Vacant job

PhD Student in Plant Biology: Functional Genomics in Conifers

Department of Physiological Botany

The Department of Physiological Botany at Umeå University is offering a PhD position within the Con-TEki project, which investigates the role of transposable elements (TEs) as drivers of regulatory innovation in conifers (spruce and pine).

The department is part of the Umeå Plant Science Centre (UPSC; www.upsc.se), an internationally leading research environment with approximately 200 researchers in plant biology, including molecular biology, genomics, physiology, and bioinformatics. UPSC offers access to advanced infrastructure for plant transformation, sequencing, computational analysis, and advanced microscopy in a highly collaborative and interdisciplinary environment.

Project Description

Conifer genomes are very large and rich in transposable elements, but the functional consequences of TE integrations for gene regulation are still poorly understood. The Con-TEki project aims to understand how TE-derived regulatory elements contribute to divergence in gene expression and adaptive responses in conifers.

This PhD project focuses on the development and implementation of methods for the functional validation of regulatory elements in conifer systems. The work will integrate large-scale regulatory genomics data with experimental molecular biology to directly test hypotheses generated from genomic data.

The project involves integrating genomic data (e.g., chromatin accessibility, gene expression, and methylation data) with experimental methods to validate candidate regulatory elements and gene regulatory mechanisms. Particular emphasis will be placed on establishing robust and reproducible workflows for functional analyses in spruce and pine.

Within the framework of the project, there are excellent opportunities to develop competence at the interface between experimental molecular biology and bioinformatics. The project will utilize transformation and validation platforms at UPSC, enabling direct testing of candidate regulatory elements in conifer systems. The project is particularly well-suited for candidates with a strong interest in the development and optimization of experimental methods. Experience with reporter gene assays, transient expression systems, or genome editing is particularly advantageous.

Responsibilities

The PhD student will be trained in:

• Developing and implementing experimental methods for the functional validation of regulatory elements
• Performing molecular biology experiments, including nucleic acid extraction and library preparation for sequencing
• Contributing to the generation, processing, and interpretation of genomic data
• Integrating experimental results with computational analyses
• Developing reproducible workflows for experimental and analytical tasks
• Participating in scientific communication through presentations and publications

Qualifications

Basic Admission Requirements

Basic eligibility is held by those who have completed an advanced level degree, fulfilled course requirements of at least 240 higher education credits, of which at least 60 credits are at an advanced level, or have otherwise acquired substantially equivalent knowledge within or outside the country. The Faculty Board may grant exceptions to the basic eligibility requirement for an individual applicant if there are special reasons. (HF 7 Chapter 39 §)

To meet the requirement for special eligibility for admission to doctoral studies in plant biology, the applicant must have fulfilled course requirements of at least 90 higher education credits at an advanced level in biology, or other subjects relevant to the research area, e.g., chemistry, physics, or computer science. Of these, at least 15 credits must be from courses with direct relevance to the research project, and at least 15 credits from an individual project work. Good knowledge of English, both written and oral, is also a requirement.

The requirements for prior knowledge as stated above are also considered met by those who have acquired substantially equivalent knowledge in another manner.

Additional Qualifications

Requirements

• Practical experience with molecular biology methods
• Good ability to work experimentally in a structured and reproducible manner
• Good ability to communicate in English, both orally and in writing

Merits

• Experience with high-throughput sequencing (e.g., RNA-seq, ATAC-seq, or similar)
• Experience working with plant material
• Experience with bioinformatics, programming, or data analysis
• Experience with method development and optimization

About the Position

The position aims at a doctoral degree, and the main task of the PhD student is to pursue their doctoral education, which includes participation in the aforementioned research project as well as doctoral education courses. Teaching and other departmental duties (max 20%) may be included in the responsibilities. The employment is time-limited to four years full-time or up to five years with part-time teaching. Salary placement is according to the established salary scale for PhD positions.

Start date: October 5, 2026, or as agreed.

Application

The application should be written in English (preferred) or Swedish and submitted via Umeå University's recruitment system, Varbi. The application deadline is July 31, 2026.

A complete application should include:

• Cover letter (max 2 pages) describing your qualifications and what motivates you to apply for the position
• CV
• Copies of degree certificates and documentation of completed higher education courses and grades
• Contact details for 2–3 references
• Any other documents the applicant wishes to submit

Contact

For questions, please contact: Professor Nathaniel R. Street, Umeå University, [email protected]