* Computational infrastructure development for analysis of microbial community functional structure, primarily using sequencing data.
* Phylogenomic approaches for functional dissection.
* Microbial community substructure such as interaction networks of minimal viable functional cohorts.
* Principles of functional guild dynamics and the determination of whether rare species contribute to community phenotype, stability, and efficiency.
* Development of lab consortia model systems.
* Modeling of microbial community population, physiological state, and genetic adaptation in response to physical, chemical, genetic, and species perturbation.
* Manipulation of natural enzymes by structural design to engender new behaviors.
* Much of this work involves developing infrastructure to support such investigations, including the Robetta protein structure prediction server (www.robetta.org), the Genome-Linked Application for Metabolic Maps (GLAMM) metabolic network viewer (glamm.lbl.gov), the MicrobesOnline (www.microbesonline.org) and metaMicrobesOnline (meta.microbesonline.org) phylogenomic analysis platforms for microbes and microbial communities, and most recently the DOE Systems Biology Knowledgebase (kbase.us) project.