PhD position in Computational biology - DTU Biosustain

Advancing Precision Fermentation: A Graph-Based Toolkit for Optimizing Fungal Microorganisms in Valuable Compound Production

Fungal microorganisms play a crucial role due to their ability to secrete a variety of enzymes and metabolites. Despite technological advancements, there is still a lack of advanced data analysis tools that can fully uncover the potential of these microorganisms. This includes detailed understanding how genes within fungal genomes interact and their connections to specific enzymes and metabolic pathways.

This project addresses this gap by designing fungal-specific graph-based methods and a comprehensive toolkit that uses high-throughput sequencing and imaging data at multiple biological levels (genomic, metabolic etc) for precision fermentation. The first objective is to achieve complete fungal genomes, including species within Aspergillus, Trichoderma, and Penicillium, enabling the exploration of gene co-occurrence patterns and their collective impact on complex metabolic pathways. The second objective involves comparing different fungal species to uncover genetic diversity and relationships, identifying gene families related to essential enzymes and metabolic pathways.

The project benefits from the PI's expertise and existing datasets at the US Joint Genome Institute/DTU Bioengineering. The resulting user-friendly, open-source toolkit will guide future experimental designs, helping users pinpoint crucial groups of genes, enzymes, and regulatory elements that significantly influence compound production. This approach advances precision fermentation, potentially enabling eco-friendly valuable compound synthesis and reducing resource dependence.

Required skills: 

• Graph methods in computational biology/bioinformatics
• Domain knowledge: Fungal microbiology and enzymology
• Proficiency in programming (python or others)
• Motivation to learn and contribute

Keywords:

• Fungal microbiology
• Bioinformatics/computational biology
• Fungal enzymes
• Precision fermentation

Your role will primarily be to perform computational modelling, write scientific publications, as well as take 30 ECTS points of relevant PhD courses as required in Danish PhD programs.

Competencies of the ideal candidate

A master's degree (120 ECTS points) or equivalent in computational biology or bioinformatics is a requirement.

We also ask that you are motivated by working in an international environment with colleagues and partners from all over the world. Added to this, the CV of the ideal candidate comprises: 

• Experience programming in Python
• Workflow/pipeline development and management
• Familiarity with large-scale data analyses
• Familiarity in Fungal microbiology and enzymology
• Interest in Precision fermentation
• Ability to work independently and as part of a team. 
• Ability to successfully work on multiple concurrent projects and meet deadlines.

We offer

You can look forward to being part of a leading research and education institution in Europe where on-going development of skills and knowledge is a part of the foundation. You will have great flexibility, as trust and respect are some of the values we build our results on. You will be supervised professionally/have your strong mentoring attention to ensure your professional training.

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.

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

. 

Further information

If you would like additional information about the position, please contact Shilpa Garg at sgargbiosustain.dtu.dk. You can read more about DTU Biosustain at www.biosustain.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. 

Salary and terms of employment

The period of employment is three years. The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. 

You can read more about career paths at DTU here

.

Application procedure 

Please submit your online application no later than 28 February 2024 (23:59 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 the application (cover letter)
• Curriculum vitae 
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale
• Research statement/plan
• Demonstration of coding/large-scale data analysis skills

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.

Technology for people

DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear mission to develop and create value using science and engineering to benefit society. That mission lives on today. DTU has 13,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.