Application Form
Senior Researcher in Genomics and AI for Microbiome Data Analysis

JobRef: 23103
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Senior Researcher in Genomics and AI for Microbiome Data Analysis

Level:Senior Researcher
POSTED:April 15, 2024
LOCATION:Bishopstown Campus, Cork
Duration:12 months, fixed term
Reports to:Dr Haithem Afli & Dr Francesca Bottacini
Salary:Remuneration will be on the Senior Researcher Salary scale (€48,660 - € 60,047) per annum in line with relevant experience
Closing Date:May 3, 2024


Please note the below is a shortened version of the full job specification. For more details please refer to the full Job Description document, which can be downloaded by clicking on the ‘Download full job spec’ button above.

Duties of the Post:
The Senior Researcher will join the Human-Centred Research Group at MTU, focusing on the development of innovative bioinformatic algorithms and pipelines that utilise Large Language Models to better understand the complexity of genomic data. As part of the project, the candidate will develop new bioinformatic algorithms and pipelines involving Deep Learning and Large Language Models for information-extraction, classification and functional prediction of genomic data obtained by NGS sequencing of human gut-related samples (both viromes and metagenomes). The conducted research will contribute to elucidating the diversity of microbial components of microbiome and virome data, improve their taxonomical classification and extend our ability for functional prediction of uncharacterised proteins using structure-based analysis and Artificial Intelligence.

This collaborative research project involving partners such as MTU, ADAPT and APC Microbiome Ireland presents the successful candidate with the opportunity to work in a supportive, exciting, fast moving and excellent technical environment, playing a guiding role in a research project. The motivation of the team is to grow this research-led initiative into effective commercialisation of the research work products. The role will also include an opportunity to carry out research in Deep Learning focusing on genomic data analysis and Artificial Intelligence for the identification and development of novel functional food products. In collaboration with the Principle Investigator, the Researcher can co-supervise and support postgraduate students working on the same topic.

The Researcher will:
▪ be responsible for designing and implementing new genomic analysis methods.
▪ be responsible for the development of new models and/or pipelines for the functional
analysis, classification and functional prediction of microbiome and virome datasets.
▪ Work on the analysis and the visualisation of the results.
▪ Actively participate in the dissemination of research findings through high-impact academic
journals, conferences, and seminars.
▪ Collaborate closely with the Principal Investigator to participate in project calls, meetings,
and presentations, both within Ireland and internationally.
▪ Assist in the preparation of project deliverables, reports, and documentation, ensuring
adherence to project timelines and goals.
▪ Contribute to the supervision of postgraduate students’ research activities, providing
mentorship and supporting their academic development.
▪ Pursue relevant training and professional development opportunities to remain at the
forefront of NLP and federated learning research fields.
▪ Perform necessary administrative tasks related to the research programme, including data
management, ethics submissions, and progress reporting.

The appointee shall carry out the lawful instructions of the President (or authorised Officer)
and comply with the requirements and regulations of the Minister for Further and Higher
Education, Research, Innovation and Science.

Qualification Requirements and Selection Criteria for role:
Qualifications (Essential):
▪ A PhD, or be near the completion of their PhD, in a relevant field of Bioinformatics,
Machine Learning and Natural Language Processing, ensuring a deep understanding of the
theoretical and practical aspects of these disciplines.
▪ A significant research experience in genomic data analysis and Artificial Intelligence,
marked by a minimum of 2 years in roles directly linked to NGS data processing, Machine
Learning and development of AI-assisted analysis methods, will also be considered. This
experience should demonstrate a tangible impact on the field and compensate for the
absence of a PhD qualification.
▪ Those close to completing a Master’s degree in Computational biology, Bioinformatics,
Data Analytics and Artificial Intelligence may be considered, especially if they have engaged
in substantial projects or research pertinent to the development and application of AI

Knowledge and experience (Essential):
▪ Previous experience working with NGS microbiome data processing and analysis.
▪ Experience in designing and conducting experiments on high-performance computing
clusters, showcasing technical proficiency and an ability to manage complex computational
▪ An established record of providing research supervision and support to students at the
postgraduate level, demonstrating a capacity for mentorship and academic leadership.
▪ A strong publication record in international peer-reviewed publications and presentations
at top-tier conferences and journals, reflecting an active and successful research career.
▪ Excellent written and verbal communication and interpersonal skills, with the ability to
convey complex technical information clearly and collaborate effectively with various

Knowledge and experience (Desirable):

  • Previous research experience in Machine Learning, Deep Learning and NLP.
    Familiarity with statistics and microbiome analysis software and working on Linux
    Previous project management or administrative experience.

NOTE: In addition to the minimum qualifications, it may be necessary to introduce further shortlisting criteria. Therefore, candidates may be shortlisted on the basis of qualifications and suitable experience based on details given in the application. Candidates should note that they may be called
for more than one interview. Upon completion of interview, a panel will be formed from appointable candidates. Other attributes:

  • Good communication and interpersonal skills
    Evidence of ability to work on own initiative as well as part of a team
    Ability and willingness to work in a collaborative environment

Application Process:
Applications by MTU eRecruitment system only. Applications will not be accepted in any other format
or through any other channel of communication. Please log on to to apply for
this position.

Closing date for receipt of completed applications is
1.00 pm on 3rd May 2024.

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