Positions Available

Masters Projects

I have supervised projects on various Masters courses. Visit my Projects Page to see past and potential Masters projects.

A one-year Research-only Masters, MSc(Res), is now available in the School of Biology. Students may start in September or January, and a rolling deadline is in place. Please see https://synergy.st-andrews.ac.uk/research/mscres/ for more information on the programme. I am happy discuss potential projects with prospective students, in any of the below areas or any other area of my research programme. Please contact me at anne.smith@st-andrews.ac.uk.

In addition to the specific projects listed on my Projects Page, some more general topics for the MSc(Res) are as follows:

Computational biology
Masters projects are available in areas of machine learning applied to molecular, neural, and ecological systems. Our group concentrates on inference of network structure from observational data, but also explores optimisation, agent-based modelling, and evolutionary algorithms, in the context of analysing biological questions. An emphasis is placed on evolutionary perspectives. Projects could be ideal bridges for students with degrees either in mathematics/computer science subjects or in biology to move into the interdisciplinary area of computational biology.

Experimental evolution in microbial systems
How repeatable is evolution? What happens to synthetically engineered gene circuits under adaptive pressures? How do microbial communities persist? Masters projects are available in experimental evolution in microbial systems, particularly yeast. The laboratory has access to a state-of-the-art Bioscreen C machine which propagates 200 microbial cultures simultaneously. Topics addressed can range from basic features of evolution and mechanisms underlying adaptation, to exploration of robustness and persistence of biodiversity in artificial microbiomes, to impact of evolutionary considerations on design of systems for synthetic biology.

Computational neuroscience: live imaging data
Collaborative with Dr Stefan Pulver, School of Psychology and Neuroscience
Live imaging of neural activity provides a wealth of data on neural activity in living animals; however, current computational analyses lag behind technological development. Masters projects are available in collaboration between a computational biologist (Smith) and an experimental neuroscientist (Pulver), developing and applying computational methods for ‘mining’ of live imaging datasets. Projects can address various aspects of analysis, from automatic image processing to answering biological questions by inferring neural information flow. Students can work entirely computationally, or have the opportunity to gain skills in experimental neuroscience.

Changing bird populations and implications for aviation
Collaborative with Dr Guy Gratton, School of Aerospace, Transport and Manufacturing, Cranfield University
“Bird strikes” are a danger for aircraft and detrimental to the wildlife involved: changes in bird populations or migratory behaviour due to climate change may influence the likelihood of such events, and require modification of current measures for mitigation. This project applies statistical analysis to historical data on avian populations and their interactions with aircraft, and makes inferences for the future. You will join an international team, including climate scientists and aerospace experts, looking at the impact of elements of climate change on the aviation industry.

Senior Honours Projects

I can supervise a wide range of projects, from wetlab work doing genetic manipulations in yeast through to exclusively computer-based projects in bioinformatics, ecology, neuroscience, or behaviour. Visit my Projects Page to see some projects done by other students in my lab as well as some potential future projects. Students interested in working with me on their senior honours project feel free to contact me (anne.smith@st-andrews.ac.uk) with questions; also you will find it useful to read the information on the Research Page and the pages linked from there describing background to the computational methods.

Other Undergraduate Research Opportunities

Students wishing to gain experience in computational biology research please feel free to contact me (anne.smith@st-andrews.ac.uk) to set up a meeting to discuss your interests and potential research opportunities. My Projects Page lists some projects done by other students in my lab as well as some potential future projects, and is worth a visit to get an idea of the type of projects possible in my lab. I have no funding for undergraduate research, but there are several opportunities for applying for academic year and summer support; if we determine that working together would be a good fit, I am willing to help students with identifying and applying for support.

Please note that funding deadlines are earlier than you may think! Many are in early February and some are as early as December, so please try to contact me sooner rather than later.