PhD scholarship in fungal genomics and predictive modelling - DTU Food

DTU; Kongens Lyngby; Remote; DKK 360,000 - 420,000; Full time

Job summary

DTU is seeking a PhD-candidate in fungal genomics to correlate genomes with phenotypes and develop online webservices. You will sequence fungi, culture and phenotype them, and implement tools for an online service.

The role requires Python, Unix experience and strong knowledge of microbial genomics, with collaboration across DTU Food and DTU Bioengineering and international partners. A two-year master’s degree or equivalent is required.

Qualifications

• Two-year master's degree or equivalent; PhD candidate status during study.
• Experience coding in Python and Unix-based systems; familiarity with machine learning.
• Extensive knowledge in microbial genomics and bioinformatics algorithms.

Responsibilities

• Create a webservice to identify fungal taxa and toxin-gene clusters.
• Perform whole-genome sequencing and build a reference genome database.
• Conduct genotype–phenotype association studies on Fusarium isolates.

Skills

Python

Unix

Machine learning

Genomics

Bioinformatics

Education

Master's degree (2-year)

Tools

Bioinformatics tools

Job description

Fungi are increasingly causing health issues globally. Such infections are not only increasing in humans and animals, but also in crops and as contamination of food products with mycotoxins.

We have recently been awarded funding to develop online webservices for genomic characterization of all pathogens capable of infecting animals, humans and plants, which includes fungi. However, genomics methods and workflows have so far not gained enough attention in relation to plant infecting or mycotoxin producing fungi.

Databases of genomes of known fungal species have already been developed, as has gene databases of mycotoxin producing gene clusters, but an extensive linkage to fungal taxa is poorly described. Furthermore, it is known that a number of fungi including some used in food production have the gene cluster for mycotoxin production but do not express them.

There is an urgent need to improve our understanding of the genomics of fungi, as well as to translate this into online services.

Thus, as part of our GPAP project (www.gpap.global) and our responsibilities as advise provider to the Danish Food Administration we are seeking a PhD-candidate in fungal genomics with a focus on correlating genomes to phenotypes and developing webservices. This will include whole genome sequencing of fungi, culturing and phenotypic characterization and implementing tools in our widely used online webservice.

Responsibilities and qualifications

Your main responsibility will be to create a webservice for identifying fungal taxa, mycotoxin-producing gene clusters and predict phenotypes under different growth conditions. You will perform complete genome sequencing (including the analyses) of a selected range of fungal to create an improved database of reference genomes.

You will also:

• develop a web-based tool for species identification and detection of known toxin-gene clusters, virulence genes and regulatory genes.
• conduct phenotype to genotype association studies based on a large collection of phenotypically characterized Fusarium isolates and develop and improve the online tool.
• With assistant from other group members, you will analyse the output, draw conclusions and present the outputs.
• communicate research results by presenting data at project meetings and international conferences and write reports and manuscripts for publication.
• engage in the general work carried out by the research group, including discussions and planning of strategies and projects, drafting research grant proposals, etc.

Daily work will be in close collaboration with other researchers in the Genomic Epidemiology group at DTU Food and the Applied Mycology group at DTU Bioengineering, as well as national and international partners.

The ideal candidate has experience in coding in python and experience with Unix-based systems and in machine and deep learning.

Other desired qualifications are:

• extensive knowledge in microbial genomics including phylogenetic analysis
• extensive knowledge of existing bioinformatic algorithms and tools.
• experience with DNA-based workload from microbes

It is a great advantage if you have experience in general microbiology and preferably fungal culturing.

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.

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. Please see DTU's salary structure for scientific staff: www.inside.dtu.dk/en/human-resources/during-employment/salary/salary-structures

The period of employment is 3 years.Starting date is 1 February 2027 (or according to mutual agreement). The position is a full-time position.

You can read more about career paths at DTU here.

Further information

The position is a collaboration between DTU Food and DTU Bioengineering, with the employment at DTU-Food. Further information may be obtained from Associate professor Christian Brinch, [e-mail] Associate professor Jakob Blæsbjerg Hoof, [e-mail].

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 "PhDrelocation to Denmark and startup "Zoom" seminar" for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU.

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply. As DTU works with research in critical technology, which is subject to special rules for security and export control, open-source background checks may be conducted on qualified candidates for the position.

DTU National Food Institute

DTU National Food Institute conducts research into and disseminates - through advice, innovation and teaching - sustainable and value-creating solutions in the area of food and health for the benefit of society. The vision is to make a difference by generating future prosperity through research into food and health. The institute works to prevent disease and promote health, develop new and better food products for a growing population and create sustainable technological solutions, including biosolutions. The institute's tasks are carried out in interdisciplinary collaboration within e.g. nutrition, chemistry, toxicology, microbiology, epidemiology, modelling, and technology. This is achieved through a strong academic environment of international top class with correspondingly skilled researchers and employees. The Institute employs approximately 390 staff members.

DTU – For the benefit of society since 1829

DTU is one of Europe's leading elite technical universities. Through research and education at an international top level, we create solutions to the major societal challenges of our time and help secure Europe's global leadership in sustainable technological development. Since Hans Christian Ørsted founded DTU almost 200 years ago, our mission has remained the same: We develop and create value through the natural and technical sciences for the benefit of society. DTU has 13,800 students, 1,600 PhD students, and 6,500 employees. We work in an international environment and have an inclusive, stimulating, and informal work culture. DTU has campuses in all parts of Denmark and in Greenland and collaborates with the best universities around the world.