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PhD Opportunities

SFI Centre for Research Training in Genomic Data Science: Creating the infrastructure in the use of genomic tools for pathogen surveillance and control in crops

School of Biological Sciences | PHD

Applications are now CLOSED
Funding
Funded
Reference Number
SBIO-2020-1208
Application Deadline
17 July 2022
Start Date
1 September 2022

Overview

Despite the recommendations of many expert groups, One Health surveillance systems have not yet improved to the point where emerging infectious threats can be better anticipated. The COVID epidemic is the latest to demonstrate that new pathogens often spread undetected for some time before being able to be diagnosed in a population. This is even more evident for pathogens in other areas such as crop production and diseases have a significant cost to agriculture.

Next-generation sequencing, particularly the use of portable genomic sequencers, offers an intriguing solution to the diagnosis and surveillance problems — it enables rapid in situ  diagnostics through amplicon-based or metagenomics approaches. Findings from analyses of whole-genome sequences show great promise for informing strategies to mitigate risks from diseases caused by phytopathogens. It also creates a stream of genomic data that can reveal critical epidemiological aspects of an outbreak or epidemic's dynamics.

Genomic epidemiology for outbreak response approaches can be used to dramatically shorten response times to outbreaks and inform disease management in novel ways. However, the use of these approaches requires expertise in working with big, complex data sets and an understanding of their pitfalls and limitations to infer well-supported communications. This has demonstrated some early successes, but there are a number of challenges to overcome — some technical and some cultural. Data sharing is one of these, but other ethical and legal issues must be considered.

The power of a genomic epidemiology approach for plant pathogens could be extended by incorporating concepts from digital disease detection and One Health. By coupling sequencing to an enhanced surveillance, response platform and even for future biocontrols, we could take a more anticipatory approach to outbreak prevention and control.

The aim of this proposal is to create a framework approach to guide the use of genomic approaches in epidemiology and diagnostics of plant pathogens. The concept is to map pathogens (especially fungi) of concern in crops to have a substantive database and be able to use their genome and geonomics databases to devise rapid point of site testing methods and design future biocontrols as a model system to create an infrastructure for an immediate response mechanism for future new pathogens.

There are >20 databases relevant to this project, the research student will receive training in working with big complex data sets from these datasets to address the key questions using BLAST, Genebank etc. The student will also receive training in sequencing techniques and data analysis and understanding of the state-of-the-art NGS methods and point of site detection methods that can be applied such as Nanopore, LAMP and LFD for pathogen detection but also for the application of biocontrol methods. The student will also receive training in literature reviews, publication and scientific writing skills and will be linked in with the QUB Graduate School for transferable skills training in Leadership. At UCD the student will receive training in metagenomic analysis from DNA extracted from spore trap samples taken across field sites to identify the wheat pathogens present. 

This project will be supervised by Professor Katrina Campbell and Dr Caroline Meharg (Queen's University Belfast) and Dr Angela Feehan (University College Dublin).

Start Date: 1 September 2022

Duration: 3 years

Skills/experience required: Besides any experience relevant to the particular project, students would benefit from having some experience with bioinformatics / computational biology tools and analyses, although training in these areas will be provided in the residential training programme at the start of the project.

How to apply: Applications must be submitted via: https://dap.qub.ac.uk/portal/user/u_login.php

Queen’s University Belfast is a partner of the SFI CRT in Genomics Data Science, which was formed in 2019. Over seven years of its operation, the Centre will train 100 PhD students in data analytical and computational skills that will help power the implementation of genomics on the island of Ireland. The Centre is built on a national cohort-based model of advanced training. At the outset of their training programme, each student cohort undertakes an intensive, semester-long series of training courses. Participation in the SFI CRT in Genomics Data Science includes a mandatory 3-month residential training programme for the students at NUI Galway, held in Semester 1 (start of September to mid-December) of Year 1 of the PhD programme. Through their experience of working and living together on this phase of the training programme, student cohorts form tight knit groups, enabling them to work collectively on the data science challenges they will encounter during their research. For more information on the SFI CRT in Genomics Data Science and the residential training programme see: https://genomicsdatascience.ie/

Funding Information

This studentship is funded by the Northern Ireland Department for the Economy (DfE).
Candidates must be normally resident in the UK for the three year period prior to 1 September 2022. For non-EU nationals, the main purpose of residence must not have been to receive full-time education. Non-UK or Irish nationals must also have pre-settled or settled status (EU nationals) or settled status (non-EU nationals).

Full eligibility criteria: https://www.economy-ni.gov.uk/sites/default/files/publications/economy/Postgraduate-studentships-terms-and-conditions.pdf

Project Summary
Supervisor


    Mode of Study

    Full-time: 3 years


    Funding Body
    DfE
    Apply now Register your interest

    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
    Industry Links
    • 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
    • Research students will have access to laboratory space as required (in our state-of-the-art research laboratories) and where relevant, also a range of field study sites and equipment (e.g. remote sensing drone equipment). They also have access to local and campus-wide high performance computing facilities and the full strength of our world-class library. Many students also benefit from the strong collaboration network maintained by our academic staff, which could result in working in the laboratories of partner organisations in industry and government as well as in the University, under specific arrangements.
    • 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.
    Internationally Renowned Experts
    • Queen's ranking for Food Science research was first in the UK in the Times and Sunday Times Good University Guide 2021.

