PhD scholarship in comparative genomics and omics-driven eukaryotic genome minimization

DTU Bioengineering
onsdag 13 sep 17

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Frist 4. oktober 2017
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Department of Biotechnology and Biomedicine is a major Danish research and teaching department in the field of systems biology and is involved in a wide range of research activities within its field.

We are seeking an ambitious PhD student to be affiliated with the Network Engineering (NetEng) group and with the Eukaryotic Molecular Cell Biology group as well as collaborations into other groups at the department.

The NetEng group has a focus on industrial biotechnology and the application of systems biology tools to understand and improve the cell factory. The group is currently 15 people and in the process of expanding by several additional members, where this position will be a key activity in one of our focus areas: Aspergillus cell factories.
The position is funded by a grant from the Independent Research Fund Denmark.

Responsibilities and tasks
Fungi of the genus Aspergillus are of large economic importance due to their widespread application in industry and their natural capabilities as highly efficient cell factories. In particular, the Aspergilli are natural enzyme producers, and preferred hosts for heterologous enzyme production, but some species also play roles in plant, animal, and human pathogenicity. All known species produce a wide range of bioactive compounds. This project is a part of our long-term efforts to whole-genome sequence the entire fungal genus of Aspergillus, more than 350 species, and to utilize this information for both fundamental and applied research, thereby building superior fungal cell factories and fungal products for the future.

This PhD position offers the unique opportunity to work with high-quality genome sequences for an entire eukaryotic genus and employ them with state-of-the-art genome engineering and editing. Specifically, the student will be a part of a team of three staff members (one post.doc and a technician), where the goal is to reduce the genome size of an Aspergillus species significantly, thereby both studying the effects of reducing the genome, and following the hypothesis that a leaner genome will generate a superior strain.

The PhD student will be responsible for a part of the overall project, focusing on identifying and deleting a specific class of genes, while developing and improving the existing methods for identification and deletion of non-essential genes.

Ideally, the successful candidate should have experience with one or more of the following disciplines:
  • Robotics for PCR, vector design, or strain construction
  • Fungal molecular biology and genetic engineering based on USER cloning or Gibson assembly
  • Data analysis from one or more of the following omics techniques:
    • Genomics
    • Transcriptomic
    • Proteomics
  • Programming in Python, R, or Perl.

Furthermore, a systematic and structured way of organizing your work would be very helpful.

Candidates should have a master's degree in engineering or a similar degree with an academic level equivalent to the master's degree in engineering.

Approval and Enrolment
The scholarships for the PhD degree are subject to academic approval, and the candidates will be enrolled in one of the general degree programmes of DTU. For information about the general requirements for enrolment and the general planning of the scholarship studies, please see the DTU PhD Guide.

The assessment of the applicants will be made by Professor MSO Mikael Rørdam Andersen.

We offer
We offer an interesting and challenging job in an international environment focusing on education, research, scientific advice and innovation, which contribute to enhancing the economy and improving social welfare. We strive for academic excellence, collegial respect and freedom tempered by responsibility. The Technical University of Denmark (DTU) is a leading technical university in northern Europe and benchmarks with the best universities in the world.

Salary and appointment terms
The salary and appointment terms are consistent with the current rules for PhD degree students. The period of employment is 3 years.

Further information
Further information may be obtained from Professor MSO Mikael Rørdam Andersen, tel.: +45 4525 2675, preferentially by mail to

You can read more about Department of Biotechnology and Biomedicine on

Please submit your online application no later than 4 October 2017. Apply online at

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:
  • 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.

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

The Department of Biotechnology and Biomedicine (DTU Bioengineering) conducts research, educates future bio-engineers, provides scientific advice and innovate within the areas of microbiology, biochemistry, biotechnology and biomedicine. The research at DTU Bioengineering is at the highest international level and focuses on the societal and scientific challenges within the field. Research is conducted within three main areas: Microbial ecology and physiology, Industrial biotechnology and cell factories, and Biomedicine and health. The department has extensive collaboration with national and international research units and industries. DTU Bioengineering has approx. 150 employees, of which 2/3 is scientific staff. The department is located at DTU Lyngby Campus.

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 10,600 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.