PhD position in plant science with focus on conifer genomics

The Department of Plant Physiology (Umeå University, Umeå Plant Science Centre, Sweden) invites applicants for a PhD position in plant science. The expected starting date is autumn 2023 or according to agreement. 

Umeå Plant Science Centre (UPSC) is one of the strongest research environments for basic plant research in Europe. Research at UPSC covers a wide range of disciplines in plant biology including ecology, computational biology, genetics, physiology, biochemistry, cell biology and molecular biology (see www.upsc.se). A PhD student position in plant science is open at the Department of Plant Physiology, which is part of Umeå Plant Science Centre. Application deadline is June 19th, 2023.

Project description

Transposable elements (TEs), major component of most plant genomes, are active and dynamic component of genome structural and functional variation and evolution. Tremendous advancements in molecular biology, genomics, and genetics have disclosed various features and roles of TEs. However, accurate and efficient tools for TEs annotation, classification, movement, lateral transfer, recombination, and evolution are still lacking or not efficacious enough especially for complex genomes, like that of conifers. 

The PhD project focuses on TE biology and the development of new computational tool. This project will focus on:

(1) The development of new TEs annotation and characterization tools by integrating alignment-free sequence analysis method with network analysis. 

(2) Using this tool to characterize the spruce genome regarding the classification and phylogenetics of TEs, and investigate how recombination, lateral transfer, and sequence capture involved in TEs diversification or even de novo origination. 

(3) Examine the spatial and temporal dynamics of TEs regeneration with mathematical or statistical modeling techniques. 

This project will potentially develop a set of new analytical tools and reveal a more insightful picture of TEs movement and evolution. Plant genome data, especially that of conifer, will be the key research systems of this project. 

This Ph.D. position is focused on developing and applying computational methods to advance our understanding of TE and its complexities reflected in plant genome. The successful candidate will work at the interface of computational biology, systems biology, and molecular biology and will have the opportunity to collaborate with experimentalists and computational scientists across a range of disciplines of plant science.

Admission requirements

To fulfil the general entry requirements for studies at third-cycle level, the applicant must have qualifications equivalent to a completed degree at second-cycle level, or completed course requirements of at least 240 ECTS credits including at least 60 ECTS credits at second-cycle level.

To fulfil the specific entry requirements to be admitted for studies at third-cycle level in Plant Science at Umeå Plant Science Centre, the successful candidate must have completed 90 ECTS relevant to the doctoral thesis project. Out of this, at least 30 ECTS have to be in a subject closely related to the research topic of the graduate program. Applicants who have acquired equivalent skills in some other educational system in Sweden or abroad are also eligible.

For this position, we are looking for a person with an academic background in plant biology, biotechnology, bioinformatics or a related field. The following skills are required:

• Experience in standard molecular biological techniques.
• Very good written and oral English language skills.
• Proficiency in working with computers and programming, e.g. in Linux Shell, R, Python, Julia etc. 

The Ph.D. student is expected to play an active role in developing this doctoral project and in the department. In addition, the Ph.D. student is expected to have a scientific, structured, flexible, and result-oriented approach to their work. The assessments of the applicants are based on their qualifications and presumed ability to take part in doctoral education.

Terms of employment

The employment is expected to result in a doctoral degree and the main assignment for the student is thus to be part of the research education, which includes participation in research but also taking relevant courses. Teaching and other departmental activities (up to a maximum of 20% time) are typically included as well. Employment is limited to four years at full time or up to five years if teaching and other departmental work is performed. The salary is fixed according to the established salary level for doctoral students. 

Application

You apply on 19 June 2023 at the latest. The application should be written in English (preferably) or Swedish and must include: 

1. A cover letter summarizing your qualifications, scientific interests and motives for applying (max two pages)
2. A curriculum Vitae
3. Certified copies of relevant degree certificate(s) translated to English or Swedish, for example Diplomas of bachelor or Master level degrees (if any).
4. Master theses work/other relevant publications (if any)
5. Transcripts with grades, with English or Swedish translation. 

Documents should be sent electronically, in MS Word or PDF format, through the recruitment system. The procedure for recruitment for the position is in accordance with the Higher Education Ordinance (chapt. 12, 2 §) and the decision regarding the position cannot be appealed. 

More information

For further information contact the Principal Investigator of the project, Associate Professor Jian-Feng Mao, jianfeng.mao@umu.se

We look forward to receiving your application!