title: In silico method for modelling metabolism and gene product expression at genome scale.
abstract: Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.
authors: Department of Bioengineering, University of California-San Diego, PFBH Room 419, 9500 Gliman Drive, La Jolla, California 92093-0412, USA.
authors: Joshua A
authors: JA
authors: Lerman
authors: Daniel R
authors: DR
authors: Hyduke
authors: Haythem
authors: H
authors: Latif
authors: Vasiliy A
authors: VA
authors: Portnoy
authors: Nathan E
authors: NE
authors: Lewis
authors: Jeffrey D
authors: JD
authors: Orth
authors: Alexandra C
authors: AC
authors: Schrimpe-Rutledge
authors: Richard D
authors: RD
authors: Smith
authors: Joshua N
authors: JN
authors: Adkins
authors: Karsten
authors: K
authors: Zengler
authors: Bernhard O
authors: BO
authors: Palsson
mesh_terms: D019295:Computational Biology / Q000379:methods*; D049490:Systems Biology / Q000379:methods*; D020124:Thermotoga maritima / Q000235:genetics; D059467:Transcriptome / Q000235:genetics