PhD fellowship in bioinformatics and metagenomics of the phyllosphere microbiome

The Department of Plant and Environmental Sciednces invites applicants for a PhD fellowship in bioinformatics and metagenomics of the phyllosphere microbiome. The project is part of the research project The MATRIX: Microbiome Assisted Triticum Resilience In X-dimensions, which is financed by the NovoNordisk Foundation.

Start date is (expected to be) April 1st, 2025 or as soon as possible thereafter.

The project
The flag leaf is a critical determinant of wheat yield, contributing up to 45% of the total yield. This PhD project aims to address the taxonomic diversity and functional potential of the wheat phyllosphere microbiome with a particular focus on the microbiome associated to the flag leaf. Today, more than one third of crop yields are lost due to abiotic and biotic stress factors, such as drought, salinity, pests and disease. In the MATRIX program several key microorganisms and regulatory mechanisms involved in wheat growth promotion and protection against biotic and abiotic stresses will be identified. By combining new microbiome-assisted approaches with machine learning and predictive modelling the MATRIX aims to quantitate and predict microbiome-mediated changes and their effect on wheat resilience and productivity under various climate change scenarios, which can be used as a novel tool to improve future wheat yield management strategies.

The research will involve high-quality sequencing data to analyze dominant bacterial communities in the wheat phyllosphere, focusing on keystone species using e.g. state of the arts genome-binning tools, Large Language Models and data integration. The project will primarily utilize unpublished metagenomic data, with future integration of available amplicon sequence variants (ASVs) and genomic data from bacterial, fungal and virus isolates to further elucidate the complexities of these microbial communities.

Who are we looking for?
We are looking for candidates within computational biology, microbiology, metagenomic analysis, network analysis, machine learning applied to microbiology, particularly with a focus on plant-microbe interactions. Applicants can have a background in fields such as microbial ecology, comparative genomics, and computational biology, with experience in genome mining, bioinformatics and different sequencing binning technologies. A strong understanding of metagenomics and the ability to integrate multi-omics data would be strongly desirable.

Our group and research- and what do we offer?
The Environmental Microbial Genomics group uses sequence-based analyses to describe genomic traits of keystone species and their prevalence and impact in natural and artificial microbial communities and metagenomes, including information on bacteriophages and how other mobile genetic elements shape microbial evolution and traits. Group activities span microbes in both natural, agricultural and health related systems. More information on the research group can be found on https://plen.ku.dk/english/research/microbial-ecology-and-biotechnology/environmental-microbial-genomics/. The group is a part of The Department of Plant and Environmental Sciences, Faculty of SCIENCE, University of Copenhagen. We are located in Copenhagen. Additionally, the work will be performed in collaboration with the Multi-modal bioinformatics group at the Novo Nordisk Foundation Center for Basic Metabolic Research at the Faculty of Health and Medical Sciences, University of Copenahgen. The multi-modal bioinformatics group has a strong history of method development and analysis of metagenomics and other data.

The candidate will be expected to conduct independent research within metagenomics, microbial network biology, machine learning and integration of multiple data types obtained from the wheat phyllosphere microbiome, in particular the wheat flag leaf. Sequenced genomes will be linked to a large set of shotgun and amplicon data from the same environment as well as metabolite datasets. We will use state-of-the-art methods for analysis and integration of these data such as TaxVAMB, MOVE and DNA language models. Finally, the candidate is expected to some degree to engage in teaching and supervision and the post may also include performance of other duties.

Candidates must have a MSc. within computational biology, microbial bioinformatics, genomic analysis, comparative genomics, network analysis, or other relevant research fields. Experience in programming in bash/Unix, R or python is strongly desirable. Also, experience within the field of plant-associated microbiomes is preferred, but not a requirement.

The candidate is expected to be enthusiastic about working in an interdisciplinary academic environment conduction research and teaching at the highest international level. The position, therefore, requires a highly motivated scientist who is comfortable working in teams, have good interpersonal skills, as well as a collaborative and open mind-set.

We offer an approximated 20 person group of creative researchers and stimulating working conditions in a dynamic and international research environment. Our research facilities include modern laboratories and In-house sequencers and bioinformatics servers.

1. Principal supervisor is Prof. Lars Hestbjerg Hansen, Department of Plant and Environmental Science. E-mail: [email protected]. Phone: +45 28752053
2. Co-supervisor is Prof. Simon Rasmussen, Center for Basic Metabolic Research. Email: [email protected]. Phone: +45 35332159

The PhD programme is a three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.

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Qualifications needed for the regular programme
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. Bioinformatics, Biotechnology. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in the PhD programme

• Carry through an independent research project under supervision
• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
• Participate in active research environments, including a stay at another research institution, preferably abroad
• Teaching and knowledge dissemination activities
• Write scientific papers aimed at high-impact journals
• Write and defend a PhD thesis on the basis of your project

We are looking for the following qualifications:

• Professional qualifications relevant to the PhD project
• Relevant publications
• Relevant work experience
• Other relevant professional activities
• Curious mind-set with a strong interest in Bioinformatics
• Good language skills

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Application and Assessment Procedure
Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include:

1. Motivated letter of application (max. one page).Your motivation for applying for the specific PhD project.
2. Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
3. Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
4. Publication list (if possible)
5. Reference letters (if available)

Application deadline:
The deadline for applications is February 1st, 23:59 GMT +1, 2025.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/.

Interviews with selected candidates are expected to be held in 2nd half of February, 2025.

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/.

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.