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Methanococcus maripaludis ReconstructionMethanococcus maripaludis is an archaeon capable of generating methane gas from carbon dioxide and hydrogen. We have reconstructed its metabolism to enable better understanding of methanogenesis, particularly for learning ways to harness the process for producing liquid fuels from methane.
Honeybee Transcriptional Regulatory NetworkUsing a brain transcriptome data set we reconstructed a Transcriptional Regulatory Network (TRN) that showed remarkably high accuracy in quantitatively predicting brain gene expression.
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.
Methanosarcina acetivorans ReconstructionIn collaboration with Bill Metcalf's lab at the University of Illinois at Urbana-Champaign, we are sequencing 20 novel Methanosarcina strains. The genomes are being analyzed to learn more about the evolution of metabolic and regulatory networks to identify environmental patterns in their evolution. As part of this analysis, we have constructed a genome scale metabolic model of Methanosarcina acetivorans C2A, a model archaeon. Along with our updated model of M. barkeri, this model serves as a platform to enhance our understanding of methanogen metabolism, a vital part of the global carbon cycle.
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.
Methanosarcina barkeri ReconstructionIn collaboration with Bill Metcalf's lab at the University of Illinois at Urbana-Champaign, we are sequencing 20 novel Methanosarcina strains. The genomes are being analyzed to learn more about the evolution of metabolic and regulatory networks to identify environmental patterns in their evolution. As part of this analysis, we have updated the genome scale metabolic model of Methanosarcina barkeri Fusaro, a model archaeon. Along with our model of M. acetivorans, this updated model serves as a platform to enhance our understanding of methanogen metabolism, a vital part of the global carbon cycle.
Clostridium beijerinckii ReconstructionClostritidium beijerinckii is an attractive organism for biofuel production because it can naturally produce high yields of butanol from sugars. In order to better understand this process, we have constructed the first genome scale metabolic model of C. beijerinckii. This model serves as a platform to generate hypotheses for how to metabolically engineer new strains with improved butanol production.