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EASTBIO Building an integrated mathematical model of a working eukaryotic nucleus

  • Full or part time
    Dr S Buonomo
    Dr R Grima
  • Application Deadline
    Sunday, January 05, 2020
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

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.

Funding Notes

The “Visit 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. Follow the instructions on the EASTBIO website (you will be directed here from our application checklist), ensuring you upload an EASTBIO application form and transcripts to your application, and ticking the box to request references. Your referees should upload their references using the EASTBIO reference form, in time for the 5th January deadline so please give them plenty of time to do this by applying early.


[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.

How good is research at University of Edinburgh in Biological Sciences?

FTE Category A staff submitted: 109.70

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