PhD scholarship in Microbial Metabolic Reconstructions

Wednesday 18 Nov 20

Apply for this job

Apply no later than 9 December 2020
Apply for the job at Center for Biosustainability by completing the following form.

Apply online

The Novo Nordisk Foundation for Biosustainability (DTU Biosustain) at the Technical University of Denmark is seeking highly motivated PhD candidates with an interest in computational approaches to microbial systems biology for the purposes of strain design.

We are looking to fill four positions in the newly established “Microbial Reconstruction Unit”, headed by DTU Biosustain CEO Prof. Bernhard Palsson and CSO Prof. Lars Keld Nielsen. Reconstructions are collections of organism-specific knowledge, such as the set of all metabolic reactions that take place within an organism or the set of all experimentally-determined protein structures. These reconstructions are invaluable resources for rational design of microbial strains for a host of applications, but their availability outside model organisms is limited.

In the Microbial Reconstruction Unit, we are developing new organism-specific reconstructions, computational tools, and databases to empower the development of microbial strains in non-model organisms for several applications, including small molecule production, bioactive compound production, and microbial foods. The team is working on a range of organisms including fermentation organisms such as Lactobacillus and Streptomyces, and C1 organisms such as acetogens, methanotrophs, and cyanobacteria.

Developing genome scale models
You will work as part of an interdisciplinary team focusing on a group of organisms, e.g., acetogens, to develop a highly curated set of reconstructions of the individual organisms. This involves working with a number of big data sources (e.g., genomes, transcriptomes, Phenotype MicroArrays), existing databases and a range of existing annotation pipelines. The end product is a high quality reconstruction that captures all codifiable information about the organism and makes it available for computational modelling. You will use these models to explore the inherent potential of the organisms as well as the potential for rational design.

Your role will primarily be to perform computational modelling, write scientific publications, as well as take 30 ECTS points of relevant PhD courses as required in Danish PhD programs.

Two-year master's degree (120 ECTS points) or equivalent in bioengineering, computational biology or bioinformatics
We are looking for candidates with a two-year master's degree (120 ECTS points) or equivalent in a relevant discipline. You will have experience in computational modelling for metabolic systems with substantial knowledge of metabolic biochemistry. You will also have intermediate skills in Python programming ideally with some experience interfacing databases and R scripting.

Collaboration is an integral part of this project and we expect that you can demonstrate a track-record for successfully collaborating with your peers. At the same time, reconstruction demands periods of exacting individual detail work and it is important that you draw satisfaction from this mode of work as well.

Approval and Enrolment
The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see the DTU PhD Guide.

Further information
If you would like additional information about the position, please contact Professor Bernhard Palsson at or Professor Lars Keld Nielsen at You can read more about DTU Biosustain at

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

Application procedure
Please submit your online application no later than 9 December 2020 (Danish time).

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

  • A letter motivating the application (cover letter)
  • Curriculum vitae
  • Grade transcripts and BSc/MSc diploma
  • Excel sheet with translation of grades to the Danish grading system (see guidelines and Excel spreadsheet here)

Candidates may apply prior to ob­tai­ning their master's degree but cannot begin before having received it.

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

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

The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain)
Recent progress in our ability to read and write genomic code, combined with advances in automation, analytics and data science, has fundamentally changed the scope and ambition of harnessing the potential of biological systems. Big data approaches and analysis of biological systems are key research instruments at the Center. DTU Biosustain utilizes these advances for microbial cell factory design to foster sustainable lifestyles in relation to three application areas: Sustainable Chemicals, Natural Products, and Microbial Foods. Learn more at

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 12,000 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. Our main campus is in Kgs. Lyngby north of Copenhagen and we have campuses in Roskilde and Ballerup and in Sisimiut in Greenland.