Regular recruitment (10 openings; deadline 10th July)
Go to the How to apply page to learn how to apply to the Doctoral Programme and get to the project.
Bioinformatics Research Group
Dr. 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.
Dr. 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
Prof. 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 the 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 developmental potential of embryos and offspring obtained following embryonic diapause.
Project description: The project will concentrate on characterization of embryonic and adult cells derived from diapaused embryos. Embryonic diapause is a reversible arrest of the blastocyst stage embryo. We are seeking for a motivated Ph.D. candidate that is interested in basic embryology and reproductive biology. The student will perform 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 University of Wurzburg (Germany). International secondments and additional funding and might become available during the course of the project.
Max Planck Laboratory
Dr. 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 for 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 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 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), the 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
Dr. Rafał Mostowy
1) Project title: Reconciling variation of bacterial mobile genetic elements using assembly
Project description: I would like to propose a PhD 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 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
Dr. 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
Prof. 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 University of Warsaw.
2) Project title: Targeting the diabetic kinome for restoration of pancreatic islet function
Project description: The successful candidate will explore the potential of pharmacological intervention into diabetic kinome for restoration of pancreatic islet cell mass and function in diabetes. The project encompasses structural characterization of target-inhibitor complexes for rational improvement of inhibitor potency and retargeting. The primary focus of the PhD 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.