Postdoc position in Structural Data Science

A joint postdoctoral position in “Structural Data Science” is available in the Taylor group (Structural Biology of Molecular Machines) and Rasmussen group (Human Proteome Variation) at the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen. We aim to recruit a scientist with extensive experience in data science and/or in silico protein folding or design to help pioneer and establish this new research field. The position is for 2 years in the first instance and can be renewed for up to 4 years in total, providing a unique long-term opportunity to work on an exciting project in a well-equipped and supportive environment. The position is available immediately, start date will be decided together with the candidate.

Background
Three of the largest technological scientific advances in past years are arguably the advent of next generation sequencing, near-atomic cryo-EM and accurate and deep learning based de novo protein folding and design. Despite the great impact of these advances on their respective and even neighboring fields, there is a great potential synergy between them that remains untapped.

We want to combine the strengths of these techniques to establish methods that will enable a functional understanding of biological processes, allowing us to simultaneously sample the effects of millions of (in-the-lab and/or in-real-life) mutations rather than just a couple. Furthermore, the proposed research will allow us to design and improve (evolve) molecular machines with unprecedented capabilities.

The recruitment of a shared postdoc between the Taylor and Rasmussen groups, with prior expertise in protein design, deep learning and/or large-scale sequence analysis, not only will establish a strong and lasting synergy between these research groups, but open up a new and unexplored field of research, which we are convinced will be a path that many biological researchers will take in the future.

If you have any questions about the position, please contact: [email protected] or [email protected],dk .

Environment

Taylor group – Structural Biology of Molecular Machines
The Taylor group (https://www.cpr.ku.dk/research/protein-structure-function-program/taylor ) studies how molecular machines transport molecules across membranes. Using a combined structural and functional approach the group tries to understand how these machines function and how they can be inhibited, with the ultimate aim to contribute fundamental insight into this key biological mechanism as well as contribute to the development of better personal medical treatments. The group uses cryo-EM as its main method of choice to achieve this goal (see e.g. Santiveri et al., Cell, 2020, and postdoctoral studies prior to CPR: Taylor et al., Nature, 2016; Taylor et al., Nature, 2017; Manolaridis et al., Nature, 2018; Jackson et al., Nat. Struct. Mol. Biol., 2018).

Rasmussen group – Human proteome variation
The Rasmussen group  https://www.cpr.ku.dk/research/protein-structure-function-program/rasmussen ) focuses on developing and applying advanced machine and deep learning methods on large-scale human genomics, proteomics, multi-omics and microbiome data. Using these approaches, we aim to increase understanding of human biology and disease and use this to pave the way for more precise diagnostics, prevention and new treatment strategies. We are developing deep learning methods for patient specific (n=1) prediction of disease from large-scale human genomics, proteomics, multi-omics and clinical data. Additionally, we develop methods to integrate human genomics and proteomics data, and use computational genetics approaches to discovery causal relationships between the genome and proteome. An example of the methodological advances from the group is the first unsupervised deep learning method for discovery of bacterial genomes in human microbiome data (Nissen et al., Nature Biotech.).

The project will be a joint effort between both groups, and the postdoc will be expected to spend time in both research environments as well as facilitate interaction between the research groups.

Responsibilities and tasks
The postdoc will use in silico protein structure prediction and design integrating sequence data (from next generation sequencing as well as databases) as well as structural cryo-EM data to obtain better structural models and provide sequence-structure-function information on a variety of molecular machines involved in health and disease.

We have direct access to Computerome 2 (for CPU and GPU computation) as well as an internal GPU cluster, as well as excellent access to a Titan Krios microscope, equipped with Falcon 3EC direct electron detector and Volta phase plates, and a Glacios microscope also with Falcon 3EC at the Core Facility for Integrated Microscopy.

Qualifications
Candidates for the postdoctoral positions must be expecting or holding a PhD degree. The successful candidate will have strong qualifications or experience within several of the following areas: 

• Protein structure prediction (Rosetta, AlphaFold, …)
• Protein design
• Data science
• Deep learning
• Large-scale sequence analysis.

Strong team player skills are required. 

Place of employment and work
The employment is Novo Nordisk Foundation Center for Protein Research (CPR) (www.cpr.ku.dk ), University of Copenhagen, located in central Copenhagen. The research environment at CPR is ambitious and international, with approx. 30 different nationalities currently represented. The center comprises modern laboratories, supercomputer resources and state-of-the-art facilities within protein science. Seminars with high-profile international speakers and regular internal research seminars are organized at the center. The selected candidate should expect some travel activity. 

For more information on working and living in Denmark, visit www.ism.ku.dk  (International staff mobility).

Terms of salary and employment
The employment as postdoc is a full time and fixed-term position for 2 years with a possibility of extension (depending on the performance, and previous employment at the University of Copenhagen).. Starting date is 1 October or after agreement.

Salary, pension and terms of employment will be in accordance with the agreement between the Danish Ministry of Finance and AC (Danish Confederation of Professional Associations). Currently, the monthly salary starts at 34,900 DKK/ approx. 4,690 Euro (April 2021-level). Depending on qualifications, a supplement may be negotiated. The employer will pay an additional 17.1 % to your pension fund.

Non-Danish and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark the last 10 years.

The position is covered by the “Memorandum on Job Structure for Academic Staff at the Universities” of June 28, 2013.

Application procedure
Your online application must be submitted in English by clicking ‘Apply now’ below. Furthermore your application must include the following documents/attachments – all in PDF format:

Application deadline:  16 August 2021, 23.59pm CET

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/

The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

University of Copenhagen wish to reflect the diversity of society and welcome applications from all qualified candidates regardless of age, disability, gender, nationality, race, religion or sexual orientation. Appointment will be based on merit alone.

Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.