Medical University of Gdańsk is seeking a candidate for the position of:

Doctoral Student

Project title: Diagnosis of High-Grade Brain Tumor Using Liquid Biopsy and Machine Learning (Diagnostyka guza mózgu o wysokim stopniu złośliwości z wykorzystaniem ciekłej biopsji i uczenia maszynowego).

Project leader: dr hab. Jakub Mieczkowski, MUG prof.

The project is carried out within the First Team programme of the Foundation for Polish Science co-financed by the European Union under the European Funds for Smart Economy 2021-2027 (FENG)

THE TASKS OF THE EMPLOYED PERSON WILL INCLUDE:

• analysis of Oxford Nanopore sequencing data, including DNA methylation patterns and fragment length distributions,
• development of predictive models using machine learning to detect tumor-derived ctDNA based on epigenomic and fragmentomic features,
• design and implementation of classification algorithms leveraging regulatory region mapping and nucleosome positioning,
• creation of a user-friendly application enabling clinicians or/and researchers to apply developed models for new data,
• preparation of clean, well-documented, and reproducible code,
• close collaboration with clinical and molecular biology teams for data interpretation and clinical validation,
• active participation in an international consortium (e.g. collaboration with the University of Zurich),
• preparation of results for scientific publications, conference presentations, and patent applications,

• participating in the Implementation Doctorate following the regulations of the Medical University of Gdańsk (MUG) regarding the external mode.

   

REQUIREMENTS:

• BSc/BEng or MSc degree in bioinformatics, mathematics, biology, biotechnology, or equivalent,
• understanding of basic molecular biology is desired, although not required,
• experience in Python and R with machine learning applications is desired,
• strong motivation for research work and interest in interdisciplinary projects,
• ability to work in a team,
• high motivation, flexibility and self-driven interest to learn new techniques,
• we also accept the candidates who have already been granted PhD student status.

WE OFFER:

• a 36-month PhD scholarship contract; approximately 11,000–12,000 PLN net per month; health, social, and accident insurance not provided – to be arranged by the candidate. Opportunity to gain and broaden expertise in the aspects of human epigenetics and liquid biopsy,
• mentoring and support from senior colleagues in the fields of epigenetics, computational biology, and biostatistics,
• opportunity to work in an international multidisciplinary training environment,
• international collaboration opportunities, including short term visits to a foreign partner (University of Zurich),
• access to state-of-the-art equipment in newly established molecular biology laboratories and computing resources,
• opportunities to attend international scientific conferences,
• living in beautiful Hanseatic Gdańsk – a city with an open-minded community that is located close to seaside, forests and landscape parks  with high-standing recreational possibilities.

APPLICATION RULES:

• Interested candidates are kindly requested to submit their application (CV, a motivation letter, references (contact details or reference in writing - nice to have) via the APPLY button. All documents should be combined into a single PDF file.
• The deadline for submitting applications is 31.07.2025 r. The deadline may be extended if necessary.
• Applications submitted in the period between the application deadline and the end of the advertisement publication may be qualified for the recruitment process.
• Planned term of employment: 01.09.2025 r.
• If you have any questions about the project, please direct them to: jakubmi@gumed.edu.pl; for issues related to the recruitment process, please contact hr@gumed.edu.pl.
• We are committed to equal opportunity and diversity. Candidates of all backgrounds, including persons with disabilities, are encouraged to apply. Our workplace is fully accessible.

PROJECT DESCRIPTION: 

The project focuses on developing analytical tools to identify samples containing circulating tumor DNA (ctDNA) originating from brain tumor cells. The core assumption is that ctDNA fragments differ from background cfDNA in several features, such as length, sequence composition, genomic location, and DNA methylation patterns.

The goal is to create a method capable of detecting whether a given sample contains a mixture of fragments derived from more than one cell population—specifically, whether the distribution of fragment features indicates the presence of tumor-derived DNA.

In practice, this involves applying statistical methods, distribution modeling, and classifiers based on fragment characteristics (e.g., fragment length, position relative to known regulatory elements, methylation probability) to flag samples as ctDNA-positive.

The work includes Oxford Nanopore sequencing data analysis, creation of custom reference datasets, design of fragment-based metrics and classification models, and evaluation of algorithm sensitivity and specificity.

RESEARCH GROUP DESCRIPTION: 

The Mieczkowski lab focuses on understanding how chromatin organization and gene regulation shape cellular identity in health and disease. A central aim is to develop computational and experimental tools for characterizing cell states and origins using epigenomic data. The group applies these approaches to liquid biopsy research, particularly in brain tumors, where circulating tumor DNA (ctDNA) is analyzed to detect cancer-specific signatures.

We integrate chromatin accessibility, nucleosome positioning, DNA methylation, and fragmentomics data generated through bulk and single-cell sequencing (e.g. ATAC-seq, ONT methylation, RNA-seq, spatial transcriptomics) to build tumor-agnostic models for ctDNA detection. Our research bridges molecular biology, bioinformatics, and translational medicine to improve non-invasive diagnostics.