Automated reverse engineering of metabolic pathways from observed data using genetic programming
Created by W.Langdon from
gp-bibliography.bib Revision:1.7989
- @InCollection{koza:2001:FSB,
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author = "John R. Koza and William Mydlowec and Guido Lanza and
Jessen Yu and Martin A. Keane",
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title = "Automated reverse engineering of metabolic pathways
from observed data using genetic programming",
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booktitle = "Foundations of Systems Biology",
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publisher = "MIT Press",
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year = "2001",
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editor = "Hiroaki Kitano",
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pages = "95--117",
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address = "Cambridge, MA, USA",
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email = "john@johnkoza.com",
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keywords = "genetic algorithms, genetic programming",
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URL = "http://www.genetic-programming.com/jkpdf/kitanochaptericsb2000.pdf",
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size = "23 pages",
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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