PhD scholarship in machine learning methods for metabolomics data analysis

Center for Biosustainability
Friday 13 Apr 18

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The iLoop (Iterative Cell Factory Development Loop) Core section at The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) is a translational research unit focused on microbial cell factory engineering. As part of the design-build-test cycle operated in the iLoop, the generation of relevant analytical data constitutes an important part of the test and design phases of cell factory engineering. In particular, mass-spectrometry data can be helpful in elucidating the internal state of engineered cells.

We seek a highly motivated PhD student to apply modern machine learning methods to the analysis of metabolomics data. Specific application areas will include raw mass-spectrometry data processing, compound identification, and biomarker elucidation.

Large amounts of data are being generated in clinical studies and medical screenings which can be used for gathering insights about various diseases. Machine learning and particularly deep learning methods allow to overcome the limitations of existing compound identification algorithms and the traditional biomarkers discovery workflow. The concrete applications would include pattern matching in raw mass-spectrometry data, alignment of peaks in different samples, and, finally, diagnostics and patients’ stratification based on disease severity.

Responsibilities and tasks
With your research you will push the boundaries of the field by increasing the throughput of metabolomics data processing and the interpretability of the data itself. Your responsibilities and tasks will include:

  • Develop the computational methods for biomarkers discovery using mass-spectrometry data
  • Analyse the performance of deep learning models in comparison with the traditional biomarkers discovery workflows for the purpose of classification and stratification of patients
  • Improve the interpretability of the results by integrating the data to the mechanistic metabolic models
  • Keep the clean and maintainable codebase, contribute to the existing open source libraries if needed
  • Be the main driver in collaborative projects involving other departments and institutes
  • Disseminate your research results to the research community as well as the general public through publications, conference talks, social media, etc.
  • Be involved in teaching activities at the Center

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 scholarship 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.

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 appointment terms
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. The period of employment is 3 years.

The workplace will be at DTU Lyngby Campus.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Nikolaus Sonnenschein (

You can read more about the Department on

Please submit your online application no later than 27 April 2018 (local time). 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.

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.