PhD position in Digital Pathology

vor 1 Tag

Bern, Schweiz talendo AG Vollzeit

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RESEARCH FIELDS: Computational Biology, Bioinformatics, Systems Biology, or a STEM-related field, such as Mathematics, Physics, Computer Science.

RESEARCHER PROFILE: Doctoral Candidate (i.e., not already in possession of a doctoral degree at the date of the recruitment).

APPLICATION DEADLINE: 30 January 2025

LOCATION: University of Bern (Switzerland)

TYPE OF CONTRACT: Temporary, 48 months.

JOB STATUS: Full-time

HOURS PER WEEK: 36

OFFER STARTING DATE: Immediately or by arrangement

EU RESEARCH FRAMEWORK PROGRAMME: HORIZON / Marie Skłodowska-Curie Actions / Doctoral Networks

MARIE CURIE GRANT AGREEMENT NUMBER: 101119370

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 that started on the 1st of February 2024.

The 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.

The PhD candidate will work on the development of multi-scale models of the immune system with a focus on investigating cardiometabolic disease (CMD).

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 publicly available single-cell data in CMD diseases.
  • 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. Candidates in the final stages of obtaining their degree are eligible to apply.

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.

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: Cornelia Mileto.

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