PhD position in Plant Science with focus on functional genomics of conifers

Project description

Conifer genomes are exceptionally large and rich in transposable elements, yet the functional consequences of TE insertions on gene regulation remain poorly understood. The Con-TEki project aims to understand how TE-derived regulatory elements contribute to gene expression divergence and adaptive responses in conifers.

This doctoral project focuses on the development and implementation of approaches for functional validation of regulatory elements in conifer systems. The work will bridge large-scale regulatory genomics with experimental molecular biology to directly test hypotheses generated from genome-wide datasets.

The project will involve the integration of genomic data (e.g. chromatin accessibility, gene expression and methylation data) with experimental approaches to validate candidate regulatory elements and gene regulatory mechanisms. Emphasis will be placed on establishing robust and reproducible workflows for functional assays in spruce and pine.

Within this framework, the position provides strong opportunities to develop expertise at the interface between experimental molecular biology and bioinformatics. The project will make use of transformation and functional validation platforms available at UPSC, enabling direct testing of candidate regulatory elements in conifer systems. This project is particularly suited to candidates with a strong interest in experimental method development and optimisation. Experience with reporter assays, transient expression systems or genome editing approaches is particularly relevant.

Work tasks

The doctoral student will be trained to:

• Develop and implement experimental approaches for functional validation of regulatory elements
• Perform molecular biology experiments, including nucleic acid extraction and sequencing library preparation
• Contribute to the generation, processing and interpretation of genome-wide datasets
• Integrate experimental results with computational analyses
• Develop reproducible workflows for experimental and analytical procedures
• Participate in scientific communication through presentations and publications

Eligibility 

To fulfil the general entry requirements, the applicant must have qualifications equivalent to a completed degree at advanced level (second cycle), or completed course requirements of at least 240 ECTS credits including at least 60 ECTS credits at advanced level, or has otherwise acquired essentially equivalent knowledge within Sweden or abroad. The faculty board may, in the case of a specific applicant, consent to an exemption from the general entry requirements if there are special reasons to do so. (cf. Higher Education Ordinance) 

To fulfil the specific entry requirements to be admitted to doctoral studies in Plant Science, the successful candidate must have completed 90 ECTS in Biology or other subjects relevant to the research area, such as Chemistry, Physics, or Computer Science/Bioinformatics. Of these, at least 15 ECTS must be in a subject directly relevant to the research topic and at least 15 ECTS from an individual project course. Good knowledge of English, both written and spoken, is also required.  

The requirements for prior knowledge as described above are also considered to be met by those who have otherwise acquired essentially equivalent knowledge. 

Qualifications

Required qualifications

• Practical experience of molecular biology techniques
• Good ability to work experimentally in a structured and reproducible manner
• Good communication skills in English, both written and spoken

Meriting qualifications

• Experience with high-throughput sequencing methods (e.g. RNA-seq, ATAC-seq or similar)
• Experience of working with plant material
• Experience with bioinformatics tools, scripting or data analysis
• Experience of method development and optimisation

About the employment

The position is intended to result in a doctoral degree. The main task of the PhD student is to pursue their doctoral studies, which include participation in research and postgraduate courses. The duties can include teaching and other departmental work (up to a maximum of 20%). The employment is limited to four years full-time or up to five years including teaching part-time. Salary is set in accordance with the established salary ladder for PhD position.

The expected starting date is October 5, 2026, or according to agreement.

Application

The application should be written in English (preferably) or Swedish and submitted via Umeå University’s e-recruitment system Varbi. The last application date is July 31, 2026.

A complete application should include:

• A personal letter (max 2 pages) describing your qualifications and motivation for applying for the position
• Curriculum vitae (CV)
• Copies of degree certificates and documentation of completed university courses and grades
• Contact details of 2–3 referees
• Other documents the applicant wishes to submit

Further information

For further information, please contact: Professor Nathaniel R. Street, Umeå University, nathaniel.street@umu.se