A fully funded PhD position in Computational Neuroscience is available at the University of Cyprus in collaboration with the University of Surrey (UK), titled “Brain Neuronal Networks Development via Multiscale Agent-based Modelling”. More details are available here. The closing date for applications is May 31st, 2024.

Project summary

Here, we will demonstrate an innovative computational approach to model and emulate biological neural networks (NNs): rather than directly modelling a brain with all its complexity, we will model NN development from a single precursor cell. In other words, by leveraging the same approach that nature uses to build brains, we aim to reproduce challenging neural complexities. Inspired by the biological brain, we will make use of developmental rules that are encoded in a gene-type manner. For instance, a rule could be that a given neural stem cell should divide under certain conditions while they could migrate under others. Similarly, neural connections develop according to well-conserved mechanisms that are adaptive to individual neurons’ activities and wiring patterns.

To inform the computational modelling, we will make use of data from experimental studies as well as synthetic, simulated data. Well-established characteristics of biological NNs will be used to inform realistic NNs, both structurally as well as functionally. We will make use of innovative machine learning techniques to match the in-silico NNs with specific organisms. In the early stages, we will employ synthetically generated NNs as a test scenario, and iteratively increase biological correspondence. We will make use of the agent-based modelling software BioDynaMo (www.biodynamo.org), an open-source software we have been actively developing for almost a decade. Notably, this project builds on previous work of the supervisory team, including for instance the simulation of a spatially embedded, functional, and biologically realistic neural network that self-organized from a single precursor cell (link).

Training

The studentship is highly interdisciplinary, because it is at the interface of computer science and neuroscience. Machine learning will constitute a core component of this studentship. This work will benefit from the prestigious BioDynaMo collaboration (www.biodynamo.org). Tight involvement with the collaboration will support the student in obtaining training in the usage of modern computational biology methodologies. Moreover, the student will benefit from weekly seminars and daily interactions with computational and experimental researchers, as well as the research groups of the supervisors (https://in-silico-modelling.ucy.ac.cy/ and www.combynelab.com).

Supervisory team

The project will be supervised by Dr Roman Bauer (r.bauer@surrey.ac.uk) and Prof. Vasileios Vavourakis (vavourakis.vasileios@ucy.ac.cy). Interested candidates are encouraged to contact either one of the supervisors in case of questions.