Postdoctoral Fellow - Uhlmann Research Group

Postdoctoral Fellow - Uhlmann Research Group

EMBL-EBI - European Bioinformatics Institute

Hinxton, United Kingdom

Organisation data: Research Groups
Job Number: EBI02056
Contract Type: Postdoctoral Fellow
Contract Duration-Length of Time (years/months): 2.5 years
Advertised Grade-Grading: Year 1 stipend - £2,952.45 per month
Closing date: 7 March 2023

About the team/job

Gonadal development is poorly understood, principally because it starts in utero and is ongoing in many mammals for several decades. Due to obvious ethical reasons, there is a limited understanding of ovarian development in humans, especially in childhood. The Single-Cell Map of the Pediatric Ovary in 3D project aims to generate paired single-cell transcriptomics and chromatin accessibility data of pediatric ovaries to define cell states and their regulatory networks. The roadmap of pediatric ovarian maturation generated in this work will be an essential resource to better understand gonadal pathophysiology, as well as illuminate the development of novel in vitro models of follicle development, with important clinical implications for infertility treatments.

The Uhlmann group develops methods to quantify morphology from microscopy images, whether they are 2D, 3D, static, dynamic, and of any imaging modality. Our overarching aim is to provide general quantification frameworks for bioimages to investigate living systems across scales and build bridges between mathematical modeling and image data.

The unique resource we consider in this project offers a challenging opportunity froman image analysis and quantification perspective since the ovary is a highly dynamic tissue with very specific cellular compositions and tissue architectures. The Uhlmann group will lead efforts towards generating a 3D map of gonadal tissue, teaming up with our research and clinician partners from the Sanger Institute (project lead), the University of Oxford, and the Oxford University Hospitals NHS Foundation Trust.

Your role

The successful candidate will develop computational tools to quantitatively characterize tissue microenvironments, and identify changes in tissue architecture across the lifespan of gonads.

The project will involve the design of a pipeline to quantify single-cell gene expression data in 3D image datasets (stitching, registration, and quantification), followed by data analysis to reconstruct and quantify follicles during development. Tissue architecture will then be characterized in 3D by combining representation learning strategies (to extract key features of tissue microenvironments in an unbiased manner) and classical algorithms for multiscale morphology description. The joint consideration of learned features and visual descriptors will help construct an interpretable and robust characterization of tissue microenvironments, which will then allow identifying and quantifying architectural changes.

We expect all code produced in this project to be developed in Python, released as fully open source and made publicly available to the research community along with analysis results following reproducible research practices.

You have

• A PhD in computational biology, bioinformatics, or data science;
• Hands-on experience with state-of-the-art algorithms for image processing and analysis;
• Solid expertise in the Python programming language, with previous experience developing Python-based analysis pipelines;
• Interest in biological research with medical applications;
• Previous research experience involving state-of-the-art machine learning;
• Independent and motivated work habits and excellent verbal and written communication skills in English;
• Strong communication skills, as necessary for inter-institutional collaborations.

You might also have

• Experience handling large bioimage datasets;
• Hands-on experience with generative modeling;
• Hands-on experience with Python-based open-source bioimage analysis platforms such as napari.

Why join us

Do something meaningful

At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity.

Join a culture of innovation

We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential. 

Enjoy lots of benefits

• Financial incentives: Monthly family and child allowances, generous stipend reviewed yearly, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances;
• Flexible working arrangements;
• Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover);
• Generous time off: 30 days annual leave per year, in addition to eight bank holidays;
• Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely);
• Family benefits: On-site nursery, 10 days of child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances;
• Benefits for non-UK residents: Visa exemption and financial support to relocate if you are based overseas.

What else you need to know

• Contract duration: This position is limited to the project duration of 2.5 years;
• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants;
• Diversity and inclusion: At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ and individuals from all nationalities;
• Job location: This role is based in Hinxton, near Cambridge, UK. You will be required to relocate if you are based overseas and you will receive a generous relocation package to support you;
• How to apply: To apply please submit a cover letter and a CV through our online system. We aim to provide a response within two weeks after the closing date; Recruitment process will take place online via Zoom and it's likely to include a seminar, panel and technical interviews and an opportunity to meet some of the group members and collaborators;
• DORA - EMBL is a signatory of DORA and is committed to hiring and training outstanding research, service, and administrative personnel.

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