Postdoc in Data-Driven Design of Cell Factories and Communities

Center for Biosustainability
Tuesday 06 Feb 18

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The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) at Technical University of Denmark (DTU) is seeking a highly motivated and skilled Postdoc. The position will be within the DD-DeCaF and Olefine consortia, two projects funded by the European Commission to develop new bioinformatics approaches that leverage system-level data for biotechnological applications (DD-DeCaF) and low-cost production of pheromones (Olefine).

With advances in synthetic biology, genomes can now be edited at unprecedented speed and fidelity allowing making multiple changes in the same genome at the same time. This increases the need for computational tools to design cells and communities of cells analogous to the tools used in Computer Aided Design (CAD) of cars, buildings and other man-made objects. The European Commission has funded a four-year collaborative project to build a CAD platform, DeCaF, for data-driven design of cells and microbial communities. Applications will range from human health to sustainable production of chemicals. Furthermore, the European Commission has funded Olefine, a project that aims to make pheromones an affordable alternative to insecticides by producing them in through a bio-process. The successful applicant will have a joint appointment with both projects and is expected to facilitate collaboration in close liaison with all partners involved.

Responsibilities and tasks
As a successful applicant, your main responsibility will be establishing the computational resources for designing microbial cell factories for the production of pheromones:

  • Curate and maintain relevant genome-scale and kinetic metabolic models of pheromone production hosts (Olefine)
  • Predict strain engineering strategies for increased pheromone production (Olefine)
  • Diagnose problems and bottlenecks in pheromone production through omics data-analysis and interpretation (Olefine)
  • Clean-up and upload data to DeCaF platform (Olefine & DD-DeCaF)
  • Implement existing and novel methods for designing microbial cell factories in core libraries such cameo and cobrapy
  • Engage in community building for open source software tools such as cobrapy and other openCOBRA (https://github.com/opencobra) related software packages
  • Engage in the community standards development such as memote (memote.readthedocs.io)
  • Optimize, test, and benchmark tools developed by academic and industrial partners within the project
  • Collaborate with partners in integrating these tools into the DeCaF platform
  • Collaborate with partners to develop omics data integration framework for the DeCaF platform
  • Participate in the dissemination of research results and scientific research software via publications in peer reviewed journals, presentations at scientific conferences, and public outreach activities 
Qualifications
Candidates should have a PhD degree or equivalent.

Further qualifications:
  • The candidate needs to hold a Ph.D. degree in Bioinformatics, Computational Systems Biology or similar field
  • Extensive experience with reconstructing genome-scale metabolic models is a must
  • Extensive experience with constraint-based modelling methods is a requirement
  • Extensive knowledge of prokaryotic and eukaryotic metabolism is required
  • Real-world project experience with scientific programming in Python is a must
  • Ability to write high-quality, structured and maintainable code

Applicants need real-world project experience with modern software development practices, including test-driven development and continuous integration.

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and an academic freedom tempered by responsibility.

Salary and terms of employment
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed with the relevant union.

Workplace and period of employment
Workplace will be at DTU, Kemitorvet, Building 220, 2800 Lyngby.

The period of employment is 2 years.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Senior Researcher Nikolaus Sonnenschein, niso@biosustain.dtu.dk

You can read more about “the Department” here www.biosustain.dtu.dk/english.

Application procedure
Please submit your online application no later than 20 February 2018.

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill in the online application form, and attach all your materials in English in one PDF file. The file must include:
  • Application (cover letter)
  • CV
  • Diploma (MSc/PhD)
  • List of publications

Applications and enclosures received after the deadline will not be considered.

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply.

DTU Biosustain is an international research center of excellence developing next generation cell factories and bioprocesses for sustainable production of high-value chemical compounds as well as protein-based products. The center uses advanced metabolic engineering techniques and computational biology ensuring efficient and cost-effective design and construction processes.

The center’s activities are a balanced mix of basic and translational research, complemented by an emphasis on business development to facilitate commercialization of new cell factories and associated technologies. DTU Biosustain offers state-of-the-art research facilities and assembles world leaders in the field thus offering a unique platform providing excellent talent development and career opportunities.

DTU is a technical university providing internationally leading research, education, innovation and scientific advice. Our staff of 5,800 advance science and technology to create innovative solutions that meet the demands of society; and our 11,000 students are being educated to address the technological challenges of the future. DTU is an independent academic university collaborating globally with business, industry, government, and public agencies.