First Team - Scientific Programmer

Location Krakow

Contract type Full-time

Region / State / Province małopolskie

About job:

Sano Scientific Programmer – FNP First Team

Project title: Scientific Programmer - A generative foundation model of the human gut microbiome for digital twin development and biomedical applications – FNP First Team

Publication date: 01.04.2026

Closing date: 30.04.2026

Level of education: MSc/PhD

Hours: 40 hours per week

Salary indication: around 15 500 PLN gross monthly (employer’s costs: 21 000 PLN gross)

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.

What are you going to do?

The Scientific Programmer will be responsible for the development and maintenance of the computational infrastructure supporting the microbiomeGPT project. The main activities include:

design and deployment of the computational infrastructure supporting the microbiome digital twin;

development and implementation of client-side applications for interacting with the digital twin system;

development of applications and tools for data collection within the project;

design and implementation of computational pipelines for microbiome data processing and model execution;

automation of analytical workflows and data processing pipelines;

optimization and maintenance of the microbiomeGPT model codebase;

integration of machine learning workflows with high-performance computing (HPC) and cloud environments;

collaboration with researchers to support the implementation of new computational methods.

What do we require?

Required background and skills of the candidate:

MSc or PhD degree in computer science, data science, bioinformatics, or a related field;

documented experience in software development projects, strong programming skills (preferably Python);

experience with high-performance computing environments (HPC) or distributed computing systems;

experience with code versioning systems (Git);

experience with containerization technologies (Docker, Apptainer/Singularity);

experience with machine learning frameworks and computational workflows;

ability to design and implement scalable computational pipelines;

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 salary, depending on relevant experience before the beginning of the employment contract, will be up to 15,500 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.

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.

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;