期刊
CHALLENGES OF SYSTEMS BIOLOGY: COMMUNITY EFFORTS TO HARNESS BIOLOGICAL COMPLEXITY
卷 1158, 期 -, 页码 234-245出版社
WILEY-BLACKWELL
DOI: 10.1111/j.1749-6632.2008.03944.x
关键词
gene regulatory networks; reverse engineering; prior knowledge; DREAM challenge
类别
资金
- Swiss National Science Foundation [200221-112060]
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).
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