Mots-Clés

single cell, multimodal single-cell data integration, computational and mathematical methods, acute leukemia, minimal residual disease

Description

PhD Position: In-Depth Analysis of Acute Leukemia MRD Dynamics Using Single-Cell Data

Location: CLIP research group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic

Duration: 36 months (full-time), extendable up to 48 months under the standard terms of the Ph.D. candidate position at the host institution

Start Date: October 1, 2025
Financing: Fully funded under the Horizon Europe Marie Skłodowska-Curie Doctoral Network (MSCA DN) program.
Application deadline: 15. 2. 2025 (see www.miracle-leukemia.eu)

Project Overview:
The heterogeneity and dynamic behavior of leukemic blasts present significant challenges for minimal residual disease (MRD) monitoring and the assessment of treatment responses. This project focuses on characterizing the dynamic processes driving acute leukemia cell evolution, including phenotypic drift and lineage switching, by integrating multimodal single-cell data with additional topological and kinetic measures (e.g., RNA velocity). 

The aim of this position is to employ advanced computational and mathematical methods—such as computational topology, stochastic modeling, or deep learning—to dissect state transitions and fate-determining processes in leukemic cells.

Key Responsibilities:
● Conduct mathematical and computational research to design novel algorithms and tools for single-cell data analysis.
● Develop and implement methods for modeling phenotypic dynamics of MRD in leukemia using spectral and mass cytometry and single-cell RNA sequencing data.
● Validate computational tools in collaboration with experimental and clinical researchers.
● Publish results in high-impact journals and present findings at international conferences.

Candidate Profile:
● A Master’s degree in computational biology, bioinformatics, mathematics, biomedical sciences, or related disciplines.
● Strong programming skills (e.g., Python, R); familiarity with machine learning or AI techniques is an advantage.
● A keen interest in interdisciplinary research and the ability to integrate computational and biological perspectives.
● Excellent communication skills in English, both written and verbal.
● Enthusiasm for teamwork in a collaborative, international research environment.

MSCA Mobility Rules: To qualify, applicants must not have resided or carried out their main activity (work, studies, etc.) in the Czech Republic for more than 12 months in the three years immediately preceding the recruitment date.

What We Offer:
● A fully funded PhD position, including a competitive salary and benefits.
● Access to state-of-the-art research facilities and resources.
● Structured training in computational and experimental methods, including workshops, advanced courses, and secondments within the MIRACLE consortium.
● The opportunity to collaborate with leading researchers and institutions across Europe, gaining exposure to academic and industry perspectives.
● A dynamic and supportive environment to develop your skills and advance your career in leukemia research.

About CLIP research group:
We are a diagnostic and translational research group with a focus on pediatric leukemia, rooted in multiple international consortia, with cutting edge genomic and cytometry facilities.

Application Process:
For detailed information about the position, application requirements, and to apply, please visit the MIRACLE consortium website.
For further information and questions, please send an email to Jan Stuchly (jan.stuchly@lfmotol.cuni.cz)