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PhD scholarship in analyzing microbiomes using long-read metagenomics and transcriptomics

Technical University of Denmark (DTU)
Copenhagen, Hovedstaden (DK)
Closing date
5 Jan 2024

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Engineering, Life Science
Job Type
PhD Studentship
Employment - Hours
Full time
Fixed term
The complete biosynthetic potential of microbiomes in marine sediments and soil is not only exceptionally large but also poorly described by traditional culturing and sequencing technologies. The purpose of this PhD is to describe the full biosynthetic potential of microbiomes in niches such as marine sediments using state-of-the-art sequencing techniques. Furthermore, the activity of this biosynthetic potential will be evaluated by transcriptomics. Also, the PhD position will work with other projects in the CeMiSt center studying transcriptomes of more defined systems. Collectively, this will also potential suggest novel compounds of biotechnological or pharmaceutical interest.

Responsibilities and qualifications
Join our dynamic research team at the Center of Microbial Secondary Metabolites (CeMiSt), in which you will be driving the use of both metagenomics and metatranscriptomics to describe the secondary metabolism of microbiomes of marine and soil environments. We are seeking a dedicated and enthusiastic PhD candidate, with a keen interest in fundamental understanding of microbiome function as well as in the potential long-term applied aspects.

Experience within the following areas of microbiology will be an advantage:
  • Molecular biology, in particular purification of high-quality DNA and RNA from complex samples
  • Sequencing on the Nanopore platform
  • Bioinformatic assembly of genomes and mRNA-classification
  • Strong programming skills, especially bash, Python and R
  • A working knowledge of data science and statistics, especially multivariate

You must be ambitious, well organized, structured and enjoy interacting with many different people including PhD students and postdocs. Also, a good sense of humor will be appreciated.

The successful candidate will become an integrated part of the Center for Excellence on Microbial Secondary Metabolites ( and the Bacterial Ecophysiology and Biotechnology Group ( We offer creative and stimulating working conditions in a dynamic and international research environment, with recently renovated laboratory facilities and state of the art equipment for bacterial molecular research. You will work closely with other scientists, including PhD students and postdocs, specialized in different disciplines such as molecular genetics, ecology, bioinformatics, natural product chemistry and big-data-analyses. The project will be carried out at the DTU campus, building 221.

We are looking for an enthusiastic and ambitious candidate within the fields of molecular biology, sequencing and bioinformatics. Documented knowledge and experience with bacterial ecology is prioritized. A good command of the English language will be required, especially in terms of writing. Creativity and independence will be highly appreciated as well.

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 DTU's rules for the PhD education.

The assessment of the candidate will be made by Associate Professor Mikael Lenz Strube, Professor Lone Gram and Postdoc Morten Dencker Schostag.

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 starting as soon as possible.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Associate Professor Mikael Lenz Strube ( and Postdoc Morten Dencker Schostag (
If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark. Furthermore, you have the option of joining our monthly free seminar “PhD relocation to Denmark and startup “Zoom” seminar” for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU.

Application procedure
Your complete online application must be submitted no later than 5 January 2024 (23:59 Danish time).

Apply at: PhD scholarship in analyzing microbiomes using long-read metagenomics and transcriptomics
Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", 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 including list of publications
  • Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale

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

Applications 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 Department of Biotechnology and Biomedicine (DTU Bioengineering) is an international leader in the areas of biotechnology and biomedicine. Our engineering approach to all aspects of biotechnology and biomedicine positions us as a valuable player with unique competences in a growing bio-based economy and with health systems transforming towards personalized medicine. We have a clear focus on the needs in the life science industry and point towards innovation, new businesses, and scientific services for the benefit of society. The department has extensive collaborations with national and international research units and industry. DTU Bioengineering has approx. 400 employees, of which 2/3 are scientific staff. The department is located at DTU Lyngby Campus. You can read more about “the Department” 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 mission to develop and create value using science and engineering to benefit society. That mission lives on today. DTU has 13,500 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.

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