Mylnefield Trust Scholars: Identification of target genes for control of economically important plant pathogens using large foundation models
1 week ago
Background: Large Foundation models (LFMs) are deep learning models that are trained on broad collections of text, images or other data and act as the basis behind many current artificial intelligence applications, such as ChatGPT. Recently, LFMs have also shown promising results in biology, drawing parallels between language (word sequences) and cells (gene and protein sequences). LFMs can also capture and make predictions on gene regulatory relationships in a context (e.g. cell type, tissue, development stage, etc). In addition, transfer learning allows LFMs to be repurposed for different tasks through finetuning with only minimum computational effort and training data required. Using LFMs to decipher gene regulations in human has shown great potential in perturbation studies, including gene deletions1-4. This project will leverage this powerful cutting-edge technology by generating LFMs for fungal gene regulatory networks using public -omics data and through transfer learning, predicting essential genes.
Objectives: (1) Develop computational models that capture the complex gene regulations of fungal species; (2) Use public condition-dependent gene essentiality data to finetune models to identify genes crucial for pathogen control; (3) Validate the model predictions using unseen Syngenta gene essentiality data.
This 4 year studentship opportunity is open to UK students and provides funding to cover stipend, UK tuition fees and consumable/travel costs.
Students must meet the eligibility criteria as outlined in the UKRI guidance on UK and international candidates. Applicants will have a first-class honours degree in a relevant subject or a 2.1 honours degree plus Masters (or equivalent).
This project is based at the Dundee site of the James Hutton Institute, UK.
We will not consider the use of 3rd party recruitment agencies for the sourcing of candidates for this position.
The James Hutton Institute is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees.
The James Hutton Institute is a: Stonewall Diversity Champion; Athena SWAN Bronze Status Holder; Disability Confident Committed Employer and a Living Wage Employer.
The James Hutton Institute is Happy to Talk Flexible Working.
-
Dundee DD DA, United Kingdom The James Hutton Institute Full time £25,000 - £40,000 per yearBackgroundMicronutrients, including copper, zinc, and iron, are elements that are necessary for healthy growth and development in plants and humans, despite being required in small amounts. In plants, copper underpins photosynthesis, which is an essential process, allowing them to grow and in the case of cereal plants, produce viable grain. Zinc is another...
-
Dundee DD DA, United Kingdom The James Hutton Institute Full time £25,000 - £35,000 per yearLegumes such as beans and peas are central to sustainable food systems, providing dietary protein and many other nutrients, contributing to sustainable soil fertility and supporting climate-resilient agriculture. However, their productivity is increasingly constrained by abiotic stresses such as drought, salinity, and extreme temperatures, which are expected...
-
Dundee DD DA, United Kingdom The James Hutton Institute Full time £30,000 - £50,000 per yearThis project is based at the James Hutton Institute (JHI), a global leader in cereal genetics and home of the International Barley Hub (IBH).The project aims at gaining novel insight into how plants acquire and maintain optimal levels of Manganese, an essential micronutrient whose availability impacts multiple aspects of plant growth and development. This...
-
Dundee DD DA, United Kingdom The James Hutton Institute Full time £25,000 - £35,000 per yearDeveloping crop cultivars that are resilient to climate change and can help mitigate its effects will be critical to supporting healthy soils and reducing the environmental impact of food production. Key to this are the interactions plants have with soil microorganisms. Plants can influence microbial communities in the soil by releasing chemicals known as...
-
Dundee DD DA, United Kingdom The James Hutton Institute Full time £25,000 - £40,000 per yearBackground – Most potato (Solanum tuberosum) varieties are highly sensitive to elevated temperature, reflecting their origin in the cool climates of the Andes in South America. This project directly targets critical knowledge gaps surrounding sustainable potato production: the loss of marketable yield and tuber quality under stress. With climate change...
-
Molecular Microbiologist/plant Pathologist
2 weeks ago
Dundee, United Kingdom The James Hutton Institute Full timeWe are seeking a motivated post-doctoral researcher in molecular microbiology or plant pathology to join our dynamic research team for a 3-year position, starting 1st October 2025, investigating the fascinating molecular mechanisms behind blackleg disease in potato, caused by _Pectobacterium atrosepticum_ (Pba). You'll lead innovative research unravelling...
-
PhD Student Vacancy Only: Leaving home
1 week ago
Dundee DD DA, United Kingdom The James Hutton Institute Full time £40,000 - £60,000 per yearCereals are our most important staple foods, supplying about 50% of global dietary energy. Cereal crops were domesticated from their wild progenitors thousands of years ago. In their wild form, mature grains naturally fall from the plant in a process called shattering. Early farmers collected and replanted wild cereals with rare mutations that prevented this...
-
Dundee DD DA, United Kingdom The James Hutton Institute Full time £30,000 - £60,000 per yearPotato genetics, unlike the genetics of other major crops, has experienced limited progress due to the complexity of its tetrasomic inheritance. However, the potato genetics group (Hein, Chen, and Adams) has made significant strides in this field. Their work has successfully developed molecular markers for disease resistances, which have been validated by...
-
Molecular Microbiologist/Plant Pathologist
2 weeks ago
Dundee, United Kingdom The James Hutton Institute Full timeWe are seeking a motivated post-doctoral researcher in molecular microbiology or plant pathology to join our dynamic research team for a 3-year position starting 1st October 2025 investigating the fascinating molecular mechanisms behind blackleg disease in potato caused by Pectobacterium atrosepticum (Pba). Youll lead innovative research unravelling how...
-
Dundee DD DA, United Kingdom The James Hutton Institute Full time £25,000 - £35,000 per yearMany governments (including UK) are encouraging regenerative agriculture via policies that support or encourage reduced tillage and cover/catch crop utilisation in agricultural rotations, however, success in northern climates has been mixed. Reduced tillage practices have been shown to benefit the soils physical attributes, but the practice is often unviable...