Linus Schumacher Research Group
Computational biology of cell populations
Tissue development and regeneration can be seen as group behaviours of cell populations. To understand development and regeneration, we need to consider the interactions between stem cells and the rest of the cells that make up a tissue. We use mathematical models and computational simulations to predict tissue behaviour from the behaviour of cells. This allows us to develop and test hypotheses in complex biological systems and discern informative patterns in experimental data.
Aims and areas of interest
The dynamics of a tissue in development and regeneration arises from the behaviour of its constituent cells and their interactions. In embryo development, initially homogeneous populations of cells have to acquire cell fates in specific proportions and spatial arrangements to enable tissue function. How do individual cells coordinate with their neighbours to achieve this? In adult tissues, cell populations have to self-regulate so as to enable regeneration after injury without over-proliferating in a malignant manner. How does regeneration only happen when needed, and how does it know when to stop?
We use mathematical models and statistical inference methods to infer from various experimental data the most likely cellular behaviours and regulatory mechanisms underlying changing tissue states. Example methods include birth-death process models of stem cell dynamics, extending such models by incorporating regulatory interactions and additional or intermediate cell states, and machine learning tools to learn cell-cell interaction models directly from data in interpretable ways. The applications range from in vitro models of embryo development to adult tissue regeneration that is disrupted in ageing or cancer.
By developing theoretical models we also bring new perspectives on how to interrogate experimental data. We work closely with experimental collaborators with the aims to formulate principles that apply to multiple biological systems, gain insight into misregulation in disease, and inform improvements to regenerative therapy.
Dan Tudor (Research Fellow)
Giuseppi Torrisi (Research Fellow)
Rodrigo Garcia (PhD Student)
Alex Richardson (PhD Student, co-supervision with Richard Blythe and Tibor Antal)
Eric Latorre Crespo (XDFellow)
Lucy Martin (XDFellow)
Miguel Robles Garcia (PhD student, co-supervision with Guillaume Blin)
Anna Popravko (PhD student, co-supervision with Elaine Dzierzak)
Viktoria Freingruber (PhD Student, co-supervision with Maria Ptashnyk & Kevin Painter)
Jaemthaworn (Keng) Thanakorn (PhD Student)
Luciana Luque (Researcher)
Cameron Kerr (PhD Student)
Tamir Chandra (University of Edinburgh)