Project title: MSc Student – A generative foundation model of the human gut microbiome for digital
twin development and biomedical applications – FNP First Team
Publication date: 08.07.2026
Closing date: 07.08.2026
Level of education: BSc/Eng
Hours: 20 hours per week (50% FTE)
Salary indication: 2500 PLN gross monthly
Supervisor:
Head Researcher: Dr. Tomasz Kościółek (Structural and Functional Genomics Research Team Leader at Sano)
Project period: 01.07.2026 – 31.12.2029
The human microbiome plays a fundamental role in many physiological processes including metabolism, immune regulation, and neurological signaling. Recent advances in metagenomic sequencing have enabled large-scale characterization of microbial communities across populations.
However, translating microbiome sequencing data into functional insights and clinically actionable predictions remains a major challenge.
The project, titled “A generative foundation model of the human gut microbiome for digital twin development and biomedical applications,” aims to create a next-generation model capable of supporting biomedical research, diagnostics, prevention, and therapy optimization.
By training microbiomeGPT on large-scale metagenomic datasets, the team will work toward identifying disease biomarkers, simulating microbiome dynamics, and generating patient digital twins to advance precision medicine. This generative approach has the potential to transform how clinicians and researchers understand and intervene in human health.
Support structure: The successful candidate will work under the Head Researcher conceptual supervision, with technical support from the Scientific Programmer (environment setup, training templates, reproducibility), and substantive guidance from prof. Ewa Szczurek (Helmholtz Munich) on AI model design and interpretation in biology.
The candidate must be enrolled in a Bachelor’s or Master’s degree programme and hold active student status.
Milestone: A defended master’s thesis plus an evaluation report comparing at least 3 architectures (ideally 5 experiments), accepted by one of Sano’s partner universities. The chosen architecture then feeds directly into Stage 4 (full training of microbiomeGPT v1.0).
What are you going to do?
MSc Student is assigned to Stage 3: Analysis of architectures for the microbiomeGPT model.
Their work will be integrated with their master’s thesis, and they’ll be the main person executing this stage. Specifically, they’re responsible for:
- literature review of candidate AI architectures
- selection of architectures to test for microbiomeGPT
- running comparative experiments across architectures, evaluating: embedding quality,
generalization ability, training efficiency (time and resources), interpretability, and stability under noisy or incomplete data - using tools like PyTorch Lightning and Hugging Face Transformers, plus explainable AI techniques
- documenting all experiments, results, and evaluation tooling
- analyzing results and producing a final report with a justified recommendation for the target architecture (considering the tradeoff between computational complexity, scalability, and expected model quality)
What do we require?
Required background and skills of the candidate:
- active student status in a Bachelor’s or Master’s degree programme in bioinformatics, computer science, biology, or a related field;
- programming skills in Python;
- knowledge of metagenomics and/or gut metabolomics;
- excellent written and spoken English communication skills.
Our offer
We offer a half-time (20h per week) contract of employment for the duration of 9 months. Two MSc student positions are planned within the project.
This will be supported by an educational plan that includes attendance of courses and international scientific meetings.
The salary, depending on relevant experience before the beginning of the employment contract, will be around 2500 PLN gross per month, based on a half-time contract (20 hours a week, 50% FTE) for the duration of 9 months. The position includes private medical care and a sports card.
Sano offers excellent opportunities for study and development, access to international conferences on computational medicine, and the possibility to work in an interdisciplinary research environment.
Questions?
Do you have any questions about this vacancy? Or do you want to know more about our organization? Please contact us at m.golabek@sanoscience.org.
About Sano
Sano Centre for Computational Medicine is a new International Scientific Foundation located in Kraków, Poland.
Sano aspires to be a major translational scientific institute, operating at the meeting point of academic science, established MedTech industry, and emerging start-up environment, combining the best of these three perspectives.
Established with support from the European Commission and the Foundation for Polish Science, Sano aims to be a major driving force behind the advancement of computational medicine for the benefit of healthcare systems worldwide.
Sano acts as a core technology and expertise provider for industry, and creator of innovation, developing state-of-the-art solutions for healthcare. Thanks to the substantial funding and excellent European partnership network, Sano will bring a critical mass to this transformational field of research, in order to translate scientific advancements into clinical practice. Sano’s ambition is to become the Reference Centre for Computational Medicine in Central Europe and build a reputation as a leading center on a global level.
As a cross-disciplinary institution, Sano uses machine learning/artificial intelligence (ML/AI), large scale computer simulations, data science, and other computational technologies towards overcoming global challenges in healthcare systems. The research agenda will be executed in close collaboration with Partners in Poland, EU and USA.
Eligibility criteria
The candidate must be enrolled in a Bachelor’s or Master’s degree programme and hold active student status.
Job application
Sano is an equal-opportunity employer. We prioritize diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.
Do you recognize yourself in the job profile? Then we look forward to receiving your application.
The recruitment process will consist of two interviews (Introductory interview and Competency-based interview) with the Recruitment Committee.
Only selected candidates will be invited for the interviewing phase.
Applications in pdf should include:
- a cover letter;
- a curriculum vitae;
Apply
https://sano.elevato.net/en/msc-student-fnp-first-team,ja,200
https://euraxess.ec.europa.eu/jobs/451298
