PhD student position in the Laboratory of Laboratory of Structural Biology

The Laboratory of Laboratory Structural Biology  https://shorturl.at/3inoD at the International Institute of Molecular and Cell Biology in Warsaw, headed by Prof. Matthias Bochtler is looking for a PhD student.

You will join the project entitled ““Stealth” asparaginases as improved protein drugs for the treatment of childhood acute lymphoblastic leukemia” carried out as the Opus grant (2024/53/B/NZ1/01841) of the National Science Centre, Poland led by prof. Matthias Bochtler.

The project aims to apply the inverse folding tools based on the Large Language Models (LLMs) or Denoising Diffusion Probabilistic Models (DDPMs) combined with immune prediction tools (MHCIIpan) to design asparaginases that are expected to be less immunogenic for a given haplotype than the clinically used wild-type protein. The asparaginases will be expressed in E. coli cells, engineered to select for high asparaginase activity. To select asparaginases in high-throughput manner, input and selected plasmid pools will be sequenced to identify the most enriched, and therefore presumably most active variants among the designed proteins. Finally, we plan to compare the predicted and actual immunogenicity of designed asparaginase variants in a mouse model of asparaginase treatment, using standard immunological readouts to experimentally quantify the extent of the induced immune response.

As a PhD student you will be predominantly responsible for testing of selected asparaginases for substrate affinity and catalytic turnover in E. coli as well as asparaginase expression, purification and in vitro characterization. The work on the project will be a team effort and thus you will also be also involved in the other steps of the grant realization. Your role will also include conducting literature reviews to contextualize your findings, actively participating in lab meetings, presenting your work at national and international conferences, and contributing to the writing of research publications and assembling your PhD thesis.

The admissions process is conducted through the Doctoral School website system. The PhD student can apply to this specific project carried out as part of the Warsaw-4-PhD doctoral school via website https://shorturl.at/cJKQY (the application system will be activated from 19^th of December 2024; deadline for sending application is 6^th January, 2025). For more information, please follow the link https://shorturl.at/mvxOR.

Candidates will be selected according to the procedure complying the rules for granting scholarships for young scientists in research projects funded by the National Science Centre (NCN Council Resolution No. 25/2024 dated March 4, 2024), recruitment procedure for the Warsaw-4-PhD and the procedure complying with the rules of the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers as a part of HR Excellence in Research Strategy https://bit.ly/3U0dydP.

Requirements for the candidate:

• Master’s degree in biochemistry or related field
• Solid knowledge in at least one of the following disciplines: molecular biology, biochemistry, immunology, or animal (mouse) models
• Hands on experience in at least one of these areas
• Knowledge of LINUX and prior experience in machine learning welcome but not required
• Written and spoken fluency in English
• Willingness to learn and take new challenges, ability to work independently, analytical thinking
• Good interpersonal skills and a collaborative attitude 

We offer: 

1. Full-time PhD scholarship 4 years (8 semesters) in amount:
2. a) before the mid-term evaluation 4800 pln net/month;
3. b) after mid-term evaluation 5300 pln net/month
4. Position with 100% focus on research (no teaching obligations)
5. Benefits including reduced-rate for an individual private medical care package and membership in MultiSport programme
6. Full technical, administrative and organizational support from professional English-speaking personnel
7. Participation in courses, scientific training, support from peers, and academic mentoring

Deadline for applications is 6^th of January, 2025. The summer semester at the Doctoral School shall begin on 24^th of February, 2025.

How to apply:

• Apply via website https://shorturl.at/cJKQY (the application system will be activated from 19^th of December, 2024; deadline for sending application is 6^th of January, 2025). If you have any enquiries about the recruitment process or the project, please send your request to This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it.
• Please include the following statement in your email: “I hereby agree to the processing of my personal data, included in the application documents by the International Institute of Molecular and Cell Biology in Warsaw, 4 Księcia Trojdena Street, 02-109 Warsaw, for the purpose of carrying out the current recruitment process.” Your personal data will be processed for the purpose of the recruitment procedure by the International Institute of Molecular and Cell Biology in Warsaw. Full information is available under the link https://bit.ly/3UFWpY2
• Procedure for reporting irregularities, taking follow-up actions, and protecting whistleblowers: https://shorturl.at/u2mww