PhD Position: EVOLF Towards an AI Model of Cell-free Gene Expression in Synthetic Cells

Do you want to contribute to the bottom-up construction of synthetic cells? Are you excited about the application of AI tools to predict gene expression levels across a synthetic genome? Then join our team as a PhD Candidate!

Future synthetic cells will require an optimised gene expression system, capable of reliable, well-controlled expression of hundreds of genes on a synthetic genome. However, we cannot predict how much and how fast proteins are produced in vitro, as we need to learn the so-called cis-regulatory code: the relationship between DNA sequence and protein levels.

The ambition of this project is to train an AI model that predicts the cis-regulatory code for synthetic genomes (i.e. for cell-free gene expression systems) and correlates the experimental conditions within the synthetic cell (crowding, concentration of nutrients, size of liposome, etc.) with gene expression levels across a synthetic genome.

To achieve this aim, you will use VASA-seq and Ribo-Seq to generate large data sets that can be used for training machine learning and deep learning models. You will work in tight collaboration with other researchers in Nijmegen, Delft and at the Hubrecht Institute (van Oudenaarden group).

Profile

• You have a Master’s degree in chemistry, biochemistry, molecular biology, or a related field.
• You are motivated by deep scientific curiosity, have excellent experimental and quantitative skills and possess a drive to learn and develop new methods and concepts.
• You have excellent verbal and written communication skills in English.
• You have a strong affinity with teamwork and thrive in an international, ambitious, multidisciplinary and highly collaborative environment.

We are

The department of Physical Organic Chemistry is an international, diverse and multidisciplinary team of chemists, physicists, biologists, engineers and AI/ML scientists at the Institute for Molecules and Materials, Radboud University (Nijmegen, Netherlands). The EVOLF research consortium includes 31 research groups across the Netherlands that have joined forces to construct bottom-up synthetic cells.

Radboud University

At Radboud University, we aim to make an impact through our work. We achieve this by conducting groundbreaking research, providing high-quality education, offering excellent support, and fostering collaborations within and outside the university. In doing so, we contribute indispensably to a healthy, free world with equal opportunities for all. To accomplish this, we need even more colleagues who, based on their expertise, are willing to search for answers. We advocate for an inclusive community and welcome employees with diverse backgrounds, cultures, and perspectives. Will you also contribute to making the world a little better? You have a part to play.

Faculty of Science
The Faculty of Science (FNWI), part of Radboud University, engages in groundbreaking research and excellent education. In doing so, we push the boundaries of scientific knowledge and pass that knowledge on to the next generation.
We seek solutions to major societal challenges, such as cybercrime and climate change and work on major scientific challenges, such as those in the quantum world. At the same time, we prepare our students for careers both within and outside the scientific field. Currently, more than 1,300 colleagues contribute to research and education, some as researchers and lecturers, others as technical and administrative support officers. The faculty has a strong international character with staff from more than 70 countries. Together, we work in an informal, accessible and welcoming environment, with attention and space for personal and professional development for all.

We offer

• We will give you a temporary employment contract (1.0 FTE) of 1.5 years, after which your performance will be evaluated. If the evaluation is positive, your contract will be extended by 2.5 years (4-year contract).
• You will receive a starting salary of €2,901 gross per month based on a 38-hour working week, which will increase to €3,707 in the fourth year.
• You will receive an 8% holiday allowance and an 8,3% end-of-year bonus.
• We offer Dual Career Coaching. The Dual Career Coaching assists your partner via support, tools, and resources to improve their chances of independently finding employment in the Netherlands.
• You will receive extra days off. With full-time employment, you can choose between 30 or 41 days of annual leave instead of the statutory 20.

Additional employment conditions

Work and science require good employment practices. Radboud University's primary and secondary employment conditions reflect this. You can make arrangements for the best possible work-life balance with flexible working hours, various leave arrangements and working from home. You are also able to compose part of your employment conditions yourself. For example, exchange income for extra leave days and receive a reimbursement for your sports membership. In addition, you receive a 34% discount on the sports and cultural activities at Radboud University as an employee. And, of course, we offer a good pension plan. We also give you plenty of room and responsibility to develop your talents and realise your ambitions. Therefore, we provide various training and development schemes.