Nathaniel Street in the UPSC bioinformatics office Photo: Fredrik Larsson

Our group has a focus on genomics research of aspen, Norway spruce and Scots pine. We perform genome assembly, transcriptome and co-expression network analyses with a focus on understanding the genetic architecture of complex traits such as leaf shape variation, wood development and specialised metabolite production and the role of non-coding RNAs in regulation and genome function.

Through collaboration with Prof. Vaughan Hurry we are also performing metagenomics and metatranscriptomics analyses to understand functional links between tree hosts, their associated microbiome and abiotic factors. The group have a strong interest in applications of new sequencing technologies and develop the web resource to make their genomics data available to the community.

We make extensive use of bioinformatics and computational approaches including machine learning, GWAS, network inference, differential, network analysis and a plethora of genome assembly and comparative genomics analysis tools. These approaches are implemented using genomic DNA, RNA-Seq, ATAC-Seq, DAP-Seq, Hi-C and other high-throughput based sequencing methods.

Five photos of aspen buds showing a closed bud on the left followed by different stages of bud burst towards the right side.Stages of leaf development in aspen. We are performing detailed characterisation of developmental profiles in aspen to support our association mapping project and to further understanding of genes functioning during leaf development.

We are also working to establish wet lab methods for validation of candidate genes and regulatory mechanisms identified from our in-silico work. The group are firm believers in implementing reproducible and transparent analyses through the use of resources such as snakmake/nextflow, git and by developing FAIR compliant tools. We make extensive use of R, python and high performance computing infrastructures.

Collection of differently formed leavesRepresentative leaf shapes from the Swedish Aspen collection, a collection of natural aspen genotypes from across Sweden that is grown in a common garden experiment near Umeå You can find out more about us at the group web site