University of Dundee

Data Analysis

MRC DTP 4 Year PhD Programme: Discovery of composite biomarkers and the role on the retina in risk prediction for systemic diseases using deep learning

Supervisors: Prof Emanuele Trucco, School of Science and Engineering, Dr Alex Doney, School of Medicine / Clinical and Molecular Medicine.

Aims and objectives. The project will use deep learning (DL) techniques to discover combinations of phenotypic and genotypic features working as predictive risk scores for high-incidence conditions (e.g. cardiovascular, diabetic complications).

MRC DTP 4 Year PhD Programme: Use of Machine Learning and Computer Vision to detect Cerebral Microbleeds in SWI MRI

Small areas of bleeding in the brain, known as cerebral microbleeds (CMB), are emerging as important features of an aging brain.  Not only are they a marker for unhealthy blood vessels associated with development of dementia, but they also indicate an increased risk of major bleeding in the brain.  This is particularly a concern in the common situation where doctors need to use medicines that stop clots from forming, and therefore increase risk of bleeding, to prevent heart attacks and ischaemic strokes.  Although CMB are common they are not checked for routinely in conventional commonly us

MRC DTP 4 Year PhD Programme: AI-Spot-Dementia (AISDA): developing machine learning algorithms to predict the risk of dementia for patients with Type 2 Diabetes

The aim of this PhD proposal is to develop novel machine learning algorithms (e.g., deep learning) to predict the risk of dementia in Type 2 diabetes, and detect early signs of such disease with association of clinical and genomic data in clinical settings. There are strong links between Type 2 Diabetes (T2D) and dementia.  With increasing numbers of people developing T2D, detecting early signs of dementia is important to better understand how it can be delayed or prevented.

MRC DTP 4 Year PhD Programme: Automatic, reliable detection of nocturnal epileptic seizures in real time via machine learning of multi-modal data.

Supervisors: (Lead): Dr Ian Morrison, Department of Neurology, Ninewells Hospital, Professor Emanuele Trucco, School of Science and Engineering, Professor Stephen McKenna, School of Science and Engineering.

Background

MRC DTP 4 Year PhD Programme: Functions & Applications of a Novel Stem Cell Signalling Pathway

The Findlay lab employs cutting-edge technologies to unravel Embryonic Stem (ES) cell signalling networks (Williams et al, Cell Rep 2016, Fernandez-Alonso et al, EMBO Rep 2017; Bustos et al, Cell Rep 2018), culminating in our recent discovery of the ERK5 pathway as an exciting new regulator of ES cell pluripotency. In order to uncover functions of ERK5 in ES cells, this project will deploy global proteomic and phosphoproteomic profiling. Novel ERK5 substrates and transcriptional networks will be characterised using biochemical and ES cell biology approaches.

MRC DTP 4 Year PhD Programme: Cell biology of a bacterial nano-weapon. Supervisors: Dr Sarah Coulthurst (Lead); Dr Colin Rickman (2nd Supervisor), Heriot-Watt

Many bacterial pathogens use the Type VI secretion system (T6SS) nanomachine to fire diverse, toxic ‘effector’ proteins directly into target cells. It is becoming increasingly apparent that the T6SS plays a key role in the virulence and competitiveness of diverse Gram-negative bacteria, including important human pathogens. Pathogens can use T6SSs to directly target eukaryotic organisms, as classical virulence factors. Alternatively, many pathogens can use T6SSs to target other bacterial cells, killing or inhibiting rivals.

MRC DTP 4 Year PhD Programme: Prediction of protein-protein interaction sites from population genetics data

Our research has focused for more than 20 years on developing effective computational methods to predict the function, structure and specificity of proteins from the amino acid sequence.  This has included work to characterise and predict protein-protein interactions from 3D structural information as well as from sequences and related data.  Much of this  experience is encapsulated in widely used software tools that include the Jalview (www.jalview.org) sequence analysis workbench which has over 70,000 regular users world-wide and JPred (

MRC DTP 4 Year PhD Programme: Prediction of protein specificity determining sites from population genetics

Our research has focused for more than 20 years on developing effective computational methods to predict the function, structure and specificity of proteins from the amino acid sequence.  This experience is encapsulated in widely used software tools which include the Jalview (www.jalview.org) sequence analysis workbench that has over 70,000 regular users world-wide and JPred (www.compbio.dundee.ac.uk/jpred) which performs up to 500,000 predictions of secondary structure and other features from the

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