Integrating genetic regulatory networks and genome-scale metabolic models using GEMINI and PROM

We have developed two genome-scale metabolic network algorithms that integrate the transcriptional regulatory network into genome-scale metabolic models.

PROM (Probabilistic Regulation of Metabolism) enables the quantitative integration of regulatory and metabolic networks to build genome-scale integrated metabolic–regulatory models. GEMINI (Gene Expression and Metabolism Integrated for Network Inference) directly connects regulatory interactions to observable phenotypes and allows rapid assessment of inferred regulatory interactions using a metabolic network.

Publications

1. Chandrasekaran S and N.D. Price, "Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis," PNAS, 2010.
2. Simeonidis E, Chandrasekaran S, Price ND. “A guide to integrating transcriptional regulatory and metabolic networks using PROM (Probabilistic Regulation of Metabolism)”, Methods in Molecular Biology: Systems Metabolic Engineering.
3. Chandrasekaran S and N.D. Price, “Metabolic Constraint-based Refinement of Transcriptional Regulatory Networks”, PLOS Computational Biology, 2013.