2026 Projects
Novel biomarkers for human gut AMPK activation using AI-driven multi-omics analysis
This PhD project will use AI-driven analysis of multi-omics data to discover blood-based biomarkers that report activation of AMPK, a key sensor of cellular “fuel deficiency” linked to obesity, diabetes and healthy ageing. The student will integrate metabolomic, proteomic, phosphoproteomic and transcriptomic datasets from human, animal and cell studies with known AMPK activators (e.g. metformin, salicylate, dietary compounds) to identify a robust molecular signature of AMPK activation. These features will be combined into an interpretable “AMPK Activation Score” and applied to samples from human dietary intervention studies to assess how foods and nutrients modulate energy metabolism in vivo. The project offers interdisciplinary training at the interface of AI, nutrition, metabolism and biomarker discovery.
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Machine learning-assisted antibacterial drug discovery
This PhD project will use machine learning to accelerate the discovery of new antibacterial drugs, focusing on plant-derived phytochemicals as a rich source of novel compounds. The student will develop predictive models that link chemical structure to antibacterial activity against multidrug-resistant (MDR) bacteria, helping to prioritise promising candidates and potentiators of existing antibiotics. These predictions will be tested experimentally using microbiology-based phenotypic assays and analytical chemistry for compound characterisation. Working at the interface of AI, microbiology and natural-product chemistry, the project aims to deliver both new methods and new leads for tackling antimicrobial resistance.
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AI-Driven Multi-Omics Biomarker Discovery and Early Detection of Mastitis in Dairy Cattle
This PhD project will use explainable AI and multi-omics integration to enable early detection of subclinical mastitis in dairy cattle. The student will combine mid-infrared milk spectra, transcriptomics, genotype data and routine milk records to identify robust molecular biomarkers and build interpretable machine-learning models for mastitis risk prediction. The work aims to deliver biologically meaningful biomarker panels and decision tools that improve herd health, reduce antimicrobial use and support precision livestock management. The project offers interdisciplinary training spanning bioinformatics, AI, microbiology and animal health, including an industrial placement at AFBI.
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Using AI-driven computer vision and high-throughput multiplexed human cell infection assays to dissect intra- and intercellular signalling networks and discover new antimicrobials
This PhD project will combine AI-driven computer vision with high-throughput, multiplexed human cell infection assays to understand how host cells and bacteria interact at single-cell resolution. The student will engineer visually barcoded libraries of mammalian cells and bacteria, track their interactions by high-content live fluorescence imaging, and develop machine-learning pipelines to decode complex intra- and intercellular signalling networks during infection. By linking specific host and bacterial phenotypes to infection outcomes and drug responses, the project will identify candidate targets for new antibiotics and host-directed therapies, followed by proof-of-concept testing with existing inhibitors.
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AI-enabled antigen discovery for vaccines targeting One-Health antimicrobial-resistant pathogens
This PhD project will harness AI to discover new vaccine antigens against antimicrobial-resistant (AMR) pathogens in a One-Health framework. Working with uniquely rich experimental datasets that link real immune responses and protection outcomes across multiple AMR bacteria, the student will develop interpretable machine-learning models to identify “protection signatures” and high-value vaccine targets. These predictions will then be tested in the lab using Streptococcus infection models, providing an iterative loop between AI and experiment. The project offers interdisciplinary training across computational biology, infection immunology and translational vaccine research, with industry exposure via the QUB spin-out VacTimmune.
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Harnessing AI to Define Extracellular Vesicle-Mediated Immune Regulation
This PhD project will use advanced AI and machine learning to uncover how extracellular vesicles (EVs) from mesenchymal stem cells regulate immune cell behaviour. The student will generate multi-omics datasets by profiling the molecular cargo of EVs and measuring how dendritic cells, B cells and T cells respond to EV treatment at the single-cell level. They will then develop and apply models (e.g. graph neural networks and multimodal autoencoders) to link EV composition to specific immune outcomes and identify key regulatory molecules or cargo combinations. Ultimately, the project aims to move from descriptive correlations to mechanistic understanding of EV-mediated immune regulation, informing future cell-free immunotherapies.
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HAPPI: Harnessing AI for personalised nutrition to promote healthy ageing in older adults
This PhD project, HAPPI, will harness AI to develop personalised nutrition solutions that help older adults prevent or reverse undernutrition and maintain independence. The student will use machine learning on large ageing cohorts (including clinical trial and NICOLA data) to identify diet–function patterns and build transparent algorithms that generate tailored diet plans. They will then co-design and test a “Healthy Ageing Diet” mobile app with older adults, creating an AI-driven tool that supports long-term dietary behaviour change and improved health and functional outcomes.
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Contextual Biological Modelling for Phenotypic Prediction
This PhD project will develop contextual probabilistic “world models” to understand and predict how cancer systems behave differently across contexts such as cell type, treatment, disease state and genetic background. Using the Contextual Probability (CP) framework, the student will model multiple biological contexts jointly, identify mechanisms that are stable or rewired between them, and build context-aware predictors of phenotypic responses. The work will focus on p53-family signalling in colorectal cancer (CRC) as a case study, using multi-omics and perturbation datasets to address a specific CRC prediction problem and generate new, testable hypotheses about context-dependent behaviour. The project offers interdisciplinary training in AI for bioscience, mathematical modelling, systems biology and computational cancer research.
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Integrating nutrition with genomics, lifestyle and environmental factors using AI to develop personalised nutrition approaches for hypertension prevention
This PhD project will use AI to integrate nutrition, genomics, lifestyle and environmental data to develop personalised nutrition approaches for preventing hypertension in older adults. Working with large ageing cohorts such as the TUDA study (>5,000 adults in Ireland) and validating findings in UK Biobank (500,000 participants), the student will apply GWAS, Mendelian randomisation and machine learning to uncover causal risk factors and novel gene–nutrient interactions (e.g. involving MTHFR and riboflavin). The project will also map hypertension incidence and antihypertensive use across Ireland by socioeconomic deprivation using GIS methods. Ultimately, the work aims to deliver evidence-based, personalised dietary strategies to reduce blood pressure and improve cardiovascular health in ageing populations.
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AI approaches to investigation of the role of folate nutrition in breast cancer prevention: epidemiological, clinical, and molecular studies
This PhD project will use AI and machine learning to investigate how folate and related B-vitamin metabolism influence breast cancer risk across epidemiological, clinical and molecular levels. Using UK Biobank data (~500,000 participants), the student will model relationships between folate status, genetic variants and breast cancer susceptibility, identifying key nutrient–gene interactions. They will then run a pilot case–control study measuring one-carbon metabolism biomarkers in blood and breast tissue from breast cancer patients and controls, alongside detailed molecular profiling of DNA damage and methylation. Together, these integrated analyses aim to clarify when folate is protective versus potentially harmful and to inform nutrition-based strategies for breast cancer prevention.
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Empowering People with Parkinson’s using Intelligent Systems for Personalised Support
This PhD project will develop AI-driven systems to support people living with Parkinson’s disease (PD) through personalised monitoring and feedback. The student will collect and integrate multimodal data from wearable sensors (e.g. movement, heart rate, skin response, activity logs) during exercise and dance-based interventions, and build machine learning models to classify motor and non-motor symptoms, identify digital biomarkers and track symptom progression. They will then design and test AI-informed tools that provide tailored prompts or feedback to help motivation, self-management and clinical decision-making. The project offers highly interdisciplinary training across wearable technology, AI, psychology and clinical collaboration within the PD-LIFE hub and industrial partner BSecur.
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Causal and Dynamic Modelling of Milk Production in Grass-Based Dairy Production System: Integrating Dietary, Environmental, and Cow–Calf Production Dynamic
This PhD project will use causal and dynamic AI modelling to understand and predict milk production in grass-based dairy systems by integrating dietary, environmental and cow–calf factors. The student will move beyond correlation-based models to identify key causal drivers, time-varying effects and feedback loops linking feed quality, energy balance, environment, calf growth and maternal physiology to milk yield. They will develop interpretable, counterfactual-ready models that can simulate “what if” scenarios to optimise feeding and management strategies under changing climatic and economic conditions. The project offers interdisciplinary training across AI, animal health, nutrition and agricultural systems in collaboration with Ulster’s AI Research Centre, NICHE and AFBI.
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