title: A whole-cell computational model predicts phenotype from genotype.
abstract: Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. Our whole-cell model accounts for all annotated gene functions and was validated against a broad range of data. The model provides insights into many previously unobserved cellular behaviors, including in vivo rates of protein-DNA association and an inverse relationship between the durations of DNA replication initiation and replication. In addition, experimental analysis directed by model predictions identified previously undetected kinetic parameters and biological functions. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery.
authors: Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA.
authors: Jonathan R
authors: JR
authors: Karr
authors: Jayodita C
authors: JC
authors: Sanghvi
authors: Derek N
authors: DN
authors: Macklin
authors: Miriam V
authors: MV
authors: Gutschow
authors: Jared M
authors: JM
authors: Jacobs
authors: Benjamin
authors: B
authors: Bolival
authors: Nacyra
authors: N
authors: Assad-Garcia
authors: John I
authors: JI
authors: Glass
authors: Markus W
authors: MW
authors: Covert
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D002453:Cell Cycle; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000378:metabolism; D008954:Models, Biological; D058977:Molecular Sequence Annotation; D045704:Mycoplasma genitalium / Q000166:cytology* / Q000235:genetics*; D010641:Phenotype
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins