Postdoc in the molecular mechanisms and evolution of fungal antimicrobial resistance - DTU Bioengineering

DTU - Technical University of Denmark; Kongens Lyngby; On-site; DKK 420,000 - 520,000; Full time

Job summary

DTU – Technical University of Denmark is seeking a postdoctoral researcher to study fungal resistance to fungicides using experimental evolution and genome re-sequencing. You will perform in vitro evolution, high-throughput phenotyping, and comprehensive genomics/transcriptomics analyses, while mentoring students and contributing to high-impact publications.

The role emphasizes English communication, collaboration in an international team, and dissemination at conferences.

Qualifications

• Demonstrated experience working with filamentous fungi in the laboratory.
• Hands-on experience with molecular lab techniques including extraction of high-molecular weight DNA/RNA for long-read sequencing and gene-editing such as CRISPR-Cas9.
• Experience with command-line bioinformatics analysis of raw sequence data, genome assembly and gene annotation, and standard RNAseq-based transcriptomics pipelines.
• High proficiency in programming languages used in bioinformatics (Python/R) and ability to work on large-scale servers.
• Strong scientific output evidenced by first-author publications in peer-reviewed journals.
• Excellent written and oral English communication skills.

Responsibilities

• Laboratory experimental evolution using in-vitro culturing of filamentous pathogenic fungi across multiple environments.
• Fungal phenotyping with high-throughput imaging and AI-assisted analysis.
• Genomics and transcriptomics: DNA/RNA extraction, sequencing, genome assembly and annotation, RNAseq analysis.
• Lead manuscript preparation for peer-reviewed journals and present findings at conferences.
• Mentor PhD, MSc and BSc students and trainees in the group.

Skills

Filamentous fungi lab experience

CRISPR-Cas9 techniques

RNAseq and transcriptomics

Python/R programming

First-author publications

English communication

Mentoring trainees

Education

PhD degree (or equivalent)

Tools

DNA/RNA extraction

Long-read sequencing

Genome assembly & gene annotation

RNA-seq pipelines

CRISPR-Cas9 workflows

Job description

If you are passionate about sustainability and interested in fungal biology and genetics, consider joining our team as postdoctoral researcher. Plant pathogenic fungi are increasingly developing resistance against multiple different classes of fungicides. This results in substantial loss of food production and compromise the effectiveness of fungicide management practices. Furthermore, this is not only a concern for agricultural food production, but also for human health as the transfer of resistance between agricultural and medical environments is exacerbated by climate change and multi-host pathogenic fungi that infect both plants and humans. In this project you will use experimental evolution and genome re-sequencing approaches to study how resistance to fungicides evolve, especially focusing on non-target site resistance and polygenic adaptation to fungicides.

Responsibilities And Qualifications

• Laboratory experimental evolution: Use fundamental mycology laboratory techniques of in-vitro culturing to perform experimental evolution of filamentous pathogenic fungi. You will be serially passaging fungi across multiple in-vitro environments and stressors.
• Fungal phenotyping: You will use state-of-the-art fungus growth phenotyping using high-throughput microscopical imaging and automated AI-assisted image analysis to assess experimentally evolved strains.
• Genomics and transcriptomics: Apply full-genome sequencing and transcriptomics analysis, starting with DNA/RNA extraction and sequencing and bioinformatics analysis involving genome assembly, gene annotation, and transcriptomic analysis using RNAseq methodology.
• Scientific Communication: Lead the preparation of manuscripts for high-impact, peer-reviewed journals and present your findings at international conferences.
• Mentorship: Provide guidance and technical mentorship to PhD, MSc, and BSc students and trainees in the group.

Qualifications

• Demonstrated experience working with filamentous fungi in the laboratory
• Hands-on experience with molecular laboratory techniques used to study molecular biology of filamentous fungi, including extraction of high-molecular weight DNA/RNA from filamentous fungi suitable for long-read sequencing and gene-editing such as CRISPR-cas9 techniques.
• Experience with command-line based bioinformatics analysis of raw sequence data, genome assembly and gene annotation, and standard RNAseq-based transcriptomics pipelines.
• High proficiency in standard programming languages used in bioinformatics (e.g., Python and/or R) and familiarity with working on large-scale computer servers.
• A strong history of scientific output, demonstrated by first-author publications in peer-reviewed journals.
• Excellent written and oral communication skills in English, with the ability to articulate complex concepts to interdisciplinary audiences, especially experimental scientists.
• Direct experience with mentoring trainees at the BSc, MSc, and PhD level in mycology and fungal genomics.

As a formal qualification, you must hold a PhD degree (or equivalent).

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 terms of employment

The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. In addition, supplements can be negotiated in accordance with DTU’s salary structure for scientific staff: www.inside.dtu.dk/en/human-resources/during-employment/salary/salary-structures .

The period of employment is 2,5 years (30 months) with a target starting date of 1 January 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

Further information may be obtained from Associate Professor Henrik H. De Fine Licht, Section for Synthetic Biology, DTU Bioengineering, [e-mail]

You can read more about DTU Bioengineeringat DTU Bioengineering .

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark .

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.

The Fungal Interactions Group in the Section for Synthetic Biology at DTU Bioengineering aims to understand the mechanisms of fungal interactions with plant and animal hosts to engineer and develop novel ways of using beneficial fungi and combating detrimental fungi in agriculture and biotechnological industries. We use a mix of computational and experimental laboratory and field approaches in our work.

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 personalised medicine. We have a clear focus on the needs in the life science- and biotech industries 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.

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 year 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.