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<font face="Arial, sans-serif"><font style="font-size:12pt">Dear
all, </font></font>
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<p style="margin-bottom:0cm;line-height:100%;background:transparent"><font face="Arial, sans-serif"><font style="font-size:12pt">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 <a href="https://www.ucy.ac.cy/hr/wp-content/uploads/sites/253/2024/04/REASON_-_PostgradResearcher_JobAnnouncement_2024.v2.pdf" style="color:rgb(0,0,128)">here</a>.
The closing date for applications is May 31st, 2024.</font></font></p>
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<p style="margin-bottom:0cm;line-height:100%;background:transparent"><font face="Arial, sans-serif"><font style="font-size:12pt"><b>Project
summary</b></font></font></p>
<p style="margin-bottom:0cm;line-height:100%;background:transparent"><font face="Arial, sans-serif"><font style="font-size:12pt">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.</font></font></p>
<p style="margin-bottom:0cm;line-height:100%;background:transparent"><font face="Arial, sans-serif"><font style="font-size:12pt">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 (<a href="http://www.biodynamo.org">www.biodynamo.org</a>), 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 (<a href="https://doi.org/10.1371/journal.pcbi.1003994" style="color:rgb(0,0,128)">link</a>).
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<p style="margin-bottom:0cm;line-height:100%;background:transparent"><font face="Arial, sans-serif"><font style="font-size:12pt"><b>Training</b></font></font></p>
<p style="margin-bottom:0cm;line-height:100%;background:transparent"><span style="font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal"><font color="#222222"><font face="Arial, sans-serif"><font style="font-size:12pt">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
(</font></font></font></span><a href="http://www.biodynamo.org/" style="color:rgb(0,0,128)"><span style="font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal"><font color="#000080"><font face="Arial, sans-serif"><font style="font-size:12pt">www.biodynamo.org</font></font></font></span></a><span style="font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal"><font color="#222222"><font face="Arial, sans-serif"><font style="font-size:12pt">).
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
(</font></font></font></span><a href="https://in-silico-modelling.ucy.ac.cy/" style="color:rgb(0,0,128)"><span style="font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal"><font color="#000080"><font face="Arial, sans-serif"><font style="font-size:12pt">https://in-silico-modelling.ucy.ac.cy/</font></font></font></span></a><span style="font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal"><font color="#222222"><font face="Arial, sans-serif"><font style="font-size:12pt"> </font></font></font></span><span style="font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal"><font color="#222222"><font face="Arial, sans-serif"><font style="font-size:12pt">and </font></font></font></span><a href="http://www.combynelab.com/" style="color:rgb(0,0,128)"><span style="font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal"><font color="#000080"><font face="Arial, sans-serif"><font style="font-size:12pt">www.combynelab.com</font></font></font></span></a><span style="font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal"><font color="#222222"><font face="Arial, sans-serif"><font style="font-size:12pt">).</font></font></font></span></p>
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<p style="margin-bottom:0cm;line-height:100%;background:transparent"><font face="Arial, sans-serif"><font style="font-size:12pt"><b>Supervisory
team</b></font></font></p>
<p style="margin-bottom:0cm;line-height:100%;background:transparent"><font face="Arial, sans-serif"><font style="font-size:12pt">The
project will be supervised by Dr Roman Bauer (<a href="mailto:r.bauer@surrey.ac.uk" style="color:rgb(0,0,128)">r.bauer@surrey.ac.uk</a>)
and Prof. Vasileios Vavourakis (<a href="mailto:vavourakis.vasileios@ucy.ac.cy" style="color:rgb(0,0,128)">vavourakis.vasileios@ucy.ac.cy</a>).
</font></font><font face="Arial, sans-serif"><font style="font-size:12pt">Interested
candidates are encouraged to contact either one of the supervisors in
case of questions.</font></font></p>
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<span style="display:inline-block;border:none;padding:0cm"><font face="Arial, sans-serif"><font style="font-size:12pt"><font color="#000000">Best
regards,</font></font></font></span></p>
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<span style="display:inline-block;border:none;padding:0cm"><font face="Arial, sans-serif"><font style="font-size:12pt"><font color="#000000">Roman</font></font></font></span></p><p style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;line-height:100%;background:transparent"><span style="display:inline-block;border:none;padding:0cm"><font face="Arial, sans-serif"><font style="font-size:12pt"><font color="#000000"><br></font></font></font></span></p>
<br><i>Roman Bauer, Ph.D.<br>Senior Lecturer<br>BioDynaMo Spokesperson<br>Computer Science Research Centre<br>University of Surrey<br>Guildford, UK</i>
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