丹麦哥本哈根大学蛋白质设计与结构数据科学博士后职位

丹麦哥本哈根大学蛋白质设计与结构数据科学博士后职位

University of Copenhagen (UCPH)

Postdoc position in Protein Design and Structural Data Science (NNF-CPR)

A postdoctoral position in Protein Design and Structural Data Science is available in the Taylor group (Structural Biology of Molecular Machines), in close collaboration with the 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 silico protein folding or design and/or data science to help pioneer and establish this new research field. The position is for 2 years in the first instance.

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 neighbouring fields, there is a great potential synergy between them that remains untapped.

We are combining the strengths of these techniques to establish methods to 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 postdoc in protein design will further extend the computational research in the Taylor group and heavily benefit from the close collaboration with the Rasmussen group.

The recruited postdoc will help modify and design protein nanomachines involved in molecular transport, in close collaboration with experimental scientists in the Taylor group and in collaboration. We are looking for a researcher with prior expertise in protein design, deep learning and/or large-scale sequence analysis, not only will further establish a strong and lasting synergy between these research groups, but open up a new and underexplored field of research.

Environment

Taylor group – Structural Biology of Molecular Machines

The Taylor group (http://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, Adaixo et al., Nat. Commun. 2022, 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  http://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 based in the Taylor Group but you will benefit from the close interaction with the Rasmussen group.

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 position 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 at 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) and www.workingconditions.ku.dk

Terms of salary and employment

The employment is a full time (37 hours per week) and fixed-term position for 2 years.

Salary, pension and other conditions of employment are set in accordance with the Agreement between the Ministry of Finance and AC (Danish Confederation of Professional Associations). Currently, the monthly salary starts at 35,500 DKK/approx. 4,770 EUR (April 2022 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 2020.

Duration:           2 years

Starting date:    1 July 2022 or after agreement

Questions

If you have any questions about the position, please contact: nicholas.taylor@cpr.ku.dk.

Foreign applicants may find this link useful: www.ism.ku.dk (International Staff Mobility).

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:

1. Motivated letter of application

2. CV incl. education, work/research experience, language skills and other skills relevant for the position.

3. A certified/signed copy of a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do.

4. A list of publications

5. Names and contact details for 3 references

Deadline for applications: 4 May 2022, 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 Appointments Committee. All applicants are then immediately notified whether their application has been passed for assessment by an expert assessment committee. Selected applicants are notified of the composition of the committee and 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 http://employment.ku.dk

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

For further information about the process, please contact SUND HR: sund-hr-cpr@sund.ku.dk

APPLY

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.