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Replaying the Evolutionary Tape: Biomimetic Reverse Engineering of Gene Networks
Author(s) -
Marbach Daniel,
Mattiussi Claudio,
Floreano Dario
Publication year - 2009
Publication title -
annals of the new york academy of sciences
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.712
H-Index - 248
eISSN - 1749-6632
pISSN - 0077-8923
DOI - 10.1111/j.1749-6632.2008.03944.x
Subject(s) - reverse engineering , computer science , gene regulatory network , sigmoid function , process (computing) , artificial intelligence , nonlinear system , gene , biology , artificial neural network , gene expression , physics , genetics , quantum mechanics , programming language , operating system
In this paper, we suggest a new approach for reverse engineering gene regulatory networks, which consists of using a reconstruction process that is similar to the evolutionary process that created these networks. The aim is to integrate prior knowledge into the reverse‐engineering procedure, thus biasing the search toward biologically plausible solutions. To this end, we propose an evolutionary method that abstracts and mimics the natural evolution of gene regulatory networks. Our method can be used with a wide range of nonlinear dynamical models. This allows us to explore novel model types such as the log‐sigmoid model introduced here. We apply the biomimetic method to a gold‐standard dataset from an in vivo gene network. The obtained results won a reverse engineering competition of the second DREAM conference (Dialogue on Reverse Engineering Assessments and Methods 2007, New York, NY).