PhD position at the University of Bern in Computational Biology - Euraxess : Job Details

Organisation/Company University of Bern Research Field Biological sciences » Other Computer science » Modelling tools Researcher Profile First Stage Researcher (R1) Positions PhD Positions Country Switzerland Application Deadline 1 Sep 2025 - 22:00 (Europe/Berlin) Type of Contract Temporary Job Status Full-time Hours Per Week 36 Is the job funded through the EU Research Framework Programme? Horizon 2020 Reference Number 101119370 Is the Job related to staff position within a Research Infrastructure? No

The University of Bern is looking for a PhD student / Doctoral Candidate (DC). This DC position is part of the MIRACLE consortium, a Marie-Sklodowska Curie Actions Doctoral Network.ABOUT THE PHD PROJECTThe PhD candidate will work on the development of interpretable deep learning for multi-omics data multi-scale models of the immune system with a focus on investigating cardiometabolic disease (CMD). We are seeking a highly motivated and ambitious PhD candidate for a project focused on developing interpretable deep learning models for the analysis of single-cell and spatially resolved multi-omics data associated with CMD. The PhD candidate will develop models that can automatically identify key molecular and morphological structures, such as clusters of cells, that are essential for making informed predictions. This project aims to enhance the use of multi-omics and spatially resolved data in clinical decision-making, hence, improving treatment guidance and prognosis.

Key Responsibilities:- Develop deep learning models for the analysis of spatially resolved data.- Train this model using both publicly available single-cell data in CMD diseases, as well as spatially resolved molecular data generated by MIRACLE partners.- Focus on model interpretability to identify significant spatial regions and immune profiles.- Investigate and address uncertainties in AI models, adapting current reliability benchmarks for the analysis of single-cell datasets.- Contribute to scientific recommendations on AI model robustness.

Expected Outcomes:- Novel interpretable deep learning models for the analysis of spatially resolved data.- A novel AI-based classifier of immune profiles.ABOUT THE SUPERVISORSThe primary supervisor for the project is Prof. María Rodríguez Martínez, an Associate Professor in the Department of Biomedical Informatics & Data Science at the Yale School of Medicine ( ), and an adjunct researcher with the Institute of Tissue Medicine and Pathology (ITMP), University of Bern. The student will be based at the University of Bern, Switzerland, and will join the group of the secondary supervisor, Prof. Inti Zlobec, a Professor of Digital Pathology at the ITMP. Collaboration between both groups is expected. To ensure this, a portion of the PhD program will be spent at Yale University.Prof. 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.Prof. Inti Zlobec is Professor of Digital Pathology at the Institute of Tissue Medicine and Pathology, University of Bern in Switzerland, where she leads to Odyssey Digital Pathology Research Group (www.digitalpathologybern.com ), an interdisciplinary computational pathology research hub, bringing computer scientists, bioinformaticians, biologists and medical doctors together to work on common projects. The aims of the research group are on the one hand, to build tools for diagnostic clinical use and on the other to gain novel biological insights into cancers by using the latest spatial (transcriptomic and protein) tissue visualisation techniques and computational methods. Inti Zlobec is Chair of the European Society of Pathology Working Group for Digital & Computational Pathology, Founder and President of the Swiss Digital Pathology Consortium (SDiPath), Executive Team member of the Center for Artificial Intelligence in Medicine (CAIM) of the University of Bern and Board member for the Bern Center for Precision Medicine (BCPM). The PhD students related to the MIRACLE programme will be embedded within the Odyssey Research Group, with additional interactions to scientists specializing in the field of cardiovascular inflammation.

ABOUT MIRACLE

This DC position is part of the MIRACLE consortium, a Marie-Sklodowska Curie Actions Doctoral Network that started on the 1st of February 2024.

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 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 associate 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: Academic Medical Center, Maastricht University, University of Lille, University of Eastern Finland, University of Bonn , BiomimX, KU Leuven, University of Bern, AstraZeneca, UC San Diego, NanoString, Science Matters, the European Macrophage- Dendritic Cell Society and the European Atherosclerosis Society.

ABOUT THE FACULTY OF MEDICINE AT THE UNIVERSITY OF BERNThe 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:

HOW TO APPLYApplications will be considered on a rolling basis. 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: [email protected] .

E-mail [email protected]

Research Field Biological sciences » Other Education Level Master Degree or equivalent

Skills/Qualifications

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.

Furthermore, the applicant should be able to perform team-oriented as well as independent work.

• 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.

Specific Requirements

• The candidate must have a bachelor's and master's degree in a relevant discipline.
• Strong interest in pursuing a career in research.
• The candidate must be a highly motivated enthusiastic and efficient researcher.
• Good communication skills in English.

Note that in order to be eligible for this position applicants:

• must not have a doctoral degree at the date of their recruitment
• can be of any nationality
• should be enrolled in a doctoral programme during the project
• should comply with the mobility rules: in general they must not have resided or carried out their main activity (work, studies, etc.) in the country of the recruiting organization for more than 12 months in the 36 months immediately before their recruitment date.

The PhD position is funded under the Marie Skłodowska-Curie Actions (MSCA) framework. The living and mobility allowance for the PhD student is approximately 4,000 EUR per month, in line with EU-MSCA requirements. If applicable, a family allowance will also be provided based on the candidate's family status assessed at recruitment. Please note that this amount is subject to taxation and deductions for the employee's national insurance contributions. All payments will be made in euros.

Eligibility criteria

Applicants can be of any nationality but cannot have been already awarded a doctoral degree. Furthermore, the applicant must not have resided or carried out their main activity (work, studies, etc.) in the country of the recruiting beneficiary (Switzerland) for more than 12 months in the 36 months immediately before their recruitment date.

Selection process

Applications will be considered on a rolling basis. 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: [email protected] .