Postdoc (2 years) in plant genomics with a focus on transposable elements

About the project

Con-TEki investigates the role of transposable elements (TEs) as drivers of regulatory innovation in conifers (Norway spruce and Scots pine), contrasting outcomes with an 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), massively parallel enhancer assays (ATAC-STARR-seq), and comparative/bayesian/deep-learning analyses, with functional validation in spruce via CRISPR-Cas9 and nanoparticle delivery.

The postdoc will join Professor Nathaniel R. Street’s team at UPSC, working closely with Laszlo Bakó (molecular biology) and Torgeir R. Hvidsten (comparative genomics). The environment provides comprehensive 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 the Integrated Science Lab (IceLab), giving access to a highly collaborative and multidisciplinary research network.

Key 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 that link TE‑derived cis‑regulatory elements (TE‑CREs) to gene expression divergence within and across species.
  - Implementing ATAC‑STARR‑seq to validate enhancer activity; mapping enhancer–promoter links via loop/TAD structures.
  - Perform comparative analyses versus Populus tremula; apply network modelling and machine learning for regulatory inference.
  - Functional validation of candidate TE‑CREs in spruce using UPSC transformation and somatic embryogenesis pipelines; evaluating drought phenotypes.
  
  
• Curate, document and analyse large, multi‑omic datasets; ensure reproducibility and FAIR data stewardship.
• Lead manuscript preparation for high‑impact journals; present at internal seminars and international conferences.
• Mentor PhD students and contribute to collaborative work 
   

Qualification requirements

To be appointed under the postdoctoral agreement, the postdoctoral fellow is required to have completed a doctoral degree or a foreign degree deemed equivalent to a doctoral degree. This qualification requirements must be fulfilled no later than at the time of the appointment decision.

To be appointed under the postdoctoral agreement, priority should be given to candidates who completed their doctoral degree, according to what is stipulated in the paragraph above, no later than three years prior. If there are special reasons, candidates who completed their doctoral degree prior to that may also be eligible. Special reasons include absence due to illness, parental leave, appointments of trust in trade union organisations, military service, or similar circumstances, as well as clinical practice or other forms of appointment/assignment relevant to the subject area.

The doctoral degree should be in in plant molecular biology, genomics/bioinformatics, systems genetics, or closely related field.

Demonstrable expertise in at least two of:

• High‑throughput sequencing assays (ATAC‑Seq, ChIP‑Seq, BS‑Seq/EM‑Seq, RNA‑Seq); library prep and QC.
• 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 commensurate with career stage; excellent scientific writing and communication. Good communication skills in English (speaking and writing) are required. 

Desirable merits

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

Terms of employment

The emplyment is full-time and time limited for two years. Starting date as soon as possible or according to agreement.

Application

Submit your application via Umeå University’s recruitment system. The last application date is February 11, 2026. Include:

• CV and publication list
• Cover letter (max 2 pages) describing your fit to Con-TEki and preferred emphasis (wet-lab vs computational; research interests)
• Names and contact details of 2–3 referees
• Evidence of PhD award (or expected award date)

Selection process

Applications are reviewed for scientific excellence, methodological match to Con-TEki, collaborative capability, and potential to drive high-impact outputs. Shortlisted candidates may be invited to present prior work and a brief research plan aligned to Con-TEki.