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EASTBIO Building an integrated mathematical model of a working eukaryotic nucleus

School of Biological Sciences

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Dr S Buonomo , Dr R Grima No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

The eukaryotic nucleus is a crowded space where millions of processes take place simultaneously. Simulations have shown that macro-molecular crowding has a strong influence on intracellular dynamics [1,2]. Hence accurate spatial organisation is likely crucial to ensure proper nuclear and cellular function.

In recent years, new technologies have helped us to collect large datasets, describing individual processes more comprehensively than in the past. However, a functional nucleus does not emerge from millions of single processes, but from their integration. In this ambitious project we will start attempting the computational integration of a large-scale data-set acquired by the Buonomo lab [3] for mouse embryonic stem cells, to incorporate DNA replication timing (Repli-seq) and gene expression data (RNA-seq) into the three-dimensional organisation of chromatin described through HiC data. The ultimate goal is to build an integrated mathematical model of a working eukaryotic nucleus. The project will be jointly supervised by Dr Buonomo and Professor Grima who have extensive expertise covering all aspects of the experimental and computational methodology.

We are looking for an enthusiastic, flexible and hard-working candidate driven by curiosity and passion for science. A strong background in computer science, applied mathematics, informatics or physics is preferred, but a deep interest in the biological world is essential.

The School of Biological Sciences is committed to Equality & Diversity:

How to Apply:
The “Institution Website” button will take you to our Online Application checklist. Complete each step and download the checklist which will provide a list of funding options and guide you through the application process.

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition fees. The fee difference will be covered by the University of Edinburgh for successful international applicants. Please refer to UKRI website ( and Annex B of the UKRI Training Grant Terms and Conditions ( for full eligibility criteria.


[1] Grima, R., and S. Schnell. "A systematic investigation of the rate laws valid in intracellular environments." Biophysical chemistry 124.1 (2006): 1-10.

[2] Smith, Stephen, Claudia Cianci, and Ramon Grima. "Macromolecular crowding directs the motion of small molecules inside cells." Journal of the Royal Society Interface 14.131 (2017): 20170047.

[3] Foti, Rossana, et al. "Nuclear architecture organized by Rif1 underpins the replication-timing program." Molecular cell 61.2 (2016): 260-273.
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