Doctoral Student - High-throughput Analysis of Protein-Protein Interactions

About the role

The Nash Lab, jointly affiliated with the Department of Chemistry at the University of Basel and the Department of Biosystems Science and Engineering of ETH Zurich, is looking for a doctoral student to develop high-throughput methods based on molecular surface display and deep sequencing to study how proteins respond to mechanical force. As a proof of concept, the project applies this platform to interactions central to blood clotting, with relevance to Von Willebrand disease. The student works at the interface of protein engineering, single-molecule biophysics and machine learning, in close collaboration with a computational biology group at D-BSSE.

Key responsibilities

• Establish and validate a quantitative, high-throughput assay for measuring the mechanical stability of a protein-protein interaction relevant to blood clotting
• Cross-validate assay results against AFM measurements
• Design and construct DNA variant libraries displayed on yeast, and use next-generation sequencing to quantify phenotypes
• Develop computational pipelines to convert sequencing data into quantitative fitness values
• Collaborate with the computational biology group to develop and benchmark machine learning models
• Prepare data and manuscripts for publication and present results at lab meetings and conferences
• Complete the requirements of the D-BSSE Doctoral program in Basel and contribute to undergraduate teaching and practical supervision

Required profile

• Master's degree in bioengineering, chemical engineering, biochemistry, molecular biology, biophysics or a related field
• Strong quantitative background and interest in protein engineering, mechanobiology and/or high-throughput methods
• Hands-on experience with molecular biology and protein expression; yeast display, directed evolution or single-molecule biophysics is an advantage but not required
• Ability to collaborate across two research groups and two institutions, and willingness to teach at bachelor level
• Fluent written and spoken English and eligibility for the D-BSSE Doctoral program

Required skills

• Computational analysis of large sequencing datasets (Python or equivalent)
• Experience with machine learning is a plus

What we offer

• Doctoral position supervised by Prof. Michael Nash and Prof. Niko Beerenwinkel, with a well-equipped lab and funding for international conferences
• Enrollment in the D-BSSE Doctoral program and competitive salary according to Swiss doctoral standards

Applications must be submitted online through the university's application portal, with a cover letter, CV, transcripts, master's thesis or project report, up to two publications and two references.