Vacant job

Postdoctoral Researcher (2 years) in Genomics focusing on Transposable Elements in Plants

About the Project

Con-TEki investigates the role of transposable elements (TEs) as drivers of regulatory innovation in conifers (spruce and pine), with a comparison to an angiosperm (asp). The project combines genomic, epigenomic, and 3D chromatin profiling methods (ATAC-Seq, easySHARE-Seq, ChIP-Seq, Micro-C/Hi-C, BS-Seq/EM-Seq), large-scale parallel enhancer assays (ATAC-STARR-seq), as well as comparative/Bayesian/deep learning analyses, with functional validation in spruce.

The postdoctoral researcher will join Professor Nathaniel R. Street’s research group at UPSC and work closely with Torgeir R. Hvidsten (NMBU, Norway). The research environment offers extensive support for large-scale multiomics data generation and analysis, as well as transformation/embryogenesis 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 strong collaborative and interdisciplinary research network.

Main Responsibilities

• Design and implement computational workflows including:
  • Analysis of chromatin accessibility, histone modifications, methylation, and chromatin conformation under drought stress and in association with ectomycorrhizal fungi in spruce/pine.
  • Perform phylogenetic analyses as well as analysis of gene duplication and gene family dynamics.
  • Build integrated analyses linking TE-derived cis-regulatory elements (TE-CREs) to divergence in gene expression within and between species.
  • Implement pipelines for the analysis of ATAC-STARR-seq data to validate enhancer activity; map enhancer–promoter connections via loop/TAD structures.
  • Perform comparative analyses against Populus tremula; apply network modeling and machine learning for regulatory inference.
  • Analyze DNA methylation data in combination with sRNA profiling.
  • Perform analysis of TE and lincRNA expression.
• Curate, document, and analyze large multiomics datasets; ensure reproducibility and FAIR data management.
• Lead manuscript writing for high-impact journals; present at internal seminars and international conferences.
• Supervise doctoral students and contribute to collaborative projects.

Qualifications

To be employed under the agreement for fixed-term employment as a postdoctoral researcher, a completed PhD degree or a foreign degree assessed as equivalent to a PhD is required. This qualification requirement must be met no later than the time the employment decision is made.

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

The PhD should be in plant molecular biology, genomics/bioinformatics, system genetics, or a related field.

Documented expertise in at least two of the following areas:

• Analysis of high-throughput sequencing data (ATAC-Seq, ChIP-Seq, BS-Seq/EM-Seq, RNA-Seq); library preparation and quality control.
• Analysis of chromatin conformation data (Hi-C/Micro-C) including TADs/compartments/loops.
• Computational genomics: co-expression networks, comparative genomics/orthology, ML/DL for regulatory inference.

A strong publication record relative to career stage and very good scientific written and oral communication skills in English are required.

Qualifications that are an advantage

• Experience with analyses of segmental duplications/WGD, TE annotation, and motif/footprint analysis.
• Experience with ATAC-STARR-seq or other MPRA methods; integration of enhancer activity with 3D genome data.
• Previous work on drought stress response, wood development, microbial interactions, or tree models.
• Experience with HPC workflows and reproducible pipelines; commitment to open science/FAIR.

Applications will be assessed based on scientific quality, methodological relevance to the Con-TEki project, teamwork skills, and potential to generate high-impact results.

Terms of Employment

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

Application

The application should be written in English (preferred) or Swedish, and attached documents should be in Word or PDF format. The application must be registered via Umeå University’s recruitment system Varbi and be received no later than June 6, 2026.

A complete application should include:

• CV and publication list.
• Cover letter (max 2 pages) describing your suitability for Con-TEki and desired focus (laboratory vs. computational work; research interests).
• Name and contact details for 2–3 references.
• Certificate of PhD degree (or expected graduation date).

Additional Information

Selected candidates may be invited to present previous work and a short research plan aligned with Con-TEki.

Contact

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