"Ph.D. student - Machine learning-based tools for multiparametric enzyme optimisation"

Workplace: RECETOX, Faculty of Science, Masaryk University in Brno, Czech Republic

Type of Contract: temporary position with 3-year contract (with possible extension), non-academic position

Working Hours: 1,0 FTE (full-time employment of 40 hours per week)

Expected Start Date: negotiable with respect to immigration timelines for non EU candidates

Number of Open Positions: 1

Pay: CZK 108 000 – 120 000 CZK depending on the eligibility for family allowance, and includes all compulsory deductions such as social security contribution, health insurance and income tax

Application Deadline: 31.03.2026

EU Researcher Profile: R1

The PhD student will be employed in Loschmidt Laboratories, one of the leading protein engineering groups in Europe and part of the RECETOX centre at the Faculty of Science of Masaryk University. The group focuses on studying the fundamental principles of enzymatic catalysis and developing proteins for environmental, chemical, and biomedical applications.

Roles and responsibilities

The PhD will be carried out in 4 years at Masaryk University under the supervision of Dr. Stanislav Mazurenko. Within this time, two research stays (2 x 3 months) are expected, at DTU (C. Acevedo) and in Provolut (J. Ivanovska). The Horizon Europe Marie Skłodowska-Curie Action (MSCA) Doctoral Network (DN) project is scheduled to start in January 2026. The date of recruitment and the start of the PhD project are planned for June 2026 and by December 2026 at the latest. Your PhD degree will be awarded based on the successful completion of the research work and fulfilling all the PhD study requirements at Masaryk University.

The PhD project will focus on:

• Development of next-generation data-driven models for protein engineering and optimisation;
• Validation of the developed models on the new data coming from the DN project;
• Integration of those models into reliable, user-friendly, state-of-the-art tools for protein engineering pipelines.

Main supervisor: Stanislav Mazurenko, Masaryk University, Brno, Czech Republic

Co-supervisor 1: Carlos Acevedo, DTU, Denmark

Co-supervisor 2: Jelena Ivanovska, Provolut (previously Exazyme), Berlin, Germany

Qualifications:

• MSc degree in Computational Biology, Machine Learning, Bioinformatics, Biotechnology or related discipline
• Experience with computational tools for protein engineering or machine learning
• Demonstrated ability in biological data analysis
• Excellent English proficiency
• Excellent communication skills for working within an interdisciplinary research team
• Strong analytical skills and ability to work independently

Preferred qualifications, but not mandatory:

• Proficiency in Python or another programming language
• Familiarity with protein modelling and analysis tools like AlphaFold, Boltz, PyMOL, Chimera, etc.
• Experience developing machine learning models
• Interest in advanced computational methods for understanding and improving protein function

Conditions of employment

You must hold a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to that of a two-year master's degree.

Eligibility Requirements:

• May not hold a doctoral degree at the date of recruitment
• May hold any nationality
• May not hold residence or have any main activity (such as work or studies) in the recruiting beneficiary's country for more than 12 months in the last 3 years
• Should meet the requirements to be enrolled in a doctoral programme

We offer

• An interesting job in a dynamically expanding university area
• Flexible working hours and occasional home office to support personal needs in family and career compatibility
• Employee benefits such as 6 weeks of paid vacation per year, pension insurance contribution or nursery/children´s group allowance, a financial meal allowance, Multisport card, vaccinations free of charge, discounted language courses, exclusive mobile tariff offer by Vodafone, childcare groups at Campus and Komenského náměstí
• Opportunity to work and live in a modern and dynamic city

Salary and appointment terms

The preferred starting date is 1st June 2026 or, according to mutual agreement. The position is full-time. The period of employment on the ELEGANCE project is 3 years, with possible extension supported by RECETOX.

Application Process

The application shall be submitted online by 31.03.2026 via an e-application. Applications must be submitted as a single PDF file containing all required materials to be considered. Please attach all your materials in English to a single PDF file.

The file must include:

• Cover letter
• Curriculum vitae
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale
• Names and contact details of at least 2 professional references