AddressPhD Scholarship in Pathogen Genomics
- Job Details
- Company
Job Details
Applications are invited from suitably qualified candidates for a full-time funded PhD scholarship starting in September 2024, affiliated to the Discipline of Bioinformatics, School of Mathematical and Statistical Sciences, at the University of Galway.
University of Galway
Located in the vibrant cultural city of Galway in the west of Ireland, the University of Galway has a distinguished reputation for teaching and research excellence
For information on moving to Ireland please see www.euraxess.ie
Detailed Project Description Since the onset of the COVID-19 pandemic, the benefits of whole-genome sequencing for pathogen research, and for understanding infectious disease transmission and evolution in a public health context, have been brought into sharp relief. Large datasets of pathogen genomes have been and continue to be published, offering substantial opportunity for new biological insights to be obtained through their (re-)analysis.
Based in the School of Mathematical and Statistical Sciences, and with primary supervision from Dr. Matthew Dorman, the student will benefit from an environment with strong expertise in quantitative data analysis. There will be scope to work with colleagues affiliated to the Discipline of Bacteriology (School of Medicine, University of Galway) and Galway University Hospital. The student will join Dr. Dorman’s newly-established group while it is in a phase of growth, and will have opportunities to contribute to shaping the team’s research direction as it matures. The student will also benefit from opportunities to interact with an international network of collaborators and contacts in acadaemia and public health.
The student will be enrolled in the four-year structured PhD programme at the University of Galway, which will involve the completion of 30 ECTS credits of level 9 taught courses. Every PhD student, in addition to a supervisor, has their own Graduate Research Committee (GRC) of three academic staff members. The formal role of the GRC is to review the student’s progress annually and to make a recommendation to the College on progression into the next year of the programme.
Living allowance (Stipend): €22,000 per annum, tax-exempt scholarship award funded by the College of Science and Engineering. University tuition fees (EU/non-EU) are waived in full.
University fees: The university tuition fees for 2024/2025 are €5,750 per annum for EU students and €15,000 per annum for non-EU students. There is an additional student levy of €140 per annum, which is mandatory for all students to pay.
Start date: September 2024
Academic Entry Requirements:
- Primary degree in a relevant subject (e.g., Genetics, Genomics, Microbiology, Data Science, Bioinformatics, Public Health, Mathematics) [essential] Postgraduate degree or work experience in a relevant subject [desirable] High standard of spoken and written English (please see here for the University’s entry requirements) [essential] Experience of guided or independent research, which may include final-year project work, summer projects, etc. [essential] Familiarity with UNIX computing environments [essential] and with working with high-performance computing systems [desirable] Familiarity with current and emerging nucleic acid sequencing technologies, such as Illumina, PacBio, and Oxford Nanopore [essential] Experience of relevant bioinformatics analysis, including but not limited to mapping and variant calling, the handling of long-read sequencing data, genome assembly, pangenome and core genome alignment calculation, phylogenetic analyses, and relevant statistical approaches [desirable] Experience in molecular microbiology which can be used to inform or validate bioinformatics research, including but not limited to targeted mutagenesis and mutant validation, transposon mutagenesis and library screening, TraDIS/Tn-seq, ChIP-seq, RNA-seq, whole genome sequencing [desirable] Experience of working as part of a team inside or outside of research, which may include international team members [desirable] Familiarity with coding, scripting, or data handling using at least one language (e.g., R, Python, etc) [desirable] Understanding of the importance of confidentiality in the handling of sensitive or potentially-identifiable (meta)data, and of best practice in the management of such research data [essential] Familiarity with the scientific publishing process, best practice for the management of research data, and research ethics principles in Ireland [essential]
Applications must address each of the entry requirements above, and the email subject line must include the position reference MJD_CSEPHD2024. Applications lacking any of the materials requested or which fail to address the entry requirements will not be considered.
Contact Name: Dr Matthew Dorman
Contact Email: matthew.dorman@universityofgalway.ie
Application Deadline: 12/04/2024, 1700h (Irish time 24hr format)
Primary Supervisor name: Dr Matthew Dorman.
