PhD scholarship in “In silico modelling of metabolism to understand and facilitate natural products biosynthesis”

Center for Biosustainability
Tuesday 11 Jul 17

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Introduction:
We are seeking three highly motivated PhD students to join our international team at the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain), Technical University of Denmark (DTU), and become part of the New Bioactive Compounds section. Within the Novo Nordisk Foundation funded Challenge Grant project “Integration of Informatics and Metabolic Engineering for the discovery of Novel Antibiotics (IIMENA)” you will actively contribute to develop and implement technologies in the field of metabolic modeling and metabolic engineering to identify and produce novel secondary metabolites as potential future antibiotics. IIMENA is an international excellence project involving partner institutions from Spain and South Korea.

Responsibilities and tasks
Position 2:
In silico modelling of metabolism to understand and facilitate natural products biosynthesis.
Within the IIMENA project, we will identify a huge number of actinomycetes producing bioactive compounds against our panel of clinical test organisms, obtain their genome sequences and identify thousands of secondary metabolite biosynthetic gene clusters.
The aim of this PhD scholarship is to develop and use metabolic modelling approaches to identify prerequisites and metabolic bottlenecks to express a selection of these pathways in heterologous hosts and conduct metabolic simulations to propose strategies to overcome these limitations.

Tasks of this thesis project include:

  • Generation and refinement of new computational resources for genome-scale metabolic modelling (e.g., generating a comprehensive manually curated reaction dataset and advancing our in-house metabolic modelling pipeline)
  • Generation of genome-scale metabolic models including secondary metabolite biosynthetic reactions
  • Application of genome-scale metabolic models to characterize working logics of secondary metabolites biosynthesis
  • Comparative analyses to identify the best expression hosts
  • Simulations to predict engineering targets, which then will be implemented by other project partners
The PhD student will work in close collaboration with the other project scientists at DTU and with the external project partners in Spain and especially South Korea.

Requirements:
  • Excellent background in computational modelling such as constrain-based reconstruction and analysis (e.g., genome-scale metabolic modelling)
  • Familiarity with principles of bioinformatics
  • Previous exposure to other related disciplines such as cheminformatics or machine learning (very positively considered)
  • Demonstrated programming skills, preferably in Python
  • Ambition, strong work ethics and attention to detail
  • Excellent methodical, communication and team-playing skills, but also the ability to work independently towards applied research goals in a multi-disciplinary international team of scientists
  • Excellent English skills for working in a highly international research group

Qualifications
Candidates should have a master's degree in chemical and biomolecular engineering, computational/systems biology, bioinformatics or a similar degree with an academic level equivalent to the master's degree in engineering. For formally required minimum grades to be accepted as a DTU PhD student, please see the DTU PhD Guide.

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.

Assessment
The assessment of the applicants will be made by Dr. Hyun Uk Kim and Dr. Tilmann Weber (IIMENA program leader)

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.

Workplace
Workplace is the Novo Nordisk Foundation Center for Biosustainability, Building 220 at DTU main campus in Kgs. Lyngby, which is approximately 10 km north of Copenhagen.

Further information
Further information may be obtained from Dr. Hyun Uk Kim (Email: ehukim@kaist.ac.kr) or Dr. Tilmann Weber, Email: tiwe@biosustain.dtu.dk.

You can read more about “DTU Biosustain” on www.biosustain.dtu.dk.

Application
Please submit your online application no later than 20 August 2017.

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.
The Center is based upon a long-term grant from the Novo Nordisk Foundation to DTU and it was inaugurated in 2011. It has now more than 220 employees and is still growing.

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.