Bioinformatics and Computational Biology

Bioinformatics and computational biology are cornerstones of modern-day molecular biology and are strongholds of the center. PSB has a longstanding expertise in many subdomains of bioinformatics, including the assembly and annotation of novel plant genome sequences, evolutionary genomics, the analysis and integration of -omics data, gene network modeling and comparative genomics. While many projects at PSB are already collaborations between experimental and bioinformatics groups, a further integration of dry- and wet-lab activities remains a key goal of the Center. Such further integration is a prerequisite for running complex integrative biology projects on climate change involving e.g. field trials, massive -omics data generation with single cell resolution, phenotyping, data integration for gene function inference, model building for trait prediction, genome editing of candidate genes, and validation experiments. Next to efforts to enhance dry-lab skills in wet-labs and vice versa, we strive to increase the number of joint projects between dry-lab and wet-lab groups tackling common research interests, and stimulate such bottom-up initiatives where possible.  

Genome editing will be pivotal for future crop improvement but when dealing with complex biological problems one of the most difficult tasks is to prioritize the list of candidate genes to target. Although great progress has already been made in model organisms such as Arabidopsis, translating this knowledge to crops is hampered by evolutionary divergence between plant species. In particular, the omnipresence of polyploidy in plants – an important research topic at PSB - hampers both direct translation of knowledge from models to crops and prioritization of candidate genes inferred from omics analyses on the crop of interest. The computational groups at PSB have ample expertise in polyploidy, ancient genome duplications, evolutionary genomics and comparative genomics, and will continue to both generate fundamental insights and develop tools in these areas. This expertise will be crucial in PSB efforts to link genes to traits in maize, wheat, poplar, and soybean, and for investigating how plants cope with climate change.