Postdoctoral Fellow - Machine learning for spatial omics
Location: EMBL Heidelberg
EMBL is Europe’s life sciences laboratory – an intergovernmental organisation with more than 110 independent research groups and service team covering the spectrum of molecular biology. It operates across six sites in Heidelberg (headquarters), Barcelona, Cambridge, Grenoble, Hamburg and Rome. Our mission is to perform basic research in molecular biology; train scientists, students and visitors at all levels; offer vital services to scientists in the public and private sectors within the member states; develop new instruments and methods; and engage actively in technology transfer.
The research group of Oliver 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-oics 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 MOPITAS 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 MOPITAS consortium.
Closing date: 2 June 2024
- Contract duration: 3 years
- Grading: Stipend Year 1
- Reference number: HD02603
Related
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 curiosity-driven, community-oriented and international. As an inclusive, equal opportunity employer, we believe that diversity enables us to collaborate more effectively and be innovative in our approaches. We are, therefore, committed to creating an inclusive and flexible culture - one where everyone can realise their full potential and make a positive contribution to our organisation.
We encourage applications from individuals who can complement our existing team – we believe that success is built on having teams whose backgrounds and personal experiences reflect the diversity of the populations that our science serves. We actively encourage applications from all genders and cultures, ethnic groups and all demographics to help us avoid perpetuating biases and oversights at this transformational point in our people strategy.
EMBL offers attractive conditions and benefits appropriate to an international research organisation with a very collegial and family-friendly working environment. Competitive salary and social security benefits, financial support for relocation, a relaxed culture, professional development, an on-site nursery, canteen and other staff facilities make EMBL a great place to work.
**Don’t meet every single requirement? We are dedicated to building a diverse, inclusive and authentic workplace, so if you’re excited about this role but your past experience doesn’t align perfectly with every qualification in the job description, we encourage you to apply nevertheless.
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.
EMBL is a signatory of DORA. Find out how we implement best practices in research assessment in our recruitment processes here.
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.
Please apply online through: www.embl.org/jobs
For questions or issues with the application process, please contact recruitment@embl.org