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Replaying the Evolutionary Tape: Biomimetic Reverse Engineering of Gene Networks.
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- Author(s): Marbach, Daniel; Mattiussi, Claudio; Floreano, Dario
- Source:
Annals of the New York Academy of Sciences; Mar2009, Vol. 1158, p234-245, 12p, 2 Diagrams, 1 Chart, 3 Graphs- Subject Terms:
- Source:
- Additional Information
- Abstract: 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). [ABSTRACT FROM AUTHOR]
- Abstract: Copyright of Annals of the New York Academy of Sciences is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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