Pre-Doctoral Researcher
2 weeks ago
The project will explore the potentially transformative value of Foundation Models (FM), generative AI (GenAI) and Agentic Workflows for accelerating scientific discovery in biological sciences, particularly in the field of glycomics. These emerging in-silico technologies have already given rise to models, such as AlphaFold, which aim to accelerate research in structural biology, drug discovery, and disease understanding. The complexity of glycomics arises from the structural diversity, branching patterns, dynamic modifications, and functional versatility of glycans. These glycans affect cell-cell communication, immune system regulation, protein folding, pathogen recognition, signal recognition and have important implications across biological systems.
Current experimental and computational methods continue to generate vast amounts of biological and glycan-related data, yet their integration and analysis remain a bottleneck in translating this information into actionable biological insights and new hypotheses. When combined, these technologies promise to handle large-scale data from multiple sources (e.g., knowledge bases, experiment databases) to learn complex patterns and carry out inferences. Additionally, the development of novel agentic tools and workflows can further bring these technologies together and unlock new research avenues. By iteratively probing multiple models, knowledge, and tools, agents may be used to design and test new hypotheses, perform and validate in-silico experiments, or suggest the most promising experiments to be designed and undertaken. These activities will generate significant novel insight into the fields of Immunology and Neuroscience, progress novel target identification and (bio)therapeutic design as well as advance computational methods and GenAI.
The student will focus on building bridges between these technologies and domains to advance the fields of glycobiology and glycoinformatics, bioinformatics and computer science.
The student will have access to rich datasets from cutting-edge facilities as well as IBM's compute infrastructure.
We offer a fully funded 4-year PhD position at the intersection between computer systems design and AI as part of a new initiative between IBM Research Europe and Trinity College Dublin (TCD).
The PhD project will be jointly supervised by Professor Gavin Davey, School of Biochemistry and Immunology, Trinity College Dublin and Dr Joao Bettencourt-Silva (IBM Research Europe).
The selected student will be employed by IBM for the duration of the PhD and be a registered student at TCD with the following benefits:
- Access to resources and expertise both at IBM Research and TCD
- Research experience in both private and public sectors
- A substantial PhD Salary (>40,000 euro per annum)
- Full TCD PhD program fees (EU or non-EU level)
Your role and responsibilities
The following research questions will be tackled by the student:
- How can emerging multimodal foundation models (e.g., for small molecules, proteins, genes), LLMs (e.g., Granite) and other domain-specific models (e.g., AlphaFold) be used together with existing tools and knowledge bases (e.g., Glycologue, UniCarb-DB) to create new, more detailed models, of glycoproteins and advance glycoprotein research?
- How may agentic workflows be developed to integrate heterogeneous experimental datasets, perform iterative hypothesis generation, and guide experimental designs?
- Can models be trained to identify novel glycan targets in human diseases like cancer and optimise antibody design and synthesis?
- How do we use agentic workflows to model glycosyltransferase and glycosidase networks and train them to generate novel glycan structures which have nutritional and therapeutic benefits?
- Investigate how agentic workflows, computational tools and models may be applied and scaled across domains within scientific discovery workflows.
Examples of models, tools and databases and references:
- Glycologue https://glycologue.org
- UniCarb-DB https://unicarb-db.expasy.org
- Alphafold [1] https://www.nature.com/articles/s41586-024-07487-w
- Multi-view Molecular Embedding with Late Fusion (MMELON) [2] https://arxiv.org/abs/2410.19704
- Molecular Aligned Multi-Modal Architecture and Language (MAMMAL) [3] https://arxiv.org/abs/2410.22367
- Otter-Knowledge: benchmarks of multimodal knowledge graph representation learning from different sources for drug discovery [4] https://arxiv.org/abs/2306.12802
- The Virtual Lab: AI Agents Design New SARS-CoV-2 Nanobodies with Experimental Validation [5] https://www.biorxiv.org/content/10.1101/2024.11.11.623004v1
- Enhancing foundation models for scientific discovery via multimodal knowledge graph representations [6] https://www.sciencedirect.com/science/article/pii/S1570826824000313
References
Visible links
1. https://www.nature.com/articles/s41586-024-07487-w
2. https://arxiv.org/abs/2410.19704
3. https://arxiv.org/abs/2410.22367
4. https://arxiv.org/abs/2306.12802
5. https://www.biorxiv.org/content/10.1101/2024.11.11.623004v1
6. https://www.sciencedirect.com/science/article/pii/S1570826824000313
Required technical and professional expertise
- An honours degree in a relevant domain.
- Master's Degree in one of the relevant fields such as Bioinformatics, Computational Biology, Data Analytics, Computer Science.
- Basic knowledge of Machine Learning and Artificial Intelligence: ML fundamentals and common Deep Learning architectures; experience with AI/ML libraries such as Pytorch.
