Zoran Nikoloski

The University of Copenhagen’s Department of Plant and Environmental Sciences invites applications for a postdoctoral position in computational biology within the Mutwil group. The project focuses on using multimodal single-cell and epigenomic data to resolve gene regulatory networks underlying crop responses to heat and drought. The research covers four Nordic crops—rapeseed, potato, wheat and barley—and examines stress responses across multiple organs, time points and conditions. The postdoctoral researcher will serve as the computational integrator of a grant investigating climate-driven crop resilience, transforming sequencing and literature-derived data into interpretable regulatory networks. The work begins with single-cell RNA-seq and ATAC-seq data generated on a 10x Genomics platform. Responsibilities include developing quality-control and integration pipelines, handling doublets and ambient RNA, annotating cell types using conserved markers, and creating reproducible workflows that can be extended by PhD students. A major research component is the inference of transcription factor–target relationships and the identification of cis-regulatory elements through known motifs, de novo motif discovery, convolutional neural networks and DNA language models. These elements will be connected into TF–CRE–target triplets, benchmarked against established frameworks such as SCENIC+ and MAESTRO, and ranked according to conservation across the four crop species. The postdoc will also connect regulatory networks with the group’s literature-derived knowledge graph, gene-function predictions and open web resources, supporting the prioritization of regulators and targets for validation in rapeseed. The role includes co-supervising PhD and master’s students and helping expand the group’s single-cell and multi-omics analysis capacity. The Mutwil group works at the intersection of comparative and evolutionary plant biology and AI-driven biological discovery. The postdoctoral researcher will collaborate with the group’s researchers and with Prof. Ryan Lister at the University of Western Australia and Prof. Zoran Nikoloski at the University of Potsdam. The position is based at the Frederiksberg Campus in Copenhagen, with access to substantial computational resources, including GPU resources through LUMI and uCloud.