The Nash Lab (Lab for Engineering Synthetic Systems) is affiliated with the Department of Chemistry at the University of Basel and the Department of Biosystems Science and Engineering of ETH Zurich in Basel. The lab operates at the interface of protein engineering, molecular biophysics, and synthetic biology, developing experimental and computational approaches to understand and engineer proteins for biomedical and industrial applications. This project focuses on developing high-throughput methods involving molecular surface display and deep sequencing to study force-dependent behavior in protein systems, with applications to blood clotting and relevance to Von Willebrand disease.
Tasks
- Establish and validate a quantitative, high-throughput assay for measuring the mechanical stability of a protein-protein interaction relevant to blood clotting
- Cross-validate high-throughput assay results against AFM measurements
- Design and construct DNA variant libraries and display them on yeast
- Apply next-generation DNA sequencing to quantify phenotypes
- Develop computational pipelines to convert sequencing data into quantitative fitness values
- Collaborate with a computational biology group at D-BSSE to develop and benchmark machine learning models
- Prepare data and manuscripts for publication and present results at lab meetings and conferences
- Enroll in and complete the requirements of the D-BSSE Doctoral program in Basel
- Contribute to undergraduate teaching and practical supervision at the University of Basel
Requirements
- A Master's degree in bioengineering, chemical engineering, biochemistry, molecular biology, biophysics, or a related field
- A strong quantitative background and genuine interest in protein engineering, mechanobiology, and/or high-throughput experimental methods
- Hands-on experience with molecular biology and protein expression techniques; prior exposure to yeast display, directed evolution, or single-molecule biophysics (e.g., AFM) is an advantage but not required
- Comfort with, or willingness to learn, computational analysis of large sequencing datasets (Python or equivalent); experience with machine learning is a plus
- Independent, careful experimental work combined with the ability to collaborate across two research groups and two institutions
- Willingness to contribute to bachelor level teaching / chemistry practicals
- Fluent written and spoken English
- Eligibility for enrollment in the D-BSSE Doctoral program in Basel
Benefits
- A Doctoral Position with primary supervision by Prof. Michael Nash and co-supervision by Prof. Niko Beerenwinkel, combining experimental and computational work
- Enrollment in the D-BSSE Doctoral program, with access to its coursework, seminar series, and interdisciplinary training environment
- A well-equipped lab at Mattenstrasse 22, 4058 Basel with established protein expression, yeast display, AFM, and high-throughput infrastructure, plus support from lab senior scientific and technical staff
- Close mentorship from a PI with an established track record in protein engineering and single-molecule biophysics, and collaboration with a leading computational biology group
- Funding to attend international conferences and present your work
- An international and interdisciplinary team of Doctoral Students, postdocs and scientists
- Exposure to ongoing projects in technology commercialization
- A collaborative, interdisciplinary project spanning molecular engineering, mechanobiology, high-throughput screening, and machine learning, with direct relevance to clinical medicine
- Competitive salary in accordance with Swiss doctoral salary standards
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Das Team
The Doctoral Student will work closely with a computational biology group at D-BSSE and be part of an international and interdisciplinary team of Doctoral Students, postdocs, and scientists, with mentorship from experienced principal investigators.