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Postdoctoral fellow in the analysis of Spatial Omics data

Employer
VIB
Location
Ghent
Closing date
18 Jul 2024

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Discipline
Life Science
Job Type
Research Assistant
Employment - Hours
Full time
Duration
Permanent
Qualification
Professional certification
Sector
Academia

Job Details

Project Overview This postdoctoral position is part of a larger project aimed at developing novel computational methods for spatial biology, establishing a new field of next-generation molecular pathology. Your research will focus on answering critical questions related to both healthy and diseased liver, utilizing data from improved wet-lab protocols from multiple biological models, complemented by in-house generated spatial omics data with optimized RNA & Protein marker panels (MERFish Vizgen, MACSima Miltenyi,). More details on the project can be found below.

Project details With the development of powerful instruments that can measure the spatial distributions of hundreds of RNA molecules (e.a. MERSCOPE instrument), proteins (e.a. MACSima instrument) or metabolites (e.a. MALDI instruments), the technological challenge has moved from the ability to acquire multiplexed spatial data to the capacity to efficiently integrate and analyze these datasets and this will require the development of novel AI-driven computational pipelines.

We will aim to develop novel AI-driven algorithms that can extract two key spatial features from tissue sections: (i) the fundamental morphological and pathological features of the tissue (tissue architecture) and (ii) the spatial organization of the cells representing the building blocks of the tissue of interest, including their precise identities and activation states (cellular organization). To achieve this goal the host labs are developing improved wet-lab protocols that allow the co-detection of RNA & Protein markers in fresh-frozen, PFA-fixed or FFPE-fixed preclinical mouse and clinical human liver samples. This will be complemented with tailored spatial multi-omic panels of RNA & Protein markers that enable identifying each of the cells within the tissue, their activation states, precise location and cellular neighbors. Altogether, the project will aim to combine improved wet-lab protocols and matching optimized RNA & Protein marker panels with the development of novel AI-driven computational pipelines that can efficiently process spatial datasets and extract meaningful biomedical insights automatically.

What you will do
  • Develop and implement advanced algorithms for the analysis of spatial omics data.
  • Integrate and analyze data from various (spatial) omics layers to gain insights into liver biology as an initial case study.
  • Contribute to the development of new computational methods and tools for spatial omics data analysis, establishing next-generation molecular pathology pipelines that will be broadly applicable across tissues and species.
Profile

Essential

  • PhD in Bioinformatics, Computational Biology, Statistics, Computer Science, Artificial Intelligence, Physics, Engineering, Bio-engineering, or equivalent.
  • Proven track record of successful research and high-ranked publications in bioinformatics
  • Experience with applying AI (deep learning, probabilistic modelling, generative AI) or machine learning in the field of systems biology
  • Proficient in Python or R programming
  • Strong communication skills in English

Desirable but not required

Preference will be given to candidates with experience with

  • Processing spatial omics data
  • High-performance computing and software containers

Key personal characteristics 

  • Strong interpersonal skills
  • Ready to be the key link between multiple researchers
  • Ready to mentor PhD students working on the same project
We offer
  • Competitive stipend and benefits package
  • Fully funded Postdoctoral fellowship for up to 4 years, but encouraged to apply for a national Postdoctoral fellowship (e.g., FWO)
  • A versatile and challenging academic position with very diverse contacts in a world-class research environment operating at an international level, and various opportunities to broaden your expertise.
  • Collaborative and supportive research environment with expertise in both the generation (wetlab) and the analysis (drylab) of single-cell and spatial multi-omic data.
  • Access to state-of-the-art compute & GPU infrastructure
  • Attendance of national and international conferences
  • Training courses in academic, technical, and career skills.
How to apply? 

Please complete the online application procedure and include a detailed CV, two reference letters, and a motivation letter.

For further information and questions, please send an email to Yvan Saeys  (yvan.saeys@ugent.be).


 

Company

VIB’s core mission is to generate disruptive insights in the molecular underpinning of life and to translate these actively into impactful innovations for patients and society. VIB is an independent research institute where some 1,800 top scientists from Belgium and abroad conduct pioneering basic research. As such, they are pushing the boundaries of what we know about molecular mechanisms and how they rule living organisms such as human beings, animals, plants, and microorganisms. Based on a close partnership with five Flemish universities – Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel, and Hasselt University – and supported by a solid funding program, VIB unites the expertise of all its collaborators and research groups in a single institute. VIB’s technology transfer activities translate research results into concrete benefits for society such as new diagnostics and therapies and agricultural innovations. These applications are often developed by young start-ups from VIB or through collaborations with other companies. This also leads to additional employment and bridges the gap between scientific research and entrepreneurship. VIB also engages actively in the public debate on biotechnology by developing and disseminating a wide range of science-based information. 

More info can be found on www.vib.be.

Company info
Website
Telephone
09446611
Location
Rijvisschestraat 120
Zwijnaarde
Belgium
9052
BE

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