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Computational image analysis assisted optimisation of retinal organoid cryopreservation

Project Description

Interested in using computers to better understand biology? Then this project might be what you are looking for! The aim is to use novel software and high-performance computers, in order to analyse retinal tissue after freezing and thawing. By improving our knowledge of how cryogenic processing affects this neural tissue, new methodologies for cryogenic processing will be studied. To this end, the student will work together with experts in the field, conduct wet-lab experiments, cryogenically process artificial retinal tissue obtained from stem cells, learn to use modern Artificial Intelligence tools to extract valuable information from experiments, and produce novel hypotheses that will generate better methodologies.

This project will enable you to gain highly interdisciplinary skills. In particular, you will be based at Newcastle University while collaborating with Liverpool University. Moreover, you will be regularly visiting Asymptote Ltd (GE Healthcare) in Cambridge. There, you will learn the usage of the latest cryogenic processing hardware and techniques. Furthermore, you will visit CERN to obtain training in modern computational biology tools (https://biodynamo.web.cern.ch).

You will be supervised by a multidisciplinary team comprising experts from the experimental, computational and industrial disciplines of cryopreservation. In particular, you will participate at weekly lab meetings of the supervisory team (Dr Roman Bauer, Professor Majlinda Lako, Dr Peter Kilbride and Dr Joao Pedro De Magalhaes), and present your findings at international conferences and scientific journals.

Informal enquiries about the project are very welcome by email to Dr Roman Bauer ().

Applications should be made by emailing with a CV (including contact details of at least two academic (or other relevant) referees), and a covering letter – clearly stating your first choice project, and optionally 2nd and 3rd ranked projects, as well as including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project(s) and at the selected University. Applications not meeting these criteria will be rejected.
In addition to the CV and covering letter, please email a completed copy of the Additional Details Form (Word document) to . A blank copy of this form can be found at: https://www.nld-dtp.org.uk/how-apply.

Funding Notes

This is a 4 year BBSRC CASE studentship under the Newcastle-Liverpool-Durham DTP. The successful applicant will receive research costs, tuition fees and stipend (£15,009 for 2019-20). The PhD will start in October 2020. Applicants should have, or be expecting to receive, a 2.1 Hons degree (or equivalent) in a relevant subject. EU candidates must have been resident in the UK for 3 years in order to receive full support. Please note, there are 2 stages to the application process.


Human‐induced pluripotent stem cells generate light responsive retinal organoids with variable and nutrient‐dependent efficiency. Stem Cells 36, no. 10 (2018): 1535-1551

Decellularised extracellular matrix-derived peptides from neural retina and retinal pigment epithelium enhance the expression of synaptic markers and light responsiveness of human pluripotent stem cell derived retinal organoids. Biomaterials 199 (2019): 63-75

Disrupted alternative splicing for genes implicated in splicing and ciliogenesis causes PRPF31 retinitis pigmentosa. Nature communications 9, no. 1 (2018): 4234

Cryoprotectant toxicity: Biochemical mechanisms and functional genomics. Cryobiology 71, no. 1 (2015): 173

A new approach for interpreting random forest models and its application to the biology of ageing. Bioinformatics 34, no. 14 (2018): 2449-2456

Structural connectivity centrality changes mark the path toward Alzheimer's disease. Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring 11 (2019): 98-107

Developmental self-construction and-configuration of functional neocortical neuronal networks. PLoS Comput Biol 10, no. 12 (2014): e1003994

Spatial considerations during cryopreservation of a large volume sample. Cryobiology 73, no. 1(2016), 47-54

Physical events occurring during the cryopreservation of immortalized human T cells. PloS ONE 14, no. 5 (2019) e0217304

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