      In the Complete University Guide 2021, Queen's was joint first in the UK for Research Intensity in Biological Sciences.
    Key Facts

    • Most of the critical problems facing humanity - disease, climate change and food security - require biological understanding to solve them.

    Course content

    Research Information

    PhD Supervisors
    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).

    Career Prospects

    Introduction
    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. Career prospects in the biological sciences are exceptionally good. To some extent it depends on the specific topic, of course, but laboratory-based and especially quantitative skills and the proven innovation of a PhD or MPhil are highly sought after. Degrees are very much in demand, both in commercial science and public sector research and development (e.g. drug discovery and development, crop and animal improvements and welfare, sustainable agriculture and resource use, human nutrition and health, animal health, ecological management, food safety and technology, scientific communications, regulation, and many more fields).

    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 Gareth Arnott
    Postgraduate Research Director
    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: biosciences-pg@qub.ac.uk. Research degrees are overseen by the School of Biological Sciences Director of Postgraduate Research, who currently is Dr Gareth Arnott.

    Learning Outcomes

    A postgraduate research degree involves the undertaking of independent research under the guidance of a professional academic supervisory team, typically using the laboratory facilities on offer in one or more of the teams' labs. The student will be expected to develop their own ideas and learn the methods needed to test them empirically and theoretically. This usually involves learning and practising both laboratory (and or field) skills as well as developing a strong theoretical background in the relevant subject.

    As well as practical work, all the activities of independent academic scholarship, such as literature searching and critical appraisal, written and verbal communications and academic networking will be developed during a research degree. Independence and innovation will be strongly encouraged, but the student will be supported by regular supervisory guidance and a wide range of courses will also be on offer, both in subject specific skills and generic skills, especially supported by the Graduate School (https://www.qub.ac.uk/graduate-school/).

    Students are encouraged to interact with one another and with members of academic staff and postdoctoral scientists to build confidence and informal learning, through a range of ‘research culture’ activities, including peer groups where students get together to discuss topical research papers, or methods, or just chat about their interests.

    Course structure

    Research degrees vary in length, but typically for a PhD they are three or four years long (full-time) and double that for part-time studies. They follow an annual cycle of progress with formal panel-based appraisals of the progress, the outcome of which is typically practical and academic advice about how to overcome problems encountered and how to move to the next stage. During each year, students are expected to supplement their studies with some tailored courses, ranging from highly specific (e.g. learning to use a piece of apparatus or technique) to generic (e.g. developing oral presentation or leadership skills). Every stage is supported by the supervisory team, augmented by an independent panel of progress monitors as well as the full support of the Graduate School.

    Assessment

    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.

    Feedback

    Supervisors will offer feedback on draft work at regular intervals throughout the period of registration on the degree.

    Facilities

    Full-time research students will have access to a shared office space and access to a desk with personal computer and internet access.

    Entrance requirements

    Graduate
    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.

    International Students

    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.

    Tuition Fees

    Northern Ireland (NI) 1 £4,596
    Republic of Ireland (ROI) 2 £4,596
    England, Scotland or Wales (GB) 1 £4,596
    EU Other 3 £22,700
    International £22,700

    1 EU citizens in the EU Settlement Scheme, with settled or pre-settled status, are expected to be charged the NI or GB tuition fee based on where they are ordinarily resident, however this is provisional and subject to the publication of the Northern Ireland Assembly Student Fees Regulations. Students who are ROI nationals resident in GB are expected to be charged the GB fee, however this is provisional and subject to the publication of the Northern Ireland Assembly student fees Regulations.

    2 It is expected that EU students who are ROI nationals resident in ROI will be eligible for NI tuition fees. The tuition fee set out above is provisional and subject to the publication of the Northern Ireland Assembly student fees Regulations.

    3 EU Other students (excludes Republic of Ireland nationals living in GB, NI or ROI) are charged tuition fees in line with international fees.

    All tuition fees quoted are for the academic year 2021-22, and relate to a single year of study unless stated otherwise. Tuition fees will be subject to an annual inflationary increase, unless explicitly stated otherwise.

    More information on postgraduate tuition fees.

    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

    All Students

    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.

    Bench fees

    Some research programmes incur an additional annual charge on top of the tuition fees, often referred to as a bench fee. Bench fees are charged when a programme (or a specific project) incurs extra costs such as those involved with specialist laboratory or field work. If you are required to pay bench fees they will be detailed on your offer letter. If you have any questions about Bench Fees these should be raised with your School at the application stage. Please note that, if you are being funded you will need to ensure your sponsor is aware of and has agreed to fund these additional costs before accepting your place.

    How do I fund my study?

    1.PhD Opportunities

    Find PhD opportunities and funded studentships by subject area.

    2.Funded Doctoral Training Programmes

    We offer numerous opportunities for funded doctoral study in a world-class research environment. Our centres and partnerships, aim to seek out and nurture outstanding postgraduate research students, and provide targeted training and skills development.

    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.

    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

    Apply using our online Postgraduate Applications Portal and follow the step-by-step instructions on 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.