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Doctoral School in Biomedical Sciences - MCB offer

Doctoral School in Biomedical Sciences - MCB offer

MCB is an international, research only, institute of the Jagiellonian University and is focused on delivering world class research in the areas of genomics, bioinformatics, cellular mechanisms, virology, plant biology and structural biology. The director and many of the group leaders are from abroad bringing a dynamic and truly international feel to the institute. Indeed over 25% of our current Ph.D. students are non-polish. The working language of the institute is English and we actively encourage applications to our doctoral school from abroad.

As a research institute established in 2013, we have grown into a thriving community of 12 principal investigators and 3 early career junior investigators with team sizes varying from about 5 to 30 people. 

Our investigators are highly successful in securing prestigious internal and international grants (such as EMBO and Horizon 2020) and this year alone, we have secured over 7M € in funding.  Indeed our Ph.D. students also regularly apply and are successful in receiving grants with 3 winners having just been announced in May. This means that research is well funded and we have well-equipped labs including some state of the art equipment enabling mass spectrometry, next-generation sequencing, flow cytometry, confocal microscopy, protein sequencing, peptide synthesis, category 3 laboratories that are enabled for coronavirus research. Access to the National Cryo-EM Centre at the neighboring Solaris synchrotron will ensure that MCB has access to state of the art facilities for structural biology. We are located close to the life-science cluster that hosts dozens of medium to small life science companies including Ryvu and Selvita and we have numerous collaborations with industrial partners. Our environment and culture have enabled publications in high impact journals such as Nature and students at MCB can participate in the vibrant and flourishing research community.

We currently host 66 Ph.D. students and the vast majority of our students are funded from project grants secured by our excellent senior and junior principal investigators with all benefits coming from it. In line with the changes across Poland, Ph.D. students apply to our doctoral schools and applications in 2020, will be the second year of entry through the Biomedical Sciences Programme, Doctoral School of Exact and Natural Sciences.y

Detailed information on the Biomedical Sciences Ph.D. programme can be found here.

Ph.D. project areas & supervision

Bioinformatics Research Group

Paweł Łabaj
1)
Project title: Fine-tuned machine learning based data science solutions for multiple bioinformatics applications
Project description: In post-genomic era of Big Data in life sciences the feature selection and dimensionality reduction of omics data is a crucial challenge. It allows to reduce the problem complexity and apply the best suited machine learning approach. The successful candidate will be responsible for developing fine-tuned machine learning based data science solutions for multiple bioinformatics applications. From one end the focus will be on application to environmental metagenomics data analysis to uncover the molecular profiles of the urban microbiome. From the other supported by multi-omics data integration will apply to patient stratification and diagnostic.

Tomasz Kościółek
1)
 Project title: New bioinformatics methods for the analysis and understanding of the human gut microbiome
Project description: We focus on the development of new bioinformatics methods for the analysis and understanding of the human gut microbiome. The project will focus on a thorough re-analysis of currently available longitudinal microbiome datasets using the newly developed machine-learning based bioinformatics techniques, as well as refinement and future development of those analytical approaches. The student is expected to have a strong quantitative background, including a good working knowledge of at least one programming language (ideally, Python) and an active interest in machine learning; interest, and experience in microbiome analyses or metagenomics is a plus.

Developmental Biology Laboratory

Grażyna Ptak
1)
Project title:  DNA damage repair ability of the embryo before implantation
Project description: The project will explore the potential of the blastocyst to be repaired from DNA damage induced by embryo/sperm irradiation. We are seeking a motivated Ph.D. candidate that is interested in experimental embryology and reproductive medicine. The student will perform molecular and image analysis of embryos and cells, oocyte micromanipulations as well as surgeries based on a mouse model. The project is based on a collaborative network with University of Wurzburg (Germany), Nencki Institute of Experimental Biology (Warsaw), and Bionanopark Ltd. (Łódź). International secondments and additional funding might become available for the student during the course of the project.

2) Project title:  In vivo and in vitro characterization of the developmental potential of embryos and offspring obtained following embryonic diapause
Project description: The project will concentrate on the characterization of embryonic and adult cells derived from diapaused embryos. Embryonic diapause is a reversible arrest of the blastocyst stage embryo. We are seeking a motivated Ph.D. candidate that is interested in basic embryology and reproductive biology. The student will perform a wide range of developmental and cell biology techniques, embryonic stem cells derivation, cell lines characterization, RNA and protein analysis, mouse surgeries ect. The project is carried out in collaboration with the University of Wurzburg (Germany). International secondments and additional funding and might become available during the course of the project.

