title: Continuous-time identification of gene expression models.
abstract: One objective of systems biology is to create predictive, quantitative models of the transcriptional regulation networks that govern numerous cellular processes. Gene expression measurements, as provided by microarrays, are commonly used in studies that attempt to infer the regulation underlying these processes. At present, most gene expression models that have been derived from microarray data are based in discrete-time, which have limited applicability to common biological data sets, and may impede the integration of gene expression models with other models of biological processes that are formulated as ordinary differential equations (ODEs). To overcome these difficulties, a continuous-time approach for process identification to identify gene expression models based in ODEs was developed. The approach utilizes the modulating functions method of parameter identification. The method was applied to three simulated systems: (1) a linear gene expression model, (2) an autoregulatory gene expression model, and (3) simulated microarray data from a nonlinear transcriptional network. In general, the approach was well suited for identifying models of gene expression dynamics, capable of accurately identifying parameters for small numbers of data samples in the presence of modest experimental noise. Additionally, numerous insights about gene expression modeling were revealed by the case studies.
authors.affiliation: Department of Chemical Engineering, University of Delaware, Newark, Delaware, USA.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Zak
authors.forename: Ronald K
authors.initials: RK
authors.lastname: Pearson
authors.forename: Rajanikanth
authors.initials: R
authors.lastname: Vadigepalli
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Gonye
authors.forename: James S
authors.initials: JS
authors.lastname: Schwaber
authors.forename: Francis J
authors.initials: FJ
authors.lastname: Doyle
mesh_terms: D003627:Data Interpretation, Statistical; D015870:Gene Expression; D006706:Homeostasis; D016014:Linear Models; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D013598:Systems Theory; D013997:Time Factors