PhD scholarship in Closed-Loop AI-Driven Protein Design at DTU Bioengineering

Are you ready to transform the future of biologics?
Are you passionate about understanding the interplay between AI-protein design, automation, and cutting-edge data science? And would you like to be part of a newly formed research collaboration between DTU and Novo Nordisk? Then you could be our new Ph.D.-student within BioAI. Read on to learn more!

About the research program – Closed Loop AI-driven Protein Binder Design
Technical University of Denmark (DTU) and Novo Nordisk have initiated a strategic partnership and created a joint cross-disciplinary research program aimed to tackle one of the life science industry’s biggest challenges: Closed-Loop Design and Optimization of Biologics. 

The research program will build on the recent advances in protein design, automation, and multi-parameter optimization and create a closed loop pipeline able to rapidly design binders to any target and optimized for developability. 

Further, the program is rooted in DALSA (DTU’s Arena for Life Science Automation), a new interdisciplinary center at DTU dedicated to merging life sciences, automation, and data-driven innovation to revolutionize research and development. 

The program combines the expertise of five DTU departments (Construct, Bioengineering, Compute, Electro, and Health Technology) and involves supervisors from both DTU and Novo Nordisk.

What you can expect 
As a PhD student, you will be at the heart of a vibrant and collaborative research environment that includes:

• Fellow PhD students, postdocs, and master’s students working on related projects with a shared overarching goal.
• Expert supervisors and mentors from DTU and Novo Nordisk. The main supervisor is affiliated with DTU, while the co-supervisor is based at Novo Nordisk. This team ensures the highest level of academic expertise to support both the project and the program.
• Opportunities to participate in conferences, symposia, and networking events to share and enhance your research.

Your role will be pivotal in driving innovation and contributing to a transformative approach to biologics development.

About the position
The PhD project is part of a larger initiative advancing closed-loop optimization for protein binder design, leveraging state-of-the-art generative AI technologies. You will contribute to developing workflows that integrate in silico library generation with high-throughput experimental validation and automation. This interdisciplinary role offers an opportunity to engage in cutting-edge research with potential applications in diagnostics, therapeutics, and reagent development.

Responsibilities and qualifications
Design and implement binder libraries using generative AI tools such as RFdiffusion and ProteinMPNN.

• Develop and optimise high-throughput experimental pipelines for cloning, expression, and characterisation of binders.
• Conduct binding assays using techniques and study binding kinetics such as Surface Plasmon Resonance (SPR) or Biolayer Interferometry (BLI).
• Analyse and refine the properties of binders, including stability, solubility, and developability metrics.
• Collaborate with automation engineers to digitise workflows and transfer analytical tests to automated platforms.
• Explore multimerisation strategies to enhance binder avidity and cross-binding capabilities.
• Contribute to the full automation of the library design and evaluation pipeline.
• Publish results in high-impact journals and present findings at scientific conferences.
• Engage in interdisciplinary training to build expertise in both computational and experimental techniques.

You must have:

• As a formal qualification, you must hold a master’s degree in a relevant field, such as bioinformatics, molecular biology, biotechnology, or a related discipline.
• Expertise in either computational protein design or wet lab techniques, with a willingness to learn the complementary skill set.
• Experience in collaborative research environments.
• Excellent communication and teamwork skills.
• A proactive attitude towards learning and applying new skills.
• It would further be beneficial if you have some of the following skills:
• Hands-on experience with protein expression systems such as bacteria, yeast, or cell-free systems.
• Basic knowledge of protein purification techniques (e.g., affinity chromatography, size exclusion chromatography).
• Familiarity with binding assays like SPR, BLI, or ELISA.
• Exposure to computational tools like RFdiffusion, ProteinMPNN, or AlphaFold2.
• Interest in automation and high-throughput experimental techniques.
• Strong analytical skills and the ability to work effectively in a collaborative, interdisciplinary research environment.

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 http://www.dtu.dk/english/about/job-and-career/working-at-dtu/career-paths.

Further information  
Further information may be obtained from Assoc. Prof. Timothy P. Jenkins ([email protected])

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 9 March 2025 (23:59 Danish time) . 

The hiring committee consists of representatives from DTU and Novo Nordisk.

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:

• A letter motivating the application (cover letter)
• Curriculum vitae 
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale

You may apply prior to ob­tai­ning your master's degree but cannot begin before having received it. 

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.

About the Novo Nordisk department where the project will be anchored – Research Bioanalysis
Departments of Research Bioanalysis is part of Global Research Technologies (GRT) area which drive the modality and technology innovation agenda by turning ideas into drugs in Research & Early Development (R&ED) at Novo Nordisk. Research Bioanalysis is located in Maaloev (Denmark). The department is responsible for establishing bioanalytical assays. We work with cutting-edge technology within their fields and support drug development projects across Novo Nordisk research portfolio.

Novo Nordisk is a leading global healthcare company with a 100-year legacy of driving change to defeat serious chronic diseases. Building on our strong legacy within diabetes, we are growing massively and expanding our commitment, reaching millions around the world and impacting more than 40 million patient lives daily. All of this has made us one of the 20 most valuable companies in the world by market cap. Our success relies on the joint potential and collaboration of our more than 63,000 employees around the world. We recognise the importance of the unique skills and perspectives our people bring to the table, and we work continuously to bring out the best in them.

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.