The arrival of next generation sequencing techniques has opened up a wide range of new research areas to study plant microbe interactions. The genomes of phytopathogenic and beneficial fungi can now be cost-effectively sequenced and gene expression profiles can be determined on a genome-wide scale for both the host plant and the pathogen or endophyte. Assembly, functional annotation and comparative analysis of the genomes of plant associated fungi will provide important novel resources to study the fungal side of plant–parasite and plant-endophyte interactions and to obtain insights into genomic (co-)evolution of interacting organisms. We focus on applying and developing computational tools to provide these resources. Our research includes collaborations with groups within the Department as well as tight communication with the local central computing facility SUSAN and the Max Planck Genome Centre Cologne (GCC). In addition to our main topics we act as a consultancy for any bioinformatics related question.