et al. Comparative phosphorylation map of Dishevelled 3 links phospho-signatures to biological outputs. Cell Commun. Signal., 2019. 17: p. 170
Harnoš J. et al. Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1. Nat. Commun., 2019. 10: p. 1804
Recommended literature:
Aleš Novotný, Jan Novotný, Iva Kejnovská, Michaela Vorlíčková, Radovan Fiala, Radek Marek. Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip. Nucleic Acids Research, 2021, 49, 11425. doi:10.1093/nar/gkab915.
Annotation:
With nearly 10 million lives claimed annually, cancer remains one of the leading causes of mortality worldwide, highlighting the urgent need for more effective treatments. One promising strategy involves mRNA-based cancer immunotherapy vaccines, which require a drug delivery system capable of reliably reaching the cytosol. Developing such delivery systems is challenging: they must ensure cytosolic delivery and therapeutic efficacy while maintaining safety, long-term stability, and compliance with scalable manufacturing standards - including high mRNA loading efficiency and uniform particle size. Current lipidand polymer-based systems offer distinct advantages but integrating lessons from both may help develop more effective next-generation carriers. A major limitation remains the incomplete understanding of nanoparticle assembly and disassembly under diverse physiological conditions (e.g., extracellular fluids, endosomal compartments, cytosol). This project will use coarse-grained molecular simulations, complemented by in-house experimental validation, to gain molecular insights in the controlled system assembly and disassembly. Our goal is to guide the rational design of improved mRNA delivery systems to advance the efficacy of cancer immunotherapy.
Requirements for candidate:
Msc in computational biophysics/chemistry/physics and related fields
Experience with Molecular Dynamics using coarse grained or atomistic models
Advantage is experience with simulations of disordered proteins/polymers and membranes
Excellent track record
Good English language – spoken and written
Motivated person with collaborative mind set
PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340
Recommended literature:
Paunovska K., et al.: Nat Rev Genet 2022, 23, 265–280, Doi: 10.1038/s41576-021-00439-4
Hou X., et al.: Nat Rev Mater 2021, 6, 1078–1094, Doi: 10.1038/s41578-021-00358-0
Yasuda I. et al.: J. Chem. Theory Comput. 2025, 21, 5, 2766–2779, Doi: 10.1021/acs.jctc.4c01646
Chew P.Y., et al.: Chem. Sci., 2023,14, 1820-1836, Doi: 10.1039/D2SC05873A
Requirements on candidates:
Motivated smart people who have the “drive” to work independently but are also willing to learn from other people in the lab and collaborate.
Candidates should have a master’s degree in Molecular biology, Biochemistry, or a similar field and have a deep interest in molecular biology and cancer cell biology.
More information: RG Microenvironment of Immune Cells
PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340
Recommended literature:
1. Hoferkova E, et al…. Mraz M. Stromal cells engineered to express T cell factors induce robust CLL cell proliferation in vitro and in PDX co-transplantations allowing the identification of RAF inhibitors as anti-proliferative drugs. Leukemia. 2024 Aug;38(8):1699-1711
2. Pavlasova G, et al…. Mraz M. Ibrutinib inhibits CD20 upregulation on CLL B cells mediated by the CXCR4/SDF-1 axis. Blood. 2016 Sep 22;128(12):1609-13. doi: 10.1182/blood-2016-04-709519. Epub 2016 Aug 1. PMID: 27480113 Free PMC article
3. Kipps et al. Chronic lymphocytic leukaemia. Nat Rev 2017 https://pubmed.ncbi.nlm.nih.gov/28102226/
4. Seda V, Mraz M. B-cell receptor signalling and its crosstalk with other pathways in normal and malignant cells. Eur J Haematol. 2015 Mar;94(3):193-205. doi: 10.1111/ejh.12427. Epub 2014 Sep 13. PMID: 25080849 Review.
Recommended literature:
1. Filbeck, S., et al., Ribosome-associated quality-control mechanisms from bacteria to humans. Mol Cell, 2022. 82(8): p. 1451-1466.
2. Ikeuchi, K., et al., Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways. EMBO J, 2019. 38(5).
3. Saito, K., et al., Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria. Nature, 2022. 603(7901): p. 503-508.
4. Narita, M., et al., A distinct mammalian disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation. Nat Commun, 2022. 13(1): p. 6411.
5. Wu, C.C., et al., Ribosome Collisions Trigger General Stress Responses to Regulate Cell Fate. Cell, 2020. 182(2): p. 404-416 e14.
Requirements for candidate: Master's degree in Chemistry/Biochemistry/Biology/Biophysics
PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340
Recommended literature:
Requirements for candidate:
Master's degree in Molecular or Cellular Biology/ Biochemistry /Chemistry / Biophysics
Prior experience with organoid production, induced pluripotent stem cells (iPSCs), or protein NMR spectroscopy is considered an asset.
PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340
Requirements on candidates:
Motivated smart people who have the “drive” to work independently but are also willing to learn from other people in the lab and collaborate.
Candidates should have a master’s degree in Molecular biology, Biochemistry, or a similar field and have a deep interest in molecular biology and cancer cell biology.
More information: RG Microenvironment of Immune Cells
PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340
Recommended literature:
1. Seda et al….Mraz FoxO1-GAB1 Axis Regulates Homing Capacity and Tonic AKT Activity in Chronic Lymphocytic Leukemia. Blood 2021 March (epub). https://pubmed.ncbi.nlm.nih.gov/33786575/
2. Pavlasova G, et al…. Mraz M. Ibrutinib inhibits CD20 upregulation on CLL B cells mediated by the CXCR4/SDF-1 axis. Blood. 2016 Sep 22;128(12):1609-13. doi: 10.1182/blood-2016-04-709519. Epub 2016 Aug 1. PMID: 27480113 Free PMC article
3. Seda V, Mraz M. B-cell receptor signalling and its crosstalk with other pathways in normal and malignant cells. Eur J Haematol. 2015 Mar;94(3):193-205. doi: 10.1111/ejh.12427. Epub 2014 Sep 13. PMID: 25080849 Review.
Provided by | Faculty of Science | |
---|---|---|
Type of studies | Doctoral | |
Mode | full-time | Yes |
combined | Yes | |
distance | No | |
Study options | single-subject studies | Yes |
single-subject studies with specialization | No | |
major/minor studies | No | |
Standard length of studies | 4 years | |
Language of instruction | Czech | |
Doctoral board and doctoral committees |
Consultant
e‑mail: |
---|