- Good programming skills: Python, version control, ability to write complex code from scratch and extend existing codes.
- Strong interest in performing basic research work, including: evaluation of existing literature, ideation of possible/alternative solutions, writing research papers.
- Ability to move quickly from idea to software prototype for evaluation and demonstration.
- Excellent spoken and written English.
Preferred technical and professional experience
- An honours degree in biological sciences, biochemistry, bioinformatics or similar.
- A background in computational and/or data-driven methods.
- Experience applying computational methods to scientific or biological data.
- Knowledge of foundation model architectures with a specific focus on models using biological data and multi-modality.
- Knowledge of Agentic Workflows, common architectures and frameworks.
- Knowledge of GenAI approaches: model architectures, fine-tuning, transfer learning.
- Advanced programming skills: Python and data preprocessing (Pandas, Xarray).
- Understanding or an interest in the fields of Glycobiology, Glycomics.
- Mass Spectrometry & Experimental techniques (optional).
- Track record of published academic papers.
#J-18808-Ljbffr
-
Pre-Doctoral Researcher
1 week ago
Dublin, Dublin City, Ireland Avature Full timeAI systems with embedded large language models (LLMs), like AI Agents, demonstrate significant potential for solving complex tasks by dynamically adapting to feedback and refining their strategies. However, ensuring responsible, safe, and secure deployment is crucial, as these systems face privacy and security risks from malicious actors – be it leakage of...
-
Research Pre-Doctoral Researcher Dublin, IE
2 weeks ago
Dublin, Dublin City, Ireland Avature Full timeAI systems with embedded large language models (LLMs), like AI Agents, demonstrate significant potential for solving complex tasks by dynamically adapting to feedback and refining their strategies. However, ensuring responsible, safe, and secure deployment is crucial, as these systems face privacy and security risks from malicious actors – be it leakage of...
-
Dublin, Dublin City, Ireland Avature Full timeThe project will explore the potentially transformative value of Foundation Models (FM) and generative AI (GenAI) approaches for scientific discovery. The ability of such approaches to handle vast amounts of data and learn complex patterns makes them particularly promising in physics for providing insights that conventional methods may miss. The last few...
-
Post Doctoral Researcher
1 week ago
Dublin, Dublin City, Ireland Technological University DublinTU Dublin Full timeApplications are invited for the following Post in the Technological University Dublin: Post: Post Doctoral Researcher - Pathways for developing New Urban Tourism in Dublin (PNUT) PROJECT - School of Tourism & Hospitality Management (Fixed Term Specified Purpose Wholetime for up to 5 years with initial funding for 2 years) (Reference: 117/2025) Location:The...
-
Dublin, Dublin City, Ireland Technological University DublinTU Dublin Full timeApplications are invited for the following Post in the Technological University Dublin: Competition ID 036523 Post: Post-Doctoral Researcher in Advanced Manufacturing & Engineering - ARISE PROJECT - School of Mechanical Engineering (Fixed Term Specified Purpose Wholetime for up to 5 years with initial funding in place for 2 years) (Reference: 112/2025)...
-
Post-doctoral Researcher
1 week ago
Dublin, Dublin City, Ireland Royal College of Surgeons (RCSI) Full timeJob Title: Post-Doctoral researcherDepartment: Department of SurgeryReporting to: Professor Leonie YoungLocation: RCSI, St Stephens Green, Dublin 2Contract/Duration: 2 YearsRemuneration: €43,371Closing Date: 17.02.2025About Our ResearchRCSI recognises that excellence in research is critical to the quality of its educational activities, its credibility,...
-
Post-doctoral Researcher
2 days ago
Dublin, Dublin City, Ireland Royal College of Surgeons (RCSI) Full timeJob Title: Post-Doctoral researcherDepartment: Department of SurgeryReporting to: Professor Leonie YoungLocation: RCSI, St Stephens Green, Dublin 2Contract/Duration: 2 YearsRemuneration: €43,371Closing Date: 17.02.2025About Our ResearchRCSI recognises that excellence in research is critical to the quality of its educational activities, its credibility,...
-
Post-doctoral Fellow
2 weeks ago
Dublin, Dublin City, Ireland Euraxess Full timeTrinity College Dublin School of ChemistryOrganisation/CompanyTrinity College Dublin School of ChemistryDepartmentSchool of ChemistryResearch FieldEngineering » OtherResearcher ProfileRecognised Researcher (R2)PositionsPostdoc PositionsCountryIrelandApplication Deadline17 Mar 2025 - 17:00 (Europe/London)Type of ContractTemporaryJob StatusFull-timeIs the job...
