Postdoctoral Researcher (2 years) in Plant Genomics with a Focus on Transposable Elements

About the Project

Con-TEki investigates transposable elements (TE) as a driving force for regulatory innovation in conifers (spruce and pine) and compares them with the angiosperm aspen.

The project combines genomic, epigenomic, and 3D chromatin profiling (ATAC-Seq, easySHARE-Seq, ChIP-Seq, Micro-C/Hi-C, BS-Seq/EM-Seq), large-scale enhancer assays (ATAC-STARR-seq), and comparative/Bayesian/deep learning analyses, with functional validation in spruce via CRISPR-Cas9 and nanoparticle technology.

The postdoctoral researcher will join Professor Nathaniel R. Streets' team at UPSC, where they will work closely with Laszlo Bakó (molecular biology) and Torgeir R. Hvidsten (comparative genomics). The research environment provides extensive support for large-scale multi-omic data generation/analysis and transformation/embryogenesis services for functional validation. Nathaniel is also an associate group leader at the Science for Life Laboratory (SciLifeLab) and Integrated Science Lab (IceLab), providing access to a highly collaborative and interdisciplinary research network.

Responsibilities

• Design and execute wet lab and/or computational workflows including:
• Profiling open chromatin, histone marks, methylation, and chromatin conformation during wood development and drought stress in spruce/pine.
• Building integrative analyses linking TE-derived cis-regulatory elements (TE CRE) to gene expression divergence within and between species.
• Implementing ATAC STARR sequencing to validate enhancer activity; mapping enhancer-promoter links via loop/TAD structures.
• Performing comparative analyses against Populus tremula; applying network modeling and machine learning for regulatory inference.
• Functional validation of candidate TE CRE in spruce using UPSC transformation and somatic embryogenesis pipelines; evaluating drought phenotypes.
• Compile, document, and analyze large multi-omic datasets; ensure reproducibility and FAIR data management.
• Lead manuscript preparations for high-impact journals; present at internal seminars and international conferences.
• Supervise PhD students and contribute to collaboration.

Qualifications

To be employed under a fixed-term postdoctoral agreement, a completed PhD or foreign degree deemed equivalent is required. This eligibility requirement must be met by the time the employment decision is made.

To be employed under the postdoctoral agreement, preference will primarily be given to those who have completed their degree as mentioned above within the last three years. If there are special reasons, those who completed their PhD earlier may be considered. Special reasons include leave due to illness, parental leave, elected positions within trade unions, service in the total defense, or other similar circumstances, as well as clinical service or relevant employment/assignments in the subject area.

The PhD must be in plant molecular biology, genomics/bioinformatics, systems genetics, or a closely related field.

Demonstrable expertise in at least two of the following:

• High-throughput sequencing analyses (ATAC Seq, ChIP Seq, BS Seq/EM Seq, RNA Seq); library preparation and quality control.
• Chromatin conformation (Hi C/Micro C) and analysis of TADs/compartments/loops.
• Computational genomics: co-expression networks, comparative genomics/orthology, ML/DL for regulatory inference.
• Plant transformation/CRISPR and phenotyping in conifers or woody species.

Strong publication record in relation to career stage; excellent scientific writing and communication. Good communication skills in English (spoken and written) are required.

Merits

Experience with segmental duplication/WGD analyses, TE annotation, and motif/footprint inference.

• Experience with segmental duplication/WGD analyses, TE annotation, and motif/footprint inference.
• Familiarity with ATAC STARR sequencing or other MPRA methods; integration of enhancer activity with 3D genome features.
• Previous work with drought stress responses, wood development, or conifer systems (spruce/pine).
• Knowledge of HPC workflows and reproducible pipelines; commitment to open science/FAIR.

Employment Conditions

The position is full-time and fixed-term for two years. Start date as soon as possible or by agreement.

Application

Please submit your application via Umeå University's recruitment system. The deadline for applications is February 11, 2026. Attach:

• CV and publication list
• Cover letter (max 2 pages) explaining why you are a good fit for Con-TEki and your preferred focus (laboratory vs bioinformatics; research interests)
• Names and contact details of 2–3 referees
• PhD diploma (or expected graduation date)

Selection Process

Applications will be assessed based on scientific excellence, methodological alignment with Con-TEki, collaborative ability, and potential to contribute to high-quality results. Selected candidates may be asked to present previous work and a brief research plan in line with Con-TEki.

The Department of Physiological Botany is part of Umeå Plant Science Centre with approximately 200 employees, including around 40 group leaders, currently representing 48 different nationalities (for more information, see http://www.upsc.se (http://www.upsc.se) or http://www.plantphys.umu.se/english/ (http://www.plantphys.umu.se/english/)). Our main activities are academic research and education covering areas such as ecology, biochemistry, plant physiology, and genomics.