PhD scholarship in Data-Driven Analysis of C1 Metabolism in Acetogens

Monday 19 Jul 21

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The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) is seeking a highly motivated researcher with an interest in computational approaches to microbial systems biology for the purposes of strain design. We are looking to fill one PhD position in the newly established C1 Metabolism group, headed by Prof. Lars Keld Nielsen and A/Prof Nikolaus Sonnenschein.

In order to realise emission reduction targets, we need to completely replace our current reliance on fossil fuels for the production of food, fibre and transportation fuel with a sustainable alternative. Plant biomass production is associated with its own challenges concerning water and land use and the disruption of the nitrogen and phosphate cycles with associated eutrophication. This challenge can be addressed by moving production to closed systems using photoautotrophic or chemoautotrophic microbes. A vast range of natural photo- and chemoautotrophic metabolisms is currently being explored. In addition, new C1 metabolisms are being invented and implemented in common fermentation microbes, such as CO2 and formate assimilation in E. coli. No system has emerged as inherently better than others, and all systems have significant shortcomings. Moreover, many of the relevant organisms are poorly characterized.

Our group’s initial focus is to develop a Global C1 Metabolic Atlas in close collaboration with leading researchers and companies working on C1 metabolism in organisms such as acetogens, methanotrophs, and cyanobacteria. Your project will be focused on reconstructing C1 metabolism of Clostridium autoethanogenum.

Responsibilities and qualifications
Based on a large multi-omics dataset encompassing gene deletions in C. autoethanogenum, constructed in a collaboration with Joint Genome Institute (JGI), University of Queensland, University of Tartu and the company Lanzatech, you will mine the data for gene functions, transcription factors and global regulatory patterns.


Specific tasks include:

  • Reconstructing of strain and species-specific metabolic networks of from genome annotations and experimental literature to enable metabolic modeling applications.
  • Pangenome analysis of solventogenic clostridia to identify new pathways.
  • Annotating protein structure and genome sequence information for the analysis of sequence variation.
  • Transcription regulatory analysis of organism gene and protein expression data
  • Contribution to development and implementation of computational methods and tools described above.
  • Participation in a team environment as part of a large academic organization developing computational tools and workflows for strain design.
  • Organization of (bi-)weekly project updates to lab management.

We are looking for a colleague with previous experience working with metabolic network reconstructions, with substantial knowledge of metabolic biochemistry. This includes familiarity with methods for computational modelling of metabolism, including constraint-based and kinetic modelling, and an understanding of the relevant methods such as linear programming and matrix decomposition.

Most of our programming is in Python/Pandas and intermediate level programming skills are essential. Experience interfacing databases and R scripting will be an advantage but not required.

Additionally, your CV will demonstrate ability to:

  • communicate technical information to internal/external audiences at various levels (undergraduates to senior scientists) and from various backgrounds (technical and non-technical personnel);
  • work independently and as part of a team; and
  • successfully work on multiple concurrent projects and meet deadlines.

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

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.

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 academic freedom tempered by responsibility.


Salary and appointment terms
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. The period of employment is 3 years.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Professor Lars Keld Nielsen (lars.nielsen@uq.edu.au) or Associate Professor Nikolaus Sonnenschein (niso@dtu.dk).

You can read more about The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) at www.biosustain.dtu.dk

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark.

Application procedure
Your complete online application must be submitted no later than 2 August 2021 (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)

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

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 biosustain.dtu.dk.  


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 12,900 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.