Project title: PhD Student – A generative foundation model of the human gut microbiome for digital twin development and biomedical applications – FNP First Team
Publication date: 13.05.2026
Closing date: 10.06.2026
Level of education: MSc
Hours: 40 hours per week
Salary indication: around 10 000 PLN gross monthly (employer’s costs: 13 000 PLN)
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.
The successful candidate will work closely with the Head Researcher and collaborate with international partners in computational biology and AI.
The PhD candidate working on this project must be enrolled at a doctoral school. The relevant topic will be available for doctoral school enrollment at the Faculty of Computer Science at AGH University. The doctoral school follows a separate recruitment and enrollment process which ends in late September 2026. As the position is available since July 1st 2026, the Candidate successful in Sano recruitment process, may start from July 1st 2026 as a Pre-doctoral Research Assistant, while awaiting the results of enrollment at the doctoral school. The position will continue as a PhD Student, as soon as the enrollment process is complete.
What are you going to do?
Selected tasks for the PhD Student:
- do original research under the supervision of the Head Researcher;
- development and testing of AI/ML algorithms for microbiome data analysis;
- analysis and interpretation of gut microbiome datasets;
- implementation of computational pipelines for data processing and model evaluation;
- biological interpretation of model outputs and generated predictions;
- participation in the integration of microbiome and clinical datasets;
- preparation of scientific publications and presentation of research results;
- preparation of a doctoral dissertation based on the results obtained within the project.
What do we require?
Required background and skills of the candidate:
- MSc degree in bioinformatics, computer science, computational biology, biology, or a related field;
- interest in artificial intelligence and machine learning methods, programming skills in Python;
- experience in data science and statistical analysis;
- knowledge or interest in metagenomics and microbiome data analysis;
- ability to analyze and interpret biological data;
- excellent written and spoken English communication skills.
Our offer
We offer a contractual setup as follows: 3-month trial period, 1 year fixed-term contract and after that a contract for the remaining duration of the project. The successful candidate will work under a full-time contract of employment (40 hours per week).
This will be supported by an educational plan that includes attendance of courses and international scientific meetings. The contract will include opportunities to participate in teaching and supervision of undergraduate and master students.
The salary, depending on relevant experience before the beginning of the employment contract, will be around 10 000 PLN gross per month, based on a full-time contract (40 hours a week) for the duration of the project. 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 PhD candidate working on this project must be enrolled at a doctoral school. The relevant topic will be available for doctoral school enrollment at the Faculty of Computer Science at AGH University. Depending on the doctoral school, additional eligibility criteria or requirements may apply. For more information regarding the eligibility criteria for enrollment at a doctoral school, please refer to the school directly.
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/sano-phd-student-fnp-first-team,ja,199
