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

Assistant professor (project role: post-doc)

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:

• isolation of cfDNA and ctDNA from plasma and urine samples, as well as preparation of sequencing libraries for Oxford Nanopore technology,
• optimization and execution of experiments related to ctDNA fragment length analysis and DNA methylation profiling, including molecular validation (e.g., PCR, qPCR, methylation-specific methods),
• organization and oversight of biological sample logistics (transport, storage, quality control), in compliance with Good Laboratory Practice (GLP) standards,
• close collaboration with the bioinformatics team to coordinate molecular analyses and computational data integration,
• active participation in the project team, including scientific support for junior team members (PhD students and students),
• data interpretation and preparation of scientific publications, presentation of results at scientific conferences, and contribution to project progress reports,
• contribution to implementation and standardization efforts, including collaboration with clinical and industrial partners,

• preparation of outreach, science communication, and dissemination materials to promote project results through media, websites, and scientific/public events.

   

REQUIREMENTS:

• PhD in biology, molecular biology, biotechnology, molecular diagnostics, or related fields, awarded no earlier than 7 years before the planned employment date (a formal requirement, in accordance with the competition regulations),
• documented scientific achievements, including at least one first-author publication in a peer-reviewed international scientific journal,
• experience in diagnostic genetics is required,
• practical experience and hands-on expertise in molecular and cell biology techniques such as DNA/RNA isolation, PCR, qPCR, cloning, Western blotting, and immunoprecipitation,
• ability to plan, conduct, and document scientific experiments independently,
• strong communication skills and the ability to work effectively in an interdisciplinary and international research team,
• fluency in English, both spoken and written,
• experience working in a foreign research institution will be considered an asset,
• a basic understanding of genome-wide bioinformatics analysis will be an additional advantage.

WE OFFER:

• Part-time employment contract – FTE 0,8.
• Employment for three years, from 1st September 2025 to 31st August 2028.
• Gross salary in the range of 8,000 – 10,000 PLN.
• 13th salary (annual bonus).
• Opportunity for scientific development.

• Collaboration with a research center in Zurich.

   

REQUIRED DOCUMENTS:

• 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. Please include “[post-doc]” before your first name in the CV.
• The application deadline is 15.08.2025.
• Applications submitted between the deadline and the end of the announcement period may still be considered.

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.