Post Doc in Bioinformatics and Metagenomics
University of Copenhagen Novo Nordisk Foundation Center for Protein Research
Denmark

Postdoc in bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research

We are looking for a highly motivated and dynamic researcher for a 2 year position, to commence on 1 January 2022 or soon hereafter. The position will be in the Human Proteome Variation group at The Novo Nordisk Foundation Center for Protein Research (CPR – www.cpr.ku.dk). CPR comprises a wide range of expertise and resources including proteomics, protein production, general characterization of disease mechanisms, and bioinformatics. The Programme for Disease Systems Biology (DSB) consists of three research groups covering many systems level aspects of biology and medicine, including large scale analysis of human variation data and integration of molecular-level and healthcare data.

The position is part of an international project that focus on developing and extending our deep learning methods for identification of plasmid sequences in hundreds of thousands of metagenome samples. We will use this method to perform large scale discovery of plasmids and link these to the spread of antimicrobial resistance genes.

Information on the department can be found at https://www.cpr.ku.dk.

Our research

The Human Proteome Variation group (https://www.cpr.ku.dk/research/disease-systems-biology/rasmussen-group/) is part of the Diseases Systems Biology program and led by Associate Professor Simon Rasmussen. The group focus on developing and applying computational methods to human variation data, especially genome, proteome, microbiome and clinical data. A focus interest of the group is to develop and apply deep learning for integration of such dataset to generate new biological knowledge. We develop bioinformatics methods using either public data or data generated from our collaborators. The team spirit is inclusive, and we promote diversity.

Your job

Your task will be to develop and extend our machine learning algorithms for discovery of plasmids in large scale metagenomics data. You will work with a curated dataset of plasmid sequences generated using short and long-read metagenomics sequencing data by a world-leading lab. You will use this curated dataset to build a machine learning algorithm that can identifying plasmids from metagenomics binning methods on hundreds of thousands of metagenomics samples. The methods that will be extended are VAMB and PHAMB that have been developed in our lab. You will work closely together with the Microbiome part of the group and will partly supervise a PhD student and take part in organizing and teaching a PhD-course on Deep Learning for Multi-omics data.

Profile

We are looking for a highly motivated and enthusiastic scientist with the following competencies and experience:

Essential experience and skills:

  • You have a PhD in Bioinformatics
  • You are highly experienced in machine learning on biological data
  • You have an active interest in metagenomics and microbiome research
  • Proficient communication skills and ability to work in teams
  • Excellent English skills written and spoken

Desirable experience and skills:

  • Experience in computational biology and using R/Python for data analysis
  • Experience in using machine learning
  • Experience in analysis of shotgun metagenomics data

Place of employment

The place of employment is at CPR, Panum Institute, 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.

Terms of employment

The employment as postdoc is a full time position for 2 years. Starting date is 1 January 2022 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. 4,650 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.

Questions

For further information please contact Simon Rasmussen; e-mail simon.rasmussen@cpr.ku.dk; www.sund.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 (max. one page).

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. List of publications.

Application deadline: 18 October 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.

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background. Appointment will be based on merit alone.

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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.

Contact

Simon Rasmussen
E-mail: simon.rasmussen@cpr.ku.dk

Info

Application deadline: 18-10-2021
Employment start: 01-01-2022
Working hours: Full time
Department/Location: Novo Nordisk Foundation Center for Protein Research


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