Automated reverse engineering of metabolic pathways from observed data using genetic programming

Created by W.Langdon from gp-bibliography.bib Revision:1.8051

@InCollection{koza:2001:FSB,

• author = "John R. Koza and William Mydlowec and Guido Lanza and Jessen Yu and Martin A. Keane",
• title = "Automated reverse engineering of metabolic pathways from observed data using genetic programming",
• booktitle = "Foundations of Systems Biology",
• publisher = "MIT Press",
• year = "2001",
• editor = "Hiroaki Kitano",
• pages = "95--117",
• address = "Cambridge, MA, USA",
• email = "john@johnkoza.com",
• keywords = "genetic algorithms, genetic programming",
• URL = "http://www.genetic-programming.com/jkpdf/kitanochaptericsb2000.pdf",
• size = "23 pages",
• abstract = "Recent work has demonstrated that genetic programming is capable of automatically creating complex networks (e.g., analog electrical circuits, controllers) whose behaviour is modelled by linear and non-linear continuous-time differential equations and whose behaviour matches prespecified output values. The concentrations of substances participating in networks of chemical reactions are modelled by non-linear continuous-time differential equations. This chapter demonstrates that it is possible to automatically create (reverse engineer) a network of chemical reactions from observed time-domain data. Genetic programming starts with observed time-domain concentrations of substances and automatically creates both the topology of the network of chemical reactions and the rates of each reaction of a network such that the behaviour of the automatically created network matches the observed time-domain data. Specifically, genetic programming automatically created a metabolic pathway involving four chemical reactions that consume glycerol and fatty acid as input, use ATP as a cofactor, and produce diacyl-glycerol as the final product. The metabolic pathway was created from 270 data points. The automatically created metabolic pathway contain three key topological features, including an internal feedback loop, a bifurcation point where one substance is distributed to two different reactions, and an accumulation point where one substance is accumulated from two sources. The topology and sizing of the entire metabolic pathway was automatically created using only the time-domain concentration values of diacyl-glycerol (the final product).",

}

Genetic Programming entries for John Koza William J Mydlowec Guido Lanza Jessen Yu Martin A Keane

Citations