A Novel Data Integration Framework for Modeling the Adverse Outcome PathwaySchool of Biological Sciences | PHD
Endocrine disrupting chemicals (EDCs) affect a variety of hormone-regulated physiological pathways in humans and wildlife. Health effects due to EDCs include reproductive dysfunction, premature puberty, neurological disorders, impaired immune function, cancer and obesity. Exposure of humans to EDCs is a worldwide problem. The primary source of EDC exposure is dietary. Many EDCs are found in plastic food containers. Canned foods and beverages are frequently coated with epoxy films. EDCs can leach into the contents of the plastic containers and cans. EDCs bind to nuclear receptors as well as key steroidogenic enzymes, disrupting normal physiological processes. The molecular mechanisms of action between EDCs and gene products are not well understood. Furthermore, correlating the effects of EDC exposures with disease incidence is a global priority . Novel analytical approaches that provide improved data processing capability and that integrate multi-dimensional statistical and computational methods to analyze, display, parse and search high dimensional toxicology data sets are urgently needed. The central hypothesis is that a novel systems level statistical framework can provide critical insights into how EDCs mediate their toxic effects. The long-term goal of this project is to develop a robust toolkit for integration into the adverse outcome pathway (AOP) conceptual framework, whereby existing knowledge linking molecular-level perturbation of a biological system and an adverse biological outcome with predictive or regulatory relevance is generated. The AOP is a pathway comprising a Molecular Initiating Event (MIE), Key Events (KE) and an Adverse Outcome (AO), causally linked together . Systematic organization of Big Data Science into AOP frameworks likely can improve regulatory decision-making through greater integration and more meaningful exploitation of mechanistic data. However, in order to develop a useful knowledge base that encompasses toxicological contexts of concern to human health risk assessment, novel tools that exploit Big Data must be developed in accordance with AOP core principles .
In this project, the successful PhD candidate will implement an informatics and statistical framework and develop software to improve identification of KEs and quantitative AOP (qAOP) causal networks, by integrating toxicogenomics data with interactome and pathological endpoints. They will also develop open source software and apply this tool kit to compound-response Omics data (e.g., those from Open TG-GATEs, the Comparative Toxicogenomics Database and DrugMatrix, which provide dose-response longitudinal measurements). The project’s multidisciplinary approach provides an excellent opportunity for training in various aspects of computational biology and advanced environmental and risk assessment analysis. Moreover, it provides an exceptional opportunity for research training in Northern Ireland whereby the successful candidate will work collaboratively across disciplines to generate new insights that transcend traditional boundaries. The project will combine aspects of computer science, biostatistics, toxicology, bioinformatics and systems biology. Consequently, subject-specific training will be offered in each of these areas. This will comprise a mix of appropriate postgraduate level training (e.g. bioinformatics, genetics, toxicology, computer science) and ‘hands on’ training in the advanced systems level methods used.
All applicants must meet the academic entry requirements: https://www.qub.ac.uk/courses/postgraduate-research/biological-sciences-phd.html#entry
Baker, M. E., Gerwick L. Šasik R, and G. Hardiman. "Endocrine disruptors. Foundations of Environmental Health-Endocrine Disruptors." Praeger Handbook of Environmental Health, Robert Friis, ed 2 (2012): 475-502.
Villeneuve DL, Garcia-Reyero N. Environ Toxicol Chem. 2011 Jan;30(1):1-8
Frey LJ. Artificial Intelligence and Integrated Genotype⁻Phenotype Identification. Genes (Basel). 2018 Dec 28;10(1). pii: E18. doi: 10.3390/genes10010018. PubMed PMID: 30597900.
Biological Sciences overview
The School of Biological Sciences provides PhD and MPhil (research degree) programmes in subjects ranging from basic biochemistry, molecular genetics and cancer research, to agricultural science, marine ecology and the economic evaluation of ecosystem services and food retailing. If you have a topic or research question in mind, please use the Find a Supervisor link (see Apply tab) to identify the most appropriate member of staff to support your idea. If not, don't worry, we regularly advertise funded projects and there is no harm in browsing our academic staff profiles for inspiration and then contacting whoever seems best: we are very open to applications from suitably qualified people interested in scientific research. In every case, a PhD or MPhil course provides the means of being part of a cutting edge scientific research team and contributing to genuine new discoveries or the development of new methods for practical use. If you cannot study full time, we offer pro-rata part time research degree programmes as well.
