Doctoral fellow

Job description

PhD Researchers on AI for drug design

Job description
ABOUT GHENT UNIVERSITY
Ghent University is a world of its own. Employing more than 15.000 people, it is actively involved in education and research, management and administration, as well as technical and social service provision on a daily basis. It is one of the largest, most exciting employers in the area and offers great career opportunities.
With its 11 faculties and more than 85 departments offering state-of-the-art study programmes grounded in research in a wide range of academic fields, Ghent University is a logical choice for its staff and students.
ABOUT IDLAB
The IDLab Ghent research group from Ghent University - imec in Belgium is extending its interdisciplinary research cluster focusing on artificial intelligence for bio-informatics, within a new collaboration project between academia and industry, focusing on the AI-driven generation and optimization of proteins for therapeutic purposes.
This vacancy encompasses 4 different PhD tracks within the same project, focusing on developing machine learning models and training strategies for the creation and adaptation of antibodies and nanobodies, with the following topics of focus:
- Topic 1: designing prediction models for the developability properties thermostability, spatial aggregation propensity, and sequence liabilities (with a strong focus on the application level),
- Topic 2: designing multi-objective guidance strategies of protein diffusion models for developability-aware generation (both fundamental and application oriented),
- Topic 3: design and training of energy-based models for unsupervised binding affinity prediction (mostly fundamental AI research),
- Topic 4: energy-based representation learning techniques for small molecules as drug candidates (more fundamental AI research).

We are seeking highly motivated and talented PhD students to join the AI-bioinformatics research cluster, with profs. Thomas Demeester, Jan Fostier, and Kathleen Marchal, combining their respective expertise in machine learning, high-performance compute in bioinformatics, and AI for biology.
The PhD fits within the recently launched imec Health Mission, a strategic research track aiming to advance the discovery and development of novel therapeutics over the next 10 years. IDLab Ghent is a key partner in the Health Mission, and leads the first mission project ADAPT (for "Affinity and Developability through AI for Protein Therapeutics"). ADAPT aims to develop AI-based models to design and optimize antibodies and nanobodies with high binding affinity and optimal developability properties, in a collaboration with several imec research groups and key industrial partners from the Ghent area specialized in nanobody technology.

The main tasks for the PhD students will include:
• Studying state-of-the-art techniques and benchmarks in the domain of antibody design with machine learning models (including protein language models and/or protein diffusion models).
• Design, implementation, and training of new models, focusing on one of the topics listed above.
• Collaboration towards proof-of-concept implementations of the created models for validation by experts in the domain of antibody engineering.
• Writing high quality publications, targeting top journals and international conferences.
In addition to these primary research responsibilities, the PhD student will actively contribute to the educational mission of our institution by providing (limited) support for courses in the area of AI and/or bioinformatics, and taking on a mentoring role by supervising master theses related to the subject of the PhD.

What we can offer you

• We offer the opportunity to do this research in an international and stimulating environment. Ghent University consistently ranks among the best 100 universities in the world. Located in the heart of Europe, Ghent is a beautiful and welcoming city with plenty of cultural and leisure activities (https://www.lonelyplanet.com/belgium/flanders/ghent).
• We offer a full-time position as a doctoral fellow, consisting of an initial period of 12 months, which - after a positive evaluation, will be extended to a total maximum of 48 months.
• The fellowship amount is 100% of the net salary of an AAP member in equal family circumstances. The individual fellowship amount is determined by the Department of Personnel and Organization based on family status and seniority. A grant that meets the conditions and criteria of the regulations for doctoral fellowships is considered free of personal income tax. Click here for more information about our salary scales
• All Ghent University staff members enjoy a number of benefits, such as a wide range of training and education opportunities, 36 days of holiday leave (on an annual basis for a full-time job) supplemented by annual fixed bridge days, bicycle allowance and eco vouchers. Click here for a complete overview of all the staff benefits (in Dutch).

Job profile

We are looking for a highly creative and motivated PhD student with the following qualifications and skills:
• You have (or will obtain before the starting date, i.e., a few months after application) a (European) master's degree in computer science, artificial intelligence, bioinformatics, mathematics, or equivalent, with excellent (‘honors’-level) grades. Your degree must be equivalent to 5 years of studies (bachelor + master) in the European Union.
• You have a strong background in at least one of the following topics,
and are excited to focus for four years on getting expert level experience in both
o machine learning (on a fundamental level)
o bioinformatics / computational biology
• You have excellent coding skills. Hands-on experience in deep learning frameworks such as PyTorch or Tensorflow is a plus, especially with language models and/or diffusion models. This is not strictly required for candidates with a background in bioinformatics.
• You have strong analytical skills to interpret the obtained research results.
• You are a team player and have strong communication skills.

How to apply

How to apply
Send your application by email to profs. Demeester (thomas.demeester@ugent.be) and Fostier (jan.fostier@ugent.be).
Please use the subject ‘Application: PhD at IDLab (AI4DD)’.

Applications should include:
• A motivation letter (highlighting why you believe you are a suitable candidate for the position & why you want this position). Please clearly mention the specific PhD topic(s) you are most interested in (see above). Make your suitability for the provided job profile explicit, and also describe relevant experience in related areas (for example, on molecular dynamics simulations).
• An academic/professional resume.
• Transcripts of study results.
• At least two reference contacts.
• A short overview describing your earlier research or technical work (e.g., scientific papers, master thesis, report on project work, etc.). Note: This may deviate from the topic of the advertised position.
After a first screening, selected candidates will be invited for an interview (in person or remotely via MS Teams).

Application deadline: December 31, 2024 (hiring will start earlier, though).
Start of the Ph.D. research: as early as October 2024, or the subsequent months.