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  4. Bio-mimetic Evolutionary Reverse Engineering of Genetic Regulatory Networks
 
conference paper

Bio-mimetic Evolutionary Reverse Engineering of Genetic Regulatory Networks

Marbach, Daniel
•
Mattiussi, Claudio  
•
Floreano, Dario  
Marchiori, E.
•
Moore, J.H.
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2007
Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Proceedings
5th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO 2007)

The effective reverse engineering of biochemical networks is one of the great challenges of systems biology. The contribution of this paper is two-fold: 1) We introduce a new method for reverse engineering genetic regulatory networks from gene expression data; 2) We demonstrate how nonlinear gene networks can be inferred from steady-state data alone. The reverse engineering method is based on an evolutionary algorithm that employs a novel representation called Analog Genetic Encoding (AGE), which is inspired from the natural encoding of genetic regulatory networks. AGE can be used with biologically plausible, nonlinear gene models where analytical approaches or local gradient based optimisation methods often fail. Recently there has been increasing interest in reverse engineering linear gene networks from steady-state data. Here we demonstrate how more accurate nonlinear dynamical models can also be inferred from steady-state data alone.

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Type
conference paper
DOI
10.1007/978-3-540-71783-6_15
Web of Science ID

WOS:000246102100015

Author(s)
Marbach, Daniel
Mattiussi, Claudio  
Floreano, Dario  
Editors
Marchiori, E.
•
Moore, J.H.
•
Rajapakse, J. C.
Date Issued

2007

Publisher

Springer-Verlag Berlin

Published in
Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Proceedings
Series title/Series vol.

Lecture Notes in Computer Science; 4447

Start page

155

End page

165

Subjects

Systems Biology

•

Gene Networks

•

Reverse Engineering

•

Steady-State Data

•

Genetic Algorithm

•

Analog Genetic Encoding

•

AGE

•

Implicit Encoding

•

Implicit Genetic Encoding

•

Evolutionary Robotics

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LIS  
Event nameEvent placeEvent date
5th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO 2007)

València

11.4.-13.4.07

Available on Infoscience
November 14, 2006
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/235758
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