-
Dublin, Dublin City, Ireland University of Galway (NUI Galway) Full timeApplications are invited from suitably qualified candidates for a full-time, fixed term position as a Postdoctoral Researcher with Civil Engineering at the University of Galway, Ireland.This position is funded by the MSCA Doctoral Networks - European Commission, and is available from 1st of July 2025 to contract end date of 30th of June 2028.Information on...
-
Researcher Position
4 days ago
Dublin, Dublin City, Ireland Technological University Dublin Full timeThe Technological University Dublin is seeking a highly qualified and experienced researcher to join our team as a Post Doctoral Researcher. This role will be based at one of our campuses, including Grangegorman, Blanchardstown or Tallaght.This is a fixed-term specified purpose appointment for up to 5 years with initial funding for 2 years. The successful...
-
Academic Researcher
4 days ago
Dublin, Dublin City, Ireland Technological University Dublin Full timeThe Technological University Dublin is seeking an exceptional researcher to join our team as a Post Doctoral Researcher. This role will involve conducting research on sustainable urban tourism futures and contributing to the development of the university's research strategy.The successful candidate will have a PhD or equivalent in human geography, urban...
-
Dublin, Dublin City, Ireland MPOWIR Mentoring Physical Oceanography Women to Increase Retention Full timeMarine Institute Post Doctoral Fellowship Call 2019The Marine Institute is pleased to announce a call for proposals for Post-Doctoral Fellowships of 3 to 5 years in duration. There are seven defined topics and one open topic under four specified research themes of the National Marine R&I Strategy. Proposals are invited from suitable Research Supervisors at...
-
Family Medicine Doctor, Ireland
2 days ago
Dublin, Dublin City, Ireland Euraxess Full timeOrganisation/Company: PhD-Jobs.NET Research Field: Medical sciences » Medicine Researcher Profile: Other Profession Positions Bachelor Positions Country: Ukraine Application Deadline: 10 May :00 (Africa/Abidjan) Type of Contract: Permanent Job Status: Full-time Is the job funded through the EU Research Framework Programme?Not funded by a EU programme...
-
Senior Research Fellow
4 days ago
Dublin, Dublin City, Ireland Technological University Dublin Full timeWe are seeking an exceptional researcher to join our team as a Post Doctoral Researcher. This role will involve conducting research on sustainable urban tourism futures and contributing to the development of the university's research strategy.The successful candidate will have a PhD or equivalent in human geography, urban studies, entrepreneurial studies,...
-
Postgraduate Research Associate
4 days ago
Dublin, Dublin City, Ireland Technological University Dublin Full timeThe Technological University Dublin is seeking a highly skilled and motivated researcher to join our team as a Post Doctoral Researcher. This role will involve conducting research on sustainable urban tourism futures and contributing to the development of the university's research strategy.The successful candidate will have a PhD or equivalent in human...
-
Research Associate
2 days ago
Dublin, Dublin City, Ireland Dublin Institute For Advanced Studies Full timeThe DIAS Solar Physics Group is offering a Research Associate position to work on the ARCAFF project, which seeks to improve flare forecasting using deep learning techniques and solar observation data. As a Research Associate, you will play a key role in the development and training of deep learning models, integrating developed models into research, and...
-
Dublin, Dublin City, Ireland Royal College of Surgeons (RCSI) Full timeJob Title: Postdoctoral Researcher or Senior Postdoctoral ResearcherDepartment: Health PsychologyReporting to: Professor Frank DoyleLocation: School of Population Health, RCSI University of Medicine and Health Sciences, Beaux Lane House, Dublin 2Contract/Duration: 24 monthsRemuneration: Aligned to the IUA Senior Postdoctoral Researcher Salary Scale...
-
Dublin, Dublin City, Ireland Trinity College Dublin Full timeTrinity is Ireland's leading university and is ranked 87th in the world (QS World University Rankings 2025). Founded in 1592, the University is steeped in history with a reputation for excellence in education, research, and innovation, which has been inspiring generations of thinkers for over 400 years. Post doctorate vacancy for a researcher to play a key...
-
Dublin, Dublin City, Ireland University of New South Wales Full timeResearch Associate in Data Science and AI, UNSW CanberraApply now Job no: 529417Work type: Full TimeLocation: Canberra, ACTCategories: Post Doctoral Research Associate, Senior Research AssociateResearch Associate in Data Science and AI, UNSW CanberraEmployment type: Fixed-term, full-timeDuration: Up to 24 monthsRemuneration: Level A, Step 6 $110,059 plus 17%...
-
Research Fellow
4 days ago
Dublin, Dublin City, Ireland Technological University DublinTU Dublin Full timeCompany OverviewTU Dublin is a leading technological university dedicated to providing high-quality education and research opportunities. Our university is committed to being fully inclusive, actively recruiting, supporting, and retaining staff from all sectors of society.SalaryThe successful candidate will be appointed at point (01) of the Post-Doctoral...
