PhD positions in ML-guided directed evolution (3.0 FTE) (V25.0085)

Are you passionate about combining the directed evolution of diverse biomolecules with deep learning approaches and contributing to the development of better (bio)catalysts and drugs? We are offering three fully-funded, 4-year PhD positions at the University of Groningen or the Technical University of Eindhoven.

Evolution is an all-purpose problem solver, which researchers mimic in the laboratory to engineer tailor-made (bio)molecules that aid us in combating diseases and in realizing a sustainable economy. While effective, such directed evolution campaigns are not only laborious and time-consuming, but also cover only a miniscule fraction of the unimaginably large sequence space available. As a result, means to guide evolutionary trajectories along a biomolecule’s fitness landscape are sought-after, as they could greatly accelerate evolutionary searches.

Within the framework of the recently funded ML-GUIDE project, we will make directed evolution guidable and, ultimately, predictable by machine learning. Specifically, you will build a first-in-class framework to expedite the design of high-affinity binders that engage with therapeutic targets or efficient (bio)catalysts for synthetic applications. By seamlessly merging cutting-edge directed evolution, next-generation sequencing, and deep learning approaches, you will establish accelerated Design-Build-Test-Learn cycles to continuously improve models via active learning and guide evolutionary trajectories toward promising but otherwise inaccessible sequence spaces.

You will be embedded in one of the three research groups involved in the ML-GUIDE project and focus your efforts on guiding engineering efforts for one particular biomolecule and its associated function.

(1) Dr Robert Pollice (https://pollicegroup.web.rug.nl/) leads the Artificial Organic Chemistry Lab at the University of Groningen and will supervise a project focusing on developing efficient peptide catalysts for powerful C-C-bond forming reactions.
(2) Prof. Francesca Grisoni (https://molecularmachinelearning.com/) leads the Molecular Machine Learning Group at the Technical University Eindhoven and will lead a project on designing potent cyclic-peptide drugs for therapeutic intervention.
(3) Prof. Clemens Mayer (https://mayerlab.nl/) leads the Molecular Evolution Group at the University of Groningen and will tackle a project on making the directed evolution of biocatalysts predictable by machine learning.

As part of the ML-GUIDE team, you will closely collaborate with researchers to identify commonalities and distinct aspects of engineering biomolecules for diverse applications!

Organisations
The University of Groningen is a research university, currently in or around the top 100 on several influential ranking lists. The Faculty of Science and Engineering (FSE) is the largest faculty within the University, offering first-rate education and research in a wide range of science and engineering disciplines. In this position, you would be embedded in the Stratingh Institute for Chemistry (https://www.rug.nl/research/stratingh/?lang=en).

Eindhoven University of Technology is an internationally top-ranking university in the Netherlands that combines scientific curiosity with a hands-on attitude. Our spirit of collaboration translates into an open culture and a top-five position in collaborating with advanced industries. Fundamental knowledge enables us to develop innovative solutions to complex societal challenges. In this position, you would be embedded in the Institute for Complex Molecular Systems (https://www.tue.nl/en/research/institutes/institute-for-complex-molecular-systems) and in the Eindhoven AI Systems Institute (https://www.tue.nl/en/education/professional-education/current-programs/eaisi-academy).

We are looking for creative, motivated, and determined candidates, who meet the following requirements:

• An MSc degree (or an equivalent university degree) in (Bio)chemistry, Biotechnology, Computational Chemistry, Synthetic Chemistry/Biology or a related field.
• Experience in one of the following areas is highly preferred: directed evolution, molecular machine learning, next-generation sequencing, or synthetic chemistry.
• An interest in working as part of a highly interdisciplinary team at the interface of synthetic biology, molecular machine learning, and synthetic chemistry.
• A research-oriented attitude with good analytical skills.
• Excellent communication and organization skill.

We offer you, following the Collective Labour Agreement for Dutch Universities:

• A salary of € 2,901 gross per month in the first year, up to a maximum of € 3,707 gross per month in the fourth and final year for a full-time working week.
• A holiday allowance of 8% gross annual income and an 8.3% year-end bonus.
• A full-time position (1.0 FTE). The successful candidate will first be offered a temporary position of one year with the option of renewal for another three years. Prolongation of the contract is contingent on sufficient progress in the first year to indicate that a successful completion of the PhD thesis within the next three years is to be expected.
• High-quality training programs and other support to grow into a self-aware, autonomous scientific researcher.
• At the University of Groningen: a PhD training programme is part of the agreement and the successful candidate will be enrolled in the Graduate School of Science and Engineering.
• At the Eindhoven University of Technology: high-quality training programs on soft skills, as well as technical skills related to research, offered by TU/e, the Institute for Complex Molecular Systems (ICMS) and the Eindhoven AI Systems Institute (EAISI).

Conditions of employment (University of Groningen Groningen): https://www.rug.nl/about-ug/work-with-us/new-staff/conditions-of-employment?lang=en
Conditions of employment (TU/e): https://www.tue.nl/index.php?id=76777&L=2

The preferred starting date is between 1 June 2025 and 1 October 2025.

Do you meet our qualification criteria? If yes, please upload the following documents to complete your application:

• A letter stating (1) your motivation to apply, (2) your key qualities relevant for this position, and (3) which research group in the ML-GUIDE consortium you would like to join.
• An up-to-date curriculum vitae.
• Diplomas (BSc and Msc (if available)) and transcript of records.
• Contact information of two academic references.

You may apply for this position until 30 April 11:59pm / before 1 May 2025 Dutch local time (CEST) by means of the electronic application form (click on "Apply" below on the advertisement on the university website).

Interviews will be held on a rolling basis and positions will be filled as soon as suitable candidates are found.

The University of Groningen strives to be a university in which students and staff are respected and feel at home, regardless of differences in background, experiences, perspectives, and identities. We believe that working on our core values of inclusion and equality are a joint responsibility and we are constructively working on creating a socially safe environment. Diversity among students and staff members enriches academic debate and contributes to the quality of our teaching and research. We therefore invite applicants from underrepresented groups in particular to apply. For more information, see also our diversity policy webpage: https://www.rug.nl/about-ug/policy-and-strategy/diversity-and-inclusion/

Our selection procedure follows the guidelines of the Recruitment code (NVP): https://www.nvp-hrnetwerk.nl/nl/sollicitatiecode and European Commission's European Code of Conduct for recruitment of researchers: https://euraxess.ec.europa.eu/jobs/charter/code

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