Location: Hamburg, Germany
Staff Category: Postdoctoral Fellow
Contract Duration: 3 years (with possibility of extension up to 5 years)
Grading: Competitive Postdoctoral Fellowship

Please apply by sending the cover letter and CV to Jan Kosinski <jan.kosinski@embl.de>

The Jan Kosinski group at EMBL Hamburg, in collaboration with the Julia Mahamid group at EMBL Heidelberg, seeks a Postdoctoral Fellow to work on computational analysis of biological cryo-electron tomography (cryo-ET) data. This position is part of the TransFORM consortium, funded by the prestigious ERC Synergy Grant, which aims to map the intricate workings of protein translation machinery in human cells using cutting-edge cryo-ET, mass spectrometry, and computational modeling of atomic structures.

Your role

• Develop algorithms to identify macromolecular complexes in cellular tomograms, using image processing techniques such as template matching and machine learning
• Investigate and implement methods to enhance the speed and accuracy of particle identification by increasing algorithm efficiency, refining scoring functions, and applying the latest deep learning techniques in computer vision
• Explore the integration of spatial constraints from other data sources to improve particle identification
• Co-develop PyTME (https://github.com/KosinskiLab/pyTME)
• Disseminate your code in well-organized, documented, and rigorously tested software packages
• Use these new methods for research projects within the TransFORM consortium

You have

• Ph.D. in Computer Science, Image Processing, Computational Structural Biology, or a related field
• Advanced programming skills in Python and a proven track record in the development and application of computational tools
• Proficiency in numerical libraries such as NumPy and SciPy
• A solid foundation in mathematics and experience in algorithm development
• At least basic knowledge of machine learning techniques
• Experience in the dissemination and management of software packages
• Strong motivation to work in a highly collaborative and multidisciplinary environment of EMBL and the TransFORM consortium

You might also have

• Experience in cryo-ET data analysis or machine learning. However, candidates with a strong background in either computer science (and a willingness to learn cryo-ET data analysis) or cryo-ET (with proven extensive programming expertise) are encouraged to apply.
• Experience with deep learning frameworks such as PyTorch, TensorFlow, or JAX.

Why join us

You will work with the Kosinski and Mahamid research groups, who have excellent track record in computational modeling of the atomic structure of biological macromolecules and cryo-ET data analysis. With us, you will find the perfect balance between academic research and software development, supported by a competitive academic salary and benefits. You will engage in exciting scientific projects within a creative environment, collaborating with research groups that regularly publish in top-tier journals such as Nature, Science, Cell, Nature Methods, and Nature Protocols. Your computational tools will have wide applications in the emerging field of in-cell structural biology. You will have access to high-quality unpublished experimental data and computing resources, including high-end server GPUs. Simultaneously, you will enhance your algorithm and software development skills, preparing you for a career in either academia or industry.

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, 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 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 1900 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. The working language of the institute is English.

EMBL is a signatory of DORA. Find out how we implement best practices in research assessment in our recruitment processes here.