Genetic Co-Occurrence Network across Sequenced MicrobesWe have developed a new phylogenetic approach and used it to identify co-occurrence patterns of orthologous genes across all sequenced microbes (at the time). This approach identifies “correlogs” that co-occur in genomes much more often than would be expected by their relative frequencies, suggesting a functional relationship.
TSEMWe have used mCADRE to reconstruct genome-scale metabolic models for 126 different human tissues and cell types to establish a Tissue-Specific Encyclopedia of Metabolism (TSEM) as a community resource—the largest collection of tissue-specific metabolic models for human to date.
MediaDBMediaDB collects chemically defined growth media from primary literature sources for fully sequenced organisms. The Price Lab maintains this database, which places emphasis on organisms with existing genome scale metabolic models. We intend for this database to serve as an aid in understanding and designing media, as well as a tool for discovering connections between media compounds and organism characteristics encoded in the genome.