Structural biology -  Max Planck Laboratory

Sebastian Glatt
1)
Project title: Single-particle cryo-EM in tRNA biology
Project description: The project is based on our fundamental interest in tRNA biology. The advent of Cryo-EM has opened the possibility to look at individual biological molecules directly without the need of forming crystals (MX) or using labeling methods (NMR). We are seeking a motivated Ph.D. candidate that is interested in working in a highly interdisciplinary project, which is placed at the interface between RNA biochemistry and bioinformatics that will provide intense training in single particle cryo-EM. The project is based on a collaborative network with the IIMCB (PL), Sichuan University (CHN), and Stanford University (USA). Additional funding might become available during the course of the project 

2) Project title: Structural and functional characterization of large macromolecular complexes involved in translational control in eukaryotes
Project description: The project will focus on the structural and functional characterization of large macromolecular complexes involved in translational control in eukaryotes. The project will include the production of different multi-subunit protein complexes in insect cells and their structural characterization using single particle Cryo-EM. We are seeking for a motivated Ph.D. candidate that is interested in protein biochemistry, biophysics and structural biology. The project is based on collaborative projects with the University of Bern (CH), University of Regensburg (GER), the MPI for biophysical chemistry (GER) and the University of Queensland (AUS). Additional funding might become available during the course of the project.

Microbial Genomics Group

Rafał Mostowy
1) Project title: Evolutionary microbial genomics and bioinformatics
Project description: I would like to propose a Ph.D. project for the MCB doctoral school in the area of evolutionary microbial genomics. The successful student would carry out the project in the Microbial Genomics Group. The goal of the project would be to use the latest advancements in bioinformatics to analyse the genetic diversity of bacterial surface molecules and of prophages in large collections of bacterial genomes and to understand how they co-evolve. The project would help us assess both qualitative and quantitatively how clinical bacteria evolve and how phages contribute to the emergence of bacterial superbugs.

Plant Molecular Biology Laboratory

Kenji Yamada
1)
 Project title: Plant defence by using the glucosinolate-myrosinase system - ER body system & myrosin cell development
Project description: Our group is investigating the plant defence system against pests and pathogens through cellular and molecular biological analysis. Cabbage family plants accumulate beta-glucosidases in myrosin cells and ER bodies to produce defensive metabolites. The successful candidate will investigate the differentiation of myrosin cells and ER body-accumulating cells during leaf development and in response to environmental stress.

Protein Crystallography Research Group

Grzegorz Dubin
1)
Project title: Structural and functional characterization of peroxisomal protein transport system (PEX)
Project description: Peroxisomal transport system (PEX) translocates functional enzymes from the cytoplasm into the peroxisomes. Several dozen PEX proteins are involved in translocation of fully folded cargo enzymes through peroxisomal membrane, but this intriguing process is currently poorly understood at the mechanistic level, a topic of vivid current investigation. The project is carried out in collaboration with Helmholtz Centrum in Munich, Technical University in Munich, Bochum University and the University of Warsaw.

2) Project title: Targeting the diabetic kinome for the restoration of pancreatic islet function
Project description: The successful candidate will explore the potential of pharmacological intervention into diabetic kinome for the restoration of pancreatic islet cell mass and function in diabetes. The project encompasses the structural characterization of target-inhibitor complexes for rational improvement of inhibitor potency and retargeting. The primary focus of the Ph.D. will be on structural biology with elements of cell biology. The inhibitors will be combined with patient-derived induced pluripotent stem cells (iPSCs) and nanodelivery systems for an effective and personalized cure for diabetes. The project is carried out in collaboration with laboratories in Germany, France, and China.

Get to know what some of our current students think:

“I’m a Ph.D. student working in prof. Dubin’s laboratory. I’m focusing mostly on structural research on a protein that acts as an adaptor protein for inflammatory signaling pathways, trying to know its molecular structure using crystallographic techniques.
The decision to begin a Ph.D. program at MCB gives me the capacity to work with gifted and inventive individuals. Lack of teaching duties gives us more time to focus on our research in the lab and it is a huge plus. Working at MCB gives me access to highly specialized equipment my lab is organized to meet every requirement for efficient protein production and crystallization for further structural studies. Not mentioning the state-of-the-art protein purifying systems, all of them significantly contributing to my Ph.D. project work."
 

~ Oskar – doctoral student’s president,  Protein Crystallography Research Group

„I came to do my Ph.D. at MCB as Dr. Yamada is one of the pioneers working on ER-bodies and their role in plant-environment interaction. Therefore working with him is the best thing that I could think of.”

~ Arpan, Plant Molecular Biology Laboratory

“We have a great environment around here at MCB, the labs are very diverse so we can really learn about detailed research in completely remote fields. The Institute is also relatively new so we can mold it to what we expect and this is truly a gift.”

~ Norhane, Max Planck Research Group (Structural biology)

“I like in Ph.D. Programme that we have freedom of thoughts, great support and great possibilities for self-development”

~ Michal, Bioinformatics Research Group

“MCB is attractive as a modern, vibrant research center, with interesting and competitive research projects. In addition, having a supportive group leader, and colleagues a conducive environment to pursue the Ph.D.”

~  Dedan, Bioinformatics Research Group