Tasks

Key Responsibilities:

• Develop a multi-scale model of the immune system to investigate inflammation by extending existing models (focused on T and B cell biology) to include macrophages.
• Train this model using both publicly available single-cell data in CMD diseases.
• Using the developed model, characterize the dynamical interplay and cellular communication between T cells and macrophages in atherosclerosis.
• Integrate spatial molecular data generated by MIRACLE partners to enable accurate cellular simulations of CMDs.
• Investigate and address uncertainties in AI models, adapting current reliability benchmarks for the analysis of single-cell datasets.

Expected Outcomes:

• Development of an accurate model for the mechanistic investigation of chronic inflammation and CMD.
• Innovative models to explore therapeutic interventions in CMD.
• Development of new interpretable deep learning methods for multi-omics data integration.

Requirements

REQUIRED EDUCATION LEVEL
A degree (MSc, or equivalent) in Computational Biology, Bioinformatics, Systems Biology, or a STEM-related field, such as Mathematics, Physics, Computer science, etc. Additionally, a good understanding of Health or Life Sciences, for example, Biology, Microbiology, Molecular Biology, Immunology, Biomedical Sciences, or Biochemistry, will be considered an asset. Candidates in the final stages of obtaining their degree are eligible to apply.
Furthermore, the applicant should be able to perform team-oriented as well as independent work. Additional requirements:

REQUIRED LANGUAGES
ENGLISH: Excellent, both written and spoken.

SKILLS/QUALIFICATIONS

Essential skills:

• Proficiency in machine learning techniques.
• Strong programming skills, preferably in Python.
• Solid foundation in mathematical modelling, probability and statistics.
• Ability to work collaboratively in an interdisciplinary team.
• Good communication skills in English (both written and spoken).

Good to have:

• Experience in computational biology.
• Familiarity with multi-omics data analysis.
• Knowledge of interpretable deep learning methods.
• Good understanding of immunology and/or microbiology.

We offer

The Faculty of Medicine at the University of Bern, one of Switzerland's largest, educates over 2200 students in human medicine and dentistry. Renowned for its unique curriculum, the faculty emphasizes practical relevance, diverse subjects, and innovation. A significant focus area is cardiovascular disease, the leading global cause of death. Through collaborative research with the University of Bern and Inselspital, Bern University Hospital, the faculty delves into cardiovascular physiology and pathophysiology, spanning fundamental science to clinical studies. This commitment to excellence in research and interdisciplinary approach positions the faculty as a leader in both education and cardiovascular research. More information can be found at the following links:

https://www.medizin.unibe.ch/index_eng.html
https://www.cvrc.unibe.ch/

Remuneration:
The per annum MSCA PhD student living and mobility allowance (plus family allowance if applicable, family status is assessed at recruitment) is in line with EU-MSCA requirements. This amount will be subject to tax and employee's National insurance deductions and will be paid in EURO.

The MIRACLE network, funded by the European Commission (2024-2028), is made up to train a new generation of researchers working on the latest advances in single-cell biology, multi-omics analysis, and the newest insights in macrophage biology in the context of cardiometabolic disease. These advances revealed heterogeneous and dynamic accumulation of (immune) cell populations in tissues that are associated with disease initiation, development, and particularly clinical outcome, a notion that has immense implications on our view of chronic inflammatory diseases and their treatment. Unique know-how is ready to be transferred to highly talented research fellows. In MIRACLE, twelve doctoral candidates will receive tailored training that enables them to study local and environmental factors that drive cardiometabolic inflammation as well as develop strategies to suppress them, via the integrated use of cutting-edge single-cell, spatial mapping, computational and disease modelling approaches. Moreover, they will be able to develop and polish skills in translational science by working with biotech- and pharma experts and clinicians pledging clinically actionable outcomes. It is aimed to organize secondments of several months for each DC to both academic and non-academic institutions in the MIRACLE network that will significantly add value to the training. The combination of high-level science with top-notch infrastructures, resources, and solid data places MIRACLE at the forefront to move single-cell biology towards cardiometabolic (precision) medicine and foster the scientists of tomorrow. The MIRACLE network consists of the following institutions and companies:

• Amsterdam UMC, location Academic Medical Center (coordinator)
• Maastricht University, NL
• University of Lille, FR
• University of Eastern Finland
• University of Bonn
• BiomimX
• Katholieke Universiteit Leuven
• University of Bern
• AstraZeneca
• University of California San Diego
• NanoString
• Science Matters
• European Macrophage Dendritic Cell Society
• European Atherosclerosis Society

MIRACLE

Applications will be considered on a rolling basis until June 30, 2024. Interested candidates should submit a short letter of interest outlining their reasons for applying to our group, a curriculum vitae including the names of two references, a list of publications, and copies of academic qualification certificates as a single PDF file by email to: E-Mail schreiben.

For more information, visit our website .