PhD fellowship in Bioinformatics/Comparative genomics

PhD Project in Comparative genomics and metabolomic potential of phyllosphere bacterial isolates

Department of Plant and Environmental Sciences
Faculty of SCIENCE

University of Copenhagen



The Department of Plant and Environmental Sciences invites applicants for a PhD fellowship in Comparative genomics and metabolomic potential of phyllosphere bacterial isolates. 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) 1 November, 2024 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 enhance crop resilience by investigating the key players within the wheat phyllosphere microbiome. The research will involve high-quality sequencing data to analyze dominant bacterial communities in the wheat phyllosphere, focusing on comparative genomics of keystone species, determining their dominance and functional roles using genome-mining tools, and assessing their metabolic potential through genome-scale metabolic models. The project will primarily utilize genomic data, with future integration of available amplicon sequence variants (ASVs) and metagenomic data to further elucidate the complexities of these microbial communities.



Who are we looking for?

We are looking for candidates within the field(s) of microbiology, genomics, and bioinformatics, particularly those 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, metabolic modeling, and different sequencing technologies. A strong understanding of metagenomics and the ability to integrate multi-omics data would also be advantageous.



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.

The candidate will be expected to conduct independent research within the area of comparative genomic analyses of an already sequenced large biobank of bacterial and fungal isolates from the wheat phyllosphere microbiome, in particular the wheat flag leaf. The analysis involves plasmid and prophage carried traits. The isolates will primarily be keystone microorganisms (pathogenic as well as beneficial) obtained in close collaboration with partners in the project. Furthermore, sequenced genomes will be linked to a large set of shotgun and amplicon data from the same environment as well as metabolite datasets. 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

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 September 8, 23:59 GMT +1, 2024.

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. 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 week 41.

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.