DC4
Project: development of a comprehensive multi-scale model of the immune system
PhD position at University of Bern
The PhD candidate (DC4) will work on the development of multi-scale models of the immune system with a focus on investigating cardiometabolic disease (CMD).
We are seeking a highly motivated PhD candidate to embark on an exciting project focusing on the development of a comprehensive multi-scale model of the immune system, with a particular emphasis on inflammation and its role in cardiometabolic diseases (CMD). The project aims to identify new therapeutic strategies to mitigate inflammation and disease progression in CMD. The PhD candidate will develop hybrid mathematical-AI models that integrate mechanistic insights with AI methodologies, addressing challenges related to data scarcity, lack of robustness and generalization of existing data-driven models. The model will be trained on multi-omics datasets and will encapsulate known macrophage and T-cell biology.
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.
ABOUT THE FACULTY OF MEDICINE AT THE UNIVERSITY OF BERN
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/
ABOUT THE SUPERVISOR
Dr. María Rodríguez Martínez
Dr. María Rodríguez Martínez has a background in physics. She transitioned to computational biology during her postdoctoral studies at the Weizmann Institute of Science (Israel) and Columbia University (USA). Between 2013 and 2023, she led the Computational Systems Biology team at IBM Research Europe (Switzerland), dedicated to the development of novel computational strategies for personalized cancer treatments. A major part of this work was developed under the umbrella of two major EU-funded consortia focused on prostate and pediatric cancers, which she successfully initiated and coordinated. Her current research integrates mechanistic and artificial intelligence models, with a particular emphasis on the development of interpretable deep learning approaches for computational biology. Recently, her research has concentrated on cancer immunology, leading to the development of predictive models for T cell receptor binding and the exploration of B cell evolution.