A list-decoding approach for inferring the dynamics of gene regulatory networks

Janis Dingel, Olgica Milenkovic

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We propose a novel algebraic method for reverse engineering the dynamics of gene regulatory networks of known topology, