Modelling Organismal Responses in Aquatic Ecosystems

About this project

The University of Hull has strong research ties to the marine environment. To strengthen these ties, the “Molecular Stress in Changing Aquatic Environments” research cluster is seeking applications to begin fully funded 3-year PhD studies in Fall 2018. Our research cluster aims to deconstruct the cause-and effect network between aquatic environmental change (climate change, human-induced pollution) and organismal stress response at the molecular level, and to utilize this information to generate tools and strategies for mitigating the ecosystem effects of global change. We take a systems approach, collaboratively bridging a variety of disciplines (ecology & evolution, toxicology, genomics, proteomics, analytical and computational chemistry, and computational biology) to achieve these goals. Some of our research at Hull has been prominently featured in a recent research outlook in the October 2017 issue of Nature.

We are seeking three PhD students to work in a combination of field, research institute / industrial (aquaculture), and lab settings, and across a range of aquatic vertebrate and invertebrate species. They will develop expertise through in-house access to biotechnology infrastructure (Genome sequencing, HPLC Mass Spec), and the largest supercomputer in the North of England (VIPER). Students will be advised by a team of academics with vibrant research programs, and work closely with collaboration partners at CCmar in Faro, Portugal; Cromarty Mussel farms, in Cromarty Firth, Scotland; the East China Fisheries Research Institute, Shanghai, China; and the British Antarctic Survey.

Our strong links with industry partners will ensure that the work will have immediately applicable outcomes and students gain industry-relevant skills and contacts. Students will also be provided with the skills and expertise necessary to succeed in policy making and academia.

Modelling organismal responses in aquatic ecosystems

This project has two key goals. Firstly, to identify universal and species-specific biochemical and genomic networks of the organismal stress response. Secondly to generate computational models to categorise individual stress responses and to assess stress in an aquacultural or environmental setting using biosensors. In order to gain insights into how ecosystem responses to stress can be predicted and its eventual outcomes, a wide collection of data sources will be used for to capture and model the data. These range from environmental stressors, biotic stressors to genetic, phenotypic and ecological data over a range of timescales. This can be achieved by exploiting new advances in artificial intelligence, which can observe huge quantities of data and map them onto a specific output. In addition, this project will utilise the University’s VIPER High Performance Computer (http://hpc.wordpress.hull.ac.uk/). This project will start using simulated parameters for this purpose, and then proceed to refine models using experimental data. By doing this, we will be able to predict future trends, tipping points, and the effects on the ecosystem as a whole. The models will be tested and further calibrated against the experimentally generated data, and to test levels of stress in our industry partner aquaculture facilities.

This position will be supervised by Dr. Alexander Turner and co-supervised by Dr. Katharina Wollenberg Valero. Additionally, Dr. Bryce Beukers-Stewart (University of York) will serve as external advisor.


You are strongly advised to contact a potential supervisor and to discuss your research proposal, well before you submit an application. Please refer to the School of Environmental Sciences research pages.

If you have any queries, please email Dr Katharina Wollenberg-Valero.

Next steps


To celebrate the University's research successes, the University of Hull is offering a full-time UK/EU PhD Scholarship or International Fees Bursary.

Entry requirements

Applicants should have or are expected to attain at least a 2.1 undergraduate degree in Computational Biology, Computer Science, or related discipline, together with relevant research experience and background in Linux programming. It is anticipated that the successful applicant will have a 1st class undergraduate degree or Masters level qualification. As this is an interdisciplinary project, ideal candidates will have a background or demonstrated interest in Computational Science, and be willing to develop skills in Computational Genomics and quantitative Ecology.

Prospective students are expected to be good team players, as their independent projects will jointly contribute to cluster research goals. Ability to pursue independent research, excellent writing, and fluency in English is expected. We encourage applications from students whose backgrounds are traditionally underrepresented in STEM fields.

How to apply

Applications for scholarship consideration at the University of Hull should be made through the Postgraduate Application system.

On the second page of your application, please select “Graduate Scholarship” as the type of scholarship you are applying for. 

Applicants are strongly encouraged to first identify and contact a potential supervisor.

Apply now

Application deadline: Monday 19 February


Full-time UK/EU PhD Scholarships will include fees at the ‘home/EU' student rate and maintenance (£14,553 in 2017/18) for three years, depending on satisfactory progress.

Full-time International Fee PhD Studentships will include full fees at the International student rate for three years, dependent on satisfactory progress.