In my research group, we use machine learning methods and large-scale genomics datasets to model how genes interact in regulatory networks, how regulatory networks evolve and how they give rise to complex properties characteristic to individuals and species.
Our main project aims to understand the process of wood formation in angiosperm and gymnosperm tree species by modelling the regulatory networks orchestrating the differentiation of stem cells into woody tissues. To this end, we are integrating large-scale multi-omics data to infer regulatory networks for several species and comparing these networks across species to identify regulatory mechanisms explaining the evolution of trees.
In another project, we work to understand how gene regulation evolves after whole genome duplication and to reveal to what degree these events, which play major roles in plant evolution, spark new regulatory innovations. To this end, we are developing phylogenetic methods for comparative analysis of omics data across multiple species.
In collaboration with Nathaniel Street, we are developing a number of online tools for facilitating comparative network analysis in plants. ComPlEx, available through the PlantGenIE portal (http://plantgenie.org), allows Comparative analysis of Plant Expression networks. AspWood (http://aspwood.popgenie.org) and NorWood (http://norwood.congenie.org) offer dedicated tools to analyze high-resolution gene expression data across wood formation in aspen and Norway spruce.