About the employer
KU Leuven is an autonomous university. It was founded in 1425. It was born of and has grown within the Catholic tradition.
Visit the employer pageKU Leuven is an autonomous university. It was founded in 1425. It was born of and has grown within the Catholic tradition.
Visit the employer pageThe Department of Oncology at KU Leuven accommodates over 500 researchers in almost 30 research groups and is one of the global leaders in multiple fields of cancer research. Laboratory for Computational Cancer Biology and Epigenomics is a new research group focusing upon computational method development and analysis of high-dimensional data to understand cancer epigenomics. Our prime interests are epigenetic mechanisms and their role in tumorigenesis. Skeletal Cell Biology and Physiology Lab led by prof. Christa Maes at the Center for Skeletal Biology and Engineering Research is a leading group in biology of quiescent stem cell biology studying mechanisms of bone formation in development and growth, postnatal homeostasis, disease and ageing, and during fracture repair.
If you are interested in our group, please find more information via the link below.
Stem cells are essential for the formation and maintenance of all tissues. Skeletal system is not an exception, with multiple stem cell populations identified in bone and cartilage, predominantly through the work in mouse models [1]. Despite these advances, details of their specific functions, regulation, phylogeny and relation to human stem cell populations are poorly understood. Furthermore, skeletal stem cells are likely giving rise to aggressive bone tumors, such as giant cell tumor of bone (GCTB) driven by a hotspot mutation in a histone variant H3.3 [2], turning them into important therapeutic targets. The Ph.D. project will focus on omics-based characterization of stem cell populations in mouse and human skeletal system and identifying their contribution to epigenetically-driven skeletal tumors. We will generate single-cell and spatial multiomics data and combine them with already existing in-house and public skeletal cell atlases. The project will also aim to further develop computational methods for cross-species single-cell multiomics integration. Our previous deep learning methods have been successfully applied to various human single-cell multiomics data analyses [3, 4]. Therefore, we plan to extend these to find a joint landscape of human and mouse single-cell multiomes and draw novel in-depth analyses on the single-cell skeletal multiomics data: integration of single-cell transcriptomes and epigenomes of human and mouse skeletal cell populations, trajectory inference for different populations and identification of most likely cell-of-origin for tumor cells.
[1] Lutsik et al. Globally altered epigenetic landscape and delayed osteogenic differentiation in H3.3-G34W-mutant giant cell tumor of bone. Nature Communications, 2020.
[2] Jeong et al. scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data. BMC Bioinformatics, 2024.
[3] Moeed et al. Identifying Effects of Disease on Single-Cells with Domain-Invariant Generative Modeling. NeurIPS workshop CRL, 2023.
[4] Trompet et al. Skeletal stem and progenitor cells in bone development and repair, Journal of Bone and Mineral Research, 2024.
We offer a full time PhD position for 48 months, given positive evaluation by the doctoral committee at the end of the first year. A successful PhD candidate will be immersed into a vibrant and highly stimulating scientific environment within the Department of Oncology, VIB-KU Leuven Center for Cancer Biology as well as Skeletal Cell Biology and Engineering Research Center, with ample possibilities to interact with researchers from other groups. For their project the candidate will obtain access to cutting-edge datasets and computational infrastructure. The project will involve regular contacts with collaboration partners across Europe, presentations at scientific conferences and meetings. Beyond that, you will have access to versatile options for personal growth and development, advanced qualification courses and mentoring available via KU Leuven and affiliated institutions.
For more information please contact prof. Pavlo Lutsik, tel.: +32 16 32 30 09, mail: pavlo.lutsik@kuleuven.be.
KU Leuven strives for an inclusive, respectful and socially safe environment. We embrace diversity among individuals and groups as an asset. Open dialogue and differences in perspective are essential for an ambitious research and educational environment. In our commitment to equal opportunity, we recognize the consequences of historical inequalities. We do not accept any form of discrimination based on, but not limited to, gender identity and expression, sexual orientation, age, ethnic or national background, skin colour, religious and philosophical diversity, neurodivergence, employment disability, health, or socioeconomic status. For questions about accessibility or support offered, we are happy to assist you at this email address.
KU Leuven is an autonomous university. It was founded in 1425. It was born of and has grown within the Catholic tradition.
Visit the employer page