PhD Position in Deep Immune Receptor Modelling - DTU Bioengineering

Join the forefront of immunoinformatics research and help revolutionise our understanding of immune receptor interactions.

Are you passionate about integrating cutting-edge machine learning with immunology?
Are you eager to develop tools that will redefine immunotherapy and immune system modelling? If so, we invite you to join the Deep Immune Receptor Modelling (DIRM) project, a pioneering initiative at the intersection of data science and immunology at the Technical University of Denmark (DTU).

About the PhD program
The DIRM project is a collaborative effort aimed at creating innovative deep machine learning tools tailored specifically to immune receptor (IR) interactions. This initiative seeks to overcome critical challenges in immunoinformatics by integrating advanced domain knowledge, cutting-edge data science, and targeted experimental validation.

The program involves collaboration with leading experts, including Professor Morten Nielsen (Immunoinformatics and Machine Learning for Immune Receptors), Assoc. Professor Timothy Jenkins (Structural Modelling and Protein Design), and Professor Sine Rekker Hadrup (Experimental Immunology with a focus on T cell recognition and detection). Together, they bring the needed expertise to guide the development of next-generation tools in immunoinformatics.

Benefiting from DTU's unique interdisciplinary ecosystem, the joint program between DTU Health Tech and DTU Bioengineering provides a vibrant and collaborative research environment where computational and experimental methodologies converge to tackle real-world challenges in immunology and immunotherapy. The whole program involves 3 PhD students and 2 Postdocs.

Your Role in the DIRM Project
As a PhD student, you will:

• Develop refined deep learning (DL) models to predict IR specificity, cross-reactivity, and functional clustering.
• Use techniques like contrastive and diffusion learning to address the scarcity and imbalance of data in immunoinformatics.
• Collaborate with domain experts to guide the design of novel, high-impact experimental datasets using active learning.
• Work at the interface of computational and experimental approaches to address real-world challenges in vaccine design, diagnostics, and immunotherapies.
• Present findings at leading conferences and publish in high-impact journals.

Responsibilities

• Design and optimize machine learning pipelines tailored for immune receptor modelling.
• Integrate structural and sequence-based data for improved prediction accuracy.
• Work on explainable AI techniques to provide biologically interpretable insights.
• Contribute to the active learning framework for data generation and refinement.
• Participate in collaborative research within a vibrant, multidisciplinary team.

You must have:

• A master’s degree in bioinformatics, computer science, biotechnology, or a related field.
• Experience in machine learning and immunology.
• A strong motivation to tackle interdisciplinary challenges and a proactive attitude towards research.

Additional skills that would be beneficial:

• Familiarity with protein structure prediction and design tools (e.g., AlphaFold, RFdiffusion).
• Experience with immune cell binding prediction tools like NetMHCpan or NetTCR.
• Interest in active learning and data augmentation strategies.
• Applied skills in ML-guided experimental design.
• Experience with (protein) representation learning (and protein language models).
• Working knowledge of immune repertoires.
• Experience with immune receptor data and structural modelling.
• Strong programming skills in Python or similar languages.

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

Approval and Enrolment 
The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see DTU's rules for the PhD education

We offer

DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility. 

Salary and appointment terms
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. The period of employment is 3 years.

You can read more about career paths at DTU here.

Further information 
May be obtained from Assoc. Prof. Timothy P. Jenkins (tpaje@dtu.dk)

You can read more about the Department of Biotechnology and Biomedicine at: www.bioengineering.dtu.dk 

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark. Furthermore, you have the option of joining our monthly free seminar “PhD relocation to Denmark and startup “Zoom” seminar” for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU. 

Application procedure 

Your complete online application must be submitted no later than 4 April 2025 (23:59 Danish time).

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• Application (cover letter)
• CV
• Academic Diplomas (MSc/PhD – in English)
• List of publications 

Applications received after the deadline will not be considered.

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply. As DTU works with research in critical technology, which is subject to special rules for security and export control, open-source background checks may be conducted on qualified candidates for the position.

The Department of Biotechnology and Biomedicine (DTU Bioengineering) is an international leader in the areas of biotechnology and biomedicine. Our engineering approach to all aspects of biotechnology and biomedicine positions us as a valuable player with unique competences in a growing bio-based economy and with health systems transforming towards personalized medicine. We have a clear focus on the needs in the life science- and biotech industries and point towards innovation, new businesses, and scientific services for the benefit of society. The department has extensive collaborations with national and international research units and industry. DTU Bioengineering has approx. 400 employees, of which 2/3 are scientific staff. The department is located at DTU Lyngby Campus.

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear mission to develop and create value using science and engineering to benefit society. That mission lives on today. DTU has 13,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.