Postdoctoral Fellow - Machine learning for Spatila Omics

Contract Type: Postdoctoral Fellow

Contract Duration-Length of Time (years/months): 3 years

About the team/job

The research group of Oliver Stegle (https://www.embl.de/research/units/genome_biology/stegle) is looking for a highly motivated computational postdoctoral fellow to join an ambitious collaborative project to develop innovative computational strategies for integrating and modelling multi-omics spatial variations across biological scales and individuals. She/he will work closely with other members of our team, colleagues at EMBL and external collaborators.

Our laboratory has a track record in computational innovations for multi-omics integration, causal inference and machine learning. The fellow will work in a highly multidisciplinary setting embedded in our group. This specific position is connected to the Novo Nordisk foundation funded MOPTIS project, which has the goal to develop novel computational strategies for modelling spatial omics and integrating such modalities with additional single-cell readouts. Among the specific challenges we seek to address is multi-scale spatial tissue reconstruction, alignment for 3D tissue atlasing and population-scale semantic spatial omics integration in human cohorts. Our group has access to unique spatial datasets in human disease contexts, which will underpin these computational aims.

Recent publications of the Stegle research group:

• Kleshchevnikov, Vitalii, et al. Cell2location maps fine-grained cell types in spatial transcriptomics. Nature Biotechnology (2022): 1-11.
• Velten, Britta, et al. Identifying temporal and spatial patterns of variation from multi-modal data using MEFISTO. Nature Methods (2022), 1-8.
• Svensson, Valentine, Sarah A. Teichmann, and Oliver Stegle. SpatialDE: identification of spatially variable genes. Nature methods 15.5 (2018): 343-346.
• Argelaguet, R., et al. Multi-Omics factor analysis disentangles heterogeneity in blood cancer. Molecular systems biology 14.6 (2018): e8124.

Your role

Your primary role will be to conduct innovative curiosity driven computational research. You will have the opportunity to closely interact with computational scientists in our team and to develop, implement and apply machine learning methods to fully exploit datasets from leading-edge spatial omics technologies. In addition to the development of novel computational methods, you will also have the opportunity to steer the experimental efforts within the MOPITUS consortium.

You have

The successful applicant will hold a doctoral degree or equivalent qualification in computer science, statistics, mathematics, physics, and/or engineering, or a degree in biological science with demonstrated experience in computational and statistical methods development. You should have a proven track record in developing and applying statistical and/or machine-learning based methods to large real-world datasets. Advanced programming skills are required. Excellent communication skills and the ability to drive your own work while collaborating within a team are essential.

You might also have

Experience in working with omics data and analysis of next-generation sequencing datasets and/or imaging data are beneficial. Prior work with spatial omics technologies is a bonus but not required.

Why join us

This is a fantastic opportunity to work in a highly collaborative scientific environment to advance the state-of-the-art in spatial omics technologies. The fellowship will provide ample opportunities to interact with experimental and computational experts at EMBL and beyond. The post will be connected to the Laboratory for Learning and Intelligent Systems (http://www.ellis.eu) at multiple levels - via the Ellis Health program (https://ellis.eu/programs/ellis-health) and the via the local ELLIS unit in Heidelberg (http://www.ellis-life-heidelberg.eu).

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits.

What else you need to know

We are Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1600 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.

Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

Please submit your application documents via our online system, including your CV and a brief letter summarizing your future research interests.

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