Postdoctoral fellow in the analysis of Spatial Omics data (27417)

→  Apply before 15/08/2024 (DD/MM/YYYY) 23:59 (Brussels Time)
→  Faculty of Sciences
→  Department: WE02 - Toegepaste Wiskunde, Informatica en Statistiek
→  Occupancy rate: 100%
→  Number of positions: 1
→  Type of employment: Contract of unlimited duration with clause
→  Term of assignment: 2 jaar
→  Wage scale: PD1 to PD4 (doctoral degree)
→  Required diploma: PhD

ABOUT GHENT UNIVERSITY

Ghent University is a world of its own. Employing more than 15,000 people, it is actively involved in education and research, management and administration, as well as technical and social service provision on a daily basis. It is one of the largest, most exciting employers in the area and offers great career opportunities. With its 11 faculties and more than 80 departments offering state-of-the-art study programmes grounded in research in a wide range of academic fields, Ghent University is a logical choice for its staff and students.

PROJECT OVERVIEW

The Saeys lab and the Martin Guilliams lab at the VIB Inflammation Research Center in Ghent, Belgium, are seeking a highly motivated and talented postdoctoral fellow to develop and apply cutting-edge algorithms for the automated analysis of spatial omics data. Join our vibrant research environment and contribute to pioneering projects in bioinformatics and computational biology.

Project Overview: This postdoctoral position is part of a larger project aimed at developing novel computational methods for spatial biology, establishing the 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.

Our aim will be 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 aim of the project will be 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 the spatial datasets and extract meaningful biomedical insights automatically.

YOUR TASKS

• At least 70% of your assignment will be spent on academic research.
• 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.

WHAT WE ARE LOOKING FOR

• You hold a thesis-based doctorate (obtained max. 6 years ago. This term of 6 years is determined by the date written on the above-mentioned required diploma). (preferably mention the desired domain)
• 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
• Preference will be given to candidates with experience with processing spatial omics data / high-performance computing and software containers
• Strong communication skills in English
• Strong interpersonal skills
• Ready to be the key link between multiple researchers
• Ready to mentor PhD students working on the same project

WHAT WE CAN OFFER YOU

• We offer you a contract of indefinite duration with maxim term of 2 years, possibly renewable for an additional 2 years, with encouragement to apply for a national Postdoctoral fellowship (e.g., FWO)
• Competitive stipend and benefits package
• Your contract will start on October 1st 2024  at the earliest.
• Your remuneration will be determined by salary scale PD1. Click here for more information about our salary scales.
• 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.
• All Ghent University staff members enjoy a number of benefits, such as a wide range of training and education opportunities, 36 days of holiday leave (on an annual basis for a full-time job) supplemented by annual fixed bridge days, a bicycle allowance and eco vouchers. Click here for a complete overview of all the staff benefits (in Dutch).

INTERESTED?

Apply online through the e-recruitment system before the application deadline (see above). We do not accept late applications or applications that are not submitted through the online system.

Your application must include the following documents:

• In the field ‘CV’: your CV and an overview of your study results (merged into one pdf file)
• In the field ‘Cover letter’: your application letter in pdf format
• In the field ‘Diploma’: a transcript of the required degree (if already in your possession). If you have a foreign diploma in a language other than our national languages (Dutch, French or German) or English, please add a translation in one of the mentioned languages.
• In the field “other documents”: at least two reference letters and an overview of your study results

Note that the maximum file size for each field is 10 MB.

As Ghent University maintains an equal opportunities and diversity policy, everyone is encouraged to apply for this position.

MORE INFORMATION

For further information and questions, please send an email to Yvan Saeys (yvan.saeys@ugent.be).  Important: do NOT send your application by email, but apply online.

Do you have a question regarding the online application process? Please read the FAQ or contact us via selecties@ugent.be or +32 9 264 34 36