Last Date: Friday, December 13, 2024
Supervisors: Dr Rachel Queen, Dr Andrew Mason, Prof Majlinda Lako
Competition Funded PhD Project (Students Worldwide)
Newcastle University MRC DiMeN Doctoral Training Partnership
About the Project
Project Overview
Age-related retinal degeneration is a leading cause of blindness and is linked to unhealthy aging and an increased risk of depression and social isolation. Precisely timed gene regulation is needed to form and maintain a healthy functioning retina, which is an intricate network of light-sensitive neurons at the back of the eye. Transposable Elements (TEs), once dismissed as “junk DNA,” are now recognised as crucial regulators of gene expression, particularly in neuronal tissues like the retina, but their role in this vital tissue has yet to be explored. Our preliminary analysis indicate these elements are active during retinal development.
This project will leverage the large datasets generated by the Human Cell Atlas (HCA) to investigate the role of TEs—especially LINE-1 (L1) elements—in retinal development, aging, and degeneration. Using cutting-edge single-cell sequencing technologies, this PhD offers an exciting opportunity to learn new skills in computational biology, develop novel bioinformatics pipelines, and unveil the contribution of TE activity to retinal health and disease.
About The Candidate
The successful candidate for this project will:
Learn advanced bioinformatics techniques for single-cell data analysis.
Develop pipelines to classify and analyse TEs in complex, high-throughput datasets.
Investigate TE-driven gene regulation in human retinal development and aging.
The ideal candidate for this PhD will be driven, self-motivated, with a passion for understanding gene-regulation and neuronal biology. They should be eager to learn, explore and develop novel computational analysis techniques. Working with leading experts in single cell technologies, retinal biology, stem cell technologies and transposable elements, will ensure that they are fully trained in highly transferable research skills, during this interdisciplinary project. These will include: bioinformatics, molecular biology, neuroscience and cell biology which will support their development as a scientist. Whilst full training will be provided, experience using R/Python would be an advantage and candidates with a degree in bioinformatics or computational biology would be particularly suited to this PhD.
Our team prioritises student wellbeing, equality, and inclusivity, and the student will be fully supported to encouraged in growth as a researcher.
Why This PhD?
Innovative Science: Be the first to study transposon activity at the single-cell level in the retina, advancing our understanding of how these elements regulate gene expression in development and aging.
Timely Impact: With the publication of the first human eye cell atlas in early 2025, you’ll have access to cutting-edge data for transformative insights into retinal biology.
Interdisciplinary Training: Gain expertise in single-cell bioinformatics, pipeline development, and neurodegeneration research—highly sought-after skills in academia and industry.
Real-world impact: Contribute to discoveries in retinal biology and neurodegeneration, with the potential to influence future treatments and therapies.
Analytical Focus: This project is 100% computational and is ideal for someone with strong analytical skills and a passion for computational biology. It provides an opportunity to develop and apply advanced bioinformatics methods with real-world applications in biomedical research.
To find out more about this project please email the supervisors and visit:
https://www.ncl.ac.uk/medical-sciences/people/profile/rachelqueen.html
https://www.york.ac.uk/biology/people/masonandrew
https://www.ncl.ac.uk/medical-sciences/people/profile/majlindalako.html
Benefits of being in the DiMeN DTP:
This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle, York and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of-the-art facilities to deliver high impact research.
We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.
Being funded by the MRC means you can access additional funding for research placements, training opportunities or internships in science policy, science communication and beyond. Further information on the programme and how to apply can be found on our website:
Funding Notes
Studentships are fully funded by the Medical Research Council (MRC) for 4yrs. Funding will cover tuition fees, stipend (£19,237 for 2024/25) and project costs. We also aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of full studentships to international applicants. Please read additional guidance here: View Website
Studentships commence: 1st October 2025
Good luck!
References
Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina, Nature Communications (2024) 15: 3567 https://pubmed.ncbi.nlm.nih.gov/38670973/
Deciphering the spatiotemporal transcriptional and chromatin accessibility of human retinal organoid development at the single-cell level, iScience (2024) 27: 109397 https://pubmed.ncbi.nlm.nih.gov/38510120/
Spatial transcriptomics reveals novel genes during the remodelling of the embryonic human arterial valves, PloS genetics (2023) 19: e1010777 https://pubmed.ncbi.nlm.nih.gov/38011284/
Exploration of the single-cell transcriptomic landscape identifies aberrant glomerular cell crosstalk in a murine model of WT1 kidney disease, The Journal of Pathology https://www.biorxiv.org/content/10.1101/2022.10.11.511555v2
A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants, BMC Biology (2023) 21:267 https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-023-01758-0
Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data, Mobile DNA (2020) 11:22
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