Natural Product Structure Prediction based on genomic data (DC1)

Are you excited of being part of our newly established Marie Skłodowska-Curie Doctoral Network MAGic-MOLFUN, funded by the European Union?

Together with 11 PhD students working at 7 leading universities, research centers and industrial partners you have the opportunity to contribute to a bio-sustainable future!

So-called “natural products” are everywhere. We use them as essential medicines, food preservatives, plant protecting agents and many more. MAGic-MOLFUN aims to integrate Natural Products Genome Mining, computational metabolomics and state-of-the art metabolic engineering and pathway discovery to develop ground-breaking tools and approaches to improve the discovery and characterization of novel natural products in bacteria and fungi, two major sources of bioactive compounds for applications in medicine, agriculture, food and biotechnology.

In this PhD project, supervised by Senior Researcher Kai Blin at the Novo Nordisk Foundation Center for Biosustainability of the Technical University of Denmark located close to Copenhagen, Denmark you will design new approaches and tools to predict Natural Product structures based on the genomic information of the producing organisms and integrate those predictions into the antiSMASH framework.

Responsibilities and qualifications
In your PhD project, you will develop bioinformatics approaches to predict the structures of Natural Product compounds based on the genomic data in their respective biosynthetic gene clusters (BGCs). This work will happen in close collaboration with the other students in the MAGic-MOLFUN doctoral network and also the antiSMASH development team.

The specific tasks in this PhD project are:

• Develop a data model for antiSMASH to represent chemical structures in memory at runtime
• Update and extend the existing enzyme classification to assess tailoring reactions
• Simulate how those tailoring reactions change the chemical structure of the cluster product
• Visualise the different structure predictions and confidence levels in antiSMASH

Specific qualifications that we are looking for:

• You have an MSc degree in bioinformatics or a related field and want to expand your knowledge and skills in natural product biosynthesis and structures
  or
  you have an MSc in biotechnology, chemistry, microbiology, or a related field and experience in natural product biosynthesis and want to expand your knowledge and skill in bioinformatics and software engineering
• Have experience in programming Python or another programming language
• You have demonstrated oral and written English communication skills
• You are a team player that enjoys working in a highly interdisciplinary and international environment and interacting with peers within the group and external partners

Additionally, it would be advantageous if you:

• Have a working knowledge of git/GitHub or another version control system
• Have experience with Machine Learning approaches
• Have a working knowledge of the biochemistry of low molecular weight compound biosynthesis

Formal qualifications
Candidates should 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 and must fulfil the criteria for a PhD enrolment at DTU (please see the DTU’s rules for the PhD education).

The Doctoral Network program requires transnational mobility (i.e., move from one country to another). At the time of recruitment, you must not have resided or carried out your main activity (work, studies, etc.) in Denmark for more than 12 months in the 3 years immediately prior to the date of recruitment.

You must not have obtained another doctoral 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.

Assessment
The evaluation of the candidates will be carried out jointly by the PhD supervisor (Kai Blin) /co-supervisor (Prof. Tilmann Weber) and at least one external evaluator among the MAGic-MOLFUN PIs. By submitting your application, you agree that your application will be shared among the doctoral network PIs in compliance with GDPR regulations.

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. Depending on seniority, the monthly salary starts at approx. DKK 29,877 / approx. EUR 4,010 (October 2022 level) plus pension and including the Marie Curie supplement allowance. It is possible to apply for family allowance. 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 Kai Blin ([email protected])

You can read more about DTU Biosustain at www.biosustain.dtu.dk and MAGic-MOLFUN at www.magic-molfun.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. 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
Please submit your online application no later than 29 January 2023 (Danish time).

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 your application and why you are interested in this topic (cover letter)
• Curriculum vitae
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale

Candidates may apply prior to obtaining their master’s degree but cannot begin before having received it.

Applications and enclosures 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.