Company
NUI Galway is recognized as a research-led University that addresses issues of global economic and societal importance. Our research strategy focuses on developing clusters of internationally recognised expertise in selected priority areas. We have developed meaningful and strategic research alliances with economic, social and cultural partners in areas of regional and national importance. This strategy has resulted in the creation of research clusters in themes that are academically challenging, economically viable and regionally and nationally relevant. We continue to develop our research priorities within the national and international context in addition to supporting emerging and cross cutting priority area development. Our priority research areas build upon our key strengths and include:
- Biomedical Science and Engineering
- Informatics, Data Analytics, Physical and Computational Sciences
- Environment, Marine and Energy
- Applied Social Sciences and Public Policy
- Humanities in Context including Digital Humanities
These priority areas seek to address the challenges and needs of society. Our research leads to life changing discoveries and polices that shape the future both nationally and internationally. Our vibrant and dynamic community attracts researcher leaders, academics, entrepreneurs and students of the highest calibre who thrive in our research focused environment. This is embodied though our research commitment , which seeks to:
1. Contribute to Knowledge
2. Create partnerships with Industry
3. Educate Future Leaders
4. Shape the Direction of Public Policy
5. Enable Regional and Cultural Advancement
Biomedical Science and Engineering
Developing innovative research programmes that promote the understanding and treatment of today’s major diseases. The core objective of this priority is to serve the needs of patients through research, to provide a real and measurable return on investment, to enhance regional and national enterprise development and to contribute to society through education and scientific outreach. Researchers focus on some of the major medical challenges that face the world today including cardiovascular disease, cancer, orthopaedic disorders and neurodegenerative diseases.
http://www.curamdevices.ie
http://www.nuigalway.ie/research/apoptosis/index.html
http://www.chromosome.ie/
http://www.remedi.ie/
http://ncbes.eurhost.net/neuroscience.aspx
Informatics, Data Analytics, Physical and Computational Sciences Science
NUI Galway’s researchers in informatics use their world-wide network of partners to take part in global standardisation efforts and to improve the way people and businesses communicate and interact. Research also addresses the problems presented by vast data sets flowing from imaging activities that need significant computing power to reduce, analyse and visualize and further research looks at modelling and simulation, which are integral to almost all physical and biological sciences.
http://www.insight-centre.org
http://www.nuigalway.ie/lighthouse
http://www.ichec.ie
Environment, Marine and Energy
This research area covers environmental change and modelling, atmospheric studies, biodiversity and bioinformatics, marine science and law, and sustainable energy. Research efforts towards enhanced energy efficiencies and conservation methods, renewable energy sources and new advanced environmental technologies, help address the dilemma between balanced economic growth and environmental impact.
http://www.ryaninstitute.ie
http://www.marei.ie
Applied Social Sciences and Public Policy
Research programmes examine economic innovation, social change, social inclusion, balanced development and health. The Whitaker Institute applies a multiperspective research approach to business and social issues, with an impact-led focus within the following research clusters:
- Business Performance, Agility and Governance
- Conflict and Collective Action
- Environment, Development and Sustainability
- Gender, Equality and the Knowledge Society
- Health and Well-Being
- Innovation: People, Place and Society
http://www.nuigalway.ie/ilas
http://www.whitakerinstitute.ie/
Humanities in Context including Digital Humanities
Humanities at NUI Galway is a vibrant research rich area for scholarship and debate. Programmes include research into Ireland’s presence within the European and Global community and its contribution to international developments, as well as the unique contribution that NUI Galway can make to the Irish language and cultural studies.
- Exemplary collection of archives in the James Hardiman Library dating from the 15th century to the present day including ; Archives of the Druid, Lyric Taibhdhearc na Gaillimhe theatres, literary papers include the archive of John McGahern, playwrights and actors papers such as Tom Kilroy papers, and film archives include the John Huston papers.
- Unique national training hub enables and encourages interaction between archival resources, digital cultures, the business economy, public policy and social opportunity.
- Research informs creative practices, production values, and strategies for the creative industries.
http://www.mooreinstitute.ie
Location
Galway takes centre stage on Ireland’s western seaboard. A spectacularly beautiful county, it is a medley of contrasts - the wildest and remotest of countryside teamed with one of Europe’s most vibrant and popular cities. Connemara is located to the west of Galway; whilst to the south, in the mouth of Galway Bay, are the Irish speaking Aran Islands where age old traditions are found along side modern living.
Cultural Galway
Galway is known as Ireland’s Cultural Heart (Croí Cultúrtha na hÉireann), attracting thousands to the many festivals throughout the year. A few of the big attractions include The Cúirt International Festival of Literature, the Galway Arts Festival, the Galway Races and the Oyster Festival.
Vibrant Galway
Even though it is one of the fastest growing cities in Europe, Galway has retained the friendly character and intimate feel that make it so popular. Galway is young at heart, with students making up 20% of the population here. Galway is the most international place in Ireland with 1 in 4 people born outside of the state.
Business In Galway
Galway is the location of choice in Europe for the medical device sector which now employs in excess of 25,000 people in over 250 companies in Ireland. Ireland is now home to 17 of the top 25 global MedTech companies and exports exceed €7.9 billion annually. Other industries include ICT, Tourism and Financial Services.
IE