To help orientation, the School is organised into three research theme clusters:
- Ecosystem Biology and Sustainability
- Microbes and Pathogen Biology
- Food Safety and Nutrition
Ecosystem Biology and Sustainability:
In this cluster, you could research biodiversity and ecosystem services for environments ranging from tropical forests to deep oceans, using field techniques and skills such as wildlife tracking, taxonomy, geostatistics, molecular and genetic ecology, foodweb-analysis, microcosm and mesocosm experiments and mathematical/computational methods. Alternatively, you could study the behaviour and temperament of wild, agricultural or domestic animals and their implications for welfare and ability to respond to environmental change. Potential research projects include phylogenetic analysis of rare and newly discovered species, examination of ecological interactions in tropical systems, agricultural soils, or marine communities, using state-of-the-art genetic analysis, surveys using drones or satellite tagging, or experiments in tanks and field plots, including careful and ethical examinations of animal behaviour. Projects range from theoretical analysis of stability in ecosystems, through discovery of new species and mechanisms of interaction, or responses to climate change, to the assessment of EU agri-environment schemes, development of new methods for commercial fisheries management and economic evaluations of conservation measures. Projects very often have an international dimension and include collaboration with other researchers worldwide.
Microbes and Pathogen Biology:
This cluster covers a diverse array of research interests united by an emphasis on molecular approaches applied to both fundamental and applied questions over the range from molecular to ecological systems. These interests include biochemistry, food safety, microbiology and parasite control with applications in human and animal health, nutrition, plant and soil sciences, and agricultural development. We have a long-standing reputation in parasite biology and in applied microbiology (for example in clearing land of contamination) as well as strong contributions to fundamental methods in understanding cancer, developing veterinary vaccines and molecular detectors for toxins and diseases. The common thread is our strong molecular approach using and developing cutting edge genomic, transcriptomic/proteomic methods. Research students in this cluster enjoy a range of strong international links across Europe, Asia, North and South America.
Food Safety and Nutrition:
Research opportunities offered by this cluster span the entire food chain "from farm to fork" with a strong emphasis on food safety and nutrition, public health and food security. In this cluster you would conduct research under the supervision of leading scientists based in the Institute for Global Food Security and benefit from integration with business experts, helping you gain leadership positions nationally and internationally.
Biological Sciences Highlights
- The School has a wide range of strong, international links with governments, academia and industry, into which postgraduate research students are integrated.
World Class Facilities
- Students will have the full use of modern, world-class laboratories, equipped with state-of-the-art, highly advanced analytical instruments and facilitated by world-class field work provision.
- Students studying in the Food Safety and Nutrition programme will gain excellent practical experience of advanced technology and bioanalytical techniques for food safety analysis and monitoring, including: 1. GC, HPLC and UPLC separation platforms; 2. ICP, IR, qToF and QqQ mass spectrometers; 3. Microbiological research facilities; 4. Antibody production and biomolecule binder development; 5. Cell culture suite and bioanalytical assay detection systems; 6. NMR, NIR and Raman spectrometers; 7. Proteomic and metabolomic profiling tools RT-PCR; 8. Transcriptomic profiling; 9. Next-generation sequencing; 10. Multiplex biosensor platforms and LFD development.
- Over 80% of science jobs are in areas of Biological Sciences.
- Most of the critical problems facing humanity - disease, climate change and food security - require biological understanding to solve them.
Information on the research interests and activities of academics in Biological Sciences can be accessed via the School website and the Find a Supervisor facility (see Apply tab).
Queen's postgraduates reap exceptional benefits. Unique initiatives, such as Degree Plus and Researcher Plus bolster our commitment to employability, while innovative leadership and executive programmes alongside sterling integration with business experts helps our students gain key leadership positions both nationally and internationally.
Employment after the Course
Graduates have gone on to be professional research scientists, consultants, or hold technical and junior executive positions in commerce and government.
People teaching you
Dr Keith Farnsworth
Chair of School Postgraduate Research Committee
School of Biological Sciences
For a PhD you will have a principal and second supervisor who advise your independent studies and will be supported by a wider team from the academic staff - who they are, of course, depends on your project. For further details on any aspect of postgraduate research degrees within the School of Biological Sciences, contact: email@example.com.
A research degree offers students an opportunity to foster their capacity for independent research and critical thought. It also allows students to explore an area of interest and so understand and solve theoretical and practical problems within the field. Undertaking a research degree can enhance a student’s written and oral communication skills and a PhD is almost always a formal requirement for an academic post.
Assessment processes for the Research Degree differ from taught degrees. Students will be expected to present drafts of their work at regular intervals to their supervisor who will provide written and oral feedback; a formal assessment process takes place annually.
This Annual Progress Review requires students to present their work in writing and orally to a panel of academics from within the School. Successful completion of this process will allow students to register for the next academic year.
The final assessment of the doctoral degree is both oral and written. Students will submit their thesis to an internal and external examining team who will review the written thesis before inviting the student to orally defend their work at a Viva Voce.
Supervisors will offer feedback on draft work at regular intervals throughout the period of registration on the degree.
FacilitiesFull-time research students will have access to a shared office space and access to a desk with personal computer and internet access.
The minimum academic requirement for admission to a research degree programme is normally an Upper Second Class Honours degree from a UK or ROI HE provider, or an equivalent qualification acceptable to the University. Further information can be obtained by contacting the School.
For information on international qualification equivalents, please check the specific information for your country.
English Language Requirements
Evidence of an IELTS* score of 6.5, with not less than 5.5 in any component, or an equivalent qualification acceptable to the University is required (*taken within the last 2 years).
International students wishing to apply to Queen's University Belfast (and for whom English is not their first language), must be able to demonstrate their proficiency in English in order to benefit fully from their course of study or research. Non-EEA nationals must also satisfy UK Visas and Immigration (UKVI) immigration requirements for English language for visa purposes.
For more information on English Language requirements for EEA and non-EEA nationals see: www.qub.ac.uk/EnglishLanguageReqs.
If you need to improve your English language skills before you enter this degree programme, INTO Queen's University Belfast offers a range of English language courses. These intensive and flexible courses are designed to improve your English ability for admission to this degree.
|Northern Ireland (NI)||£4,407|
|England, Scotland or Wales (GB)||£4,407|
|Other (non-UK) EU||£4,407|
Biological Sciences costs
Students may incur additional costs for small items of clothing and/or equipment necessary for lab or field work
Additional course costs
Depending on the programme of study, there may also be other extra costs which are not covered by tuition fees, which students will need to consider when planning their studies . Students can borrow books and access online learning resources from any Queen's library. If students wish to purchase recommended texts, rather than borrow them from the University Library, prices per text can range from £30 to £100. Students should also budget between £30 to £100 per year for photocopying, memory sticks and printing charges. Students may wish to consider purchasing an electronic device; costs will vary depending on the specification of the model chosen. There are also additional charges for graduation ceremonies, and library fines. In undertaking a research project students may incur costs associated with transport and/or materials, and there will also be additional costs for printing and binding the thesis. There may also be individually tailored research project expenses and students should consult directly with the School for further information.
How do I fund my study?1.PhD Opportunities
Find PhD opportunities and funded studentships by subject area.2.Doctoral Training Centres at Queen's
Queen's has eight outstanding competitive Doctoral Training Centres, with each one providing funding for a number of PhD positions and most importantly a hub for carrying out world class research in key disciplines.3.PhD loans
The Government offers doctoral loans of up to £26,445 for PhDs and equivalent postgraduate research programmes for English- or Welsh-resident UK and EU students, £10,000 for students in Scotland and up to £5,500 for Northern Ireland students.4.International Scholarships
Information on Postgraduate Research scholarships for international students.
Funding and Scholarships
The Funding & Scholarship Finder helps prospective and current students find funding to help cover costs towards a whole range of study related expenses.
How to Apply
Find a supervisor
If you're interested in a particular project, we suggest you contact the relevant academic before you apply, to introduce yourself and ask questions.
To find a potential supervisor aligned with your area of interest, or if you are unsure of who to contact, look through the staff profiles linked here.
You might be asked to provide a short outline of your proposal to help us identify potential supervisors.