Research Highlights for Milestone 3: Computing
- Progress is being made in data reduction and analysis for mass spectrometric experiments, integration of databases containing heterogeneous data sets, and use of myriad approaches to metabolic and regulatory network modeling.
- The computational framework for comparative analysis of functional genomic data and computational models is being developed for data on the behavior of microbial gene regulatory networks in response to environmental conditions.
- Whole-cell flux-balance models are being used to understand aspects of natural behavior and for comparative analysis of different microbial strains.
- Computational methods are being developed to predict the wiring diagrams of various response networks, which consist of signaling, regulatory, and metabolic components. These include carbon fixation, phosphorus assimilation, and nitrogen-assimilation networks encoded in cyanobacterial genomes. Research is ongoing to apply the framework to Shewanella. These methods use predictions of operons and regulons and interaction relationships among candidate genes whose proteins appear to be expressed together or coordinately (see Synechococcus Encyclopedia).
- Computational models are being built to predict the activity of natural microbial communities for application of robust bioremediation technologies. Teams also are learning how to simulate growth and activity of metal-reducing organisms in their natural environments.
