Phd Position in Digital Pathology

vor 4 Wochen

Bern, Schweiz Universität Bern Vollzeit

RESEARCH FIELDS: Computational Biology, Bioinformatics, Systems Biology, or a STEM-related field, such as Mathematics, Physics, Computer science.
APPLICATION DEADLINE: 31 March 2024 18:00h - Europe/Brussels
LOCATION: University of Bern (Switzerland)
TYPE OF CONTRACT: Temporary, 48 months.
JOB STATUS: Full-time
HOURS PER WEEK: 36
OFFER STARTING DATE: Flexible starting April - October 2024
EU RESEARCH FRAMEWORK PROGRAMME: HORIZON / Marie Skłodowska-Curie Actions / Doctoral Networks
MARIE CURIE GRANT AGREEMENT NUMBER: 101119370

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.

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

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

Remuneration:

- 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

For more information, visit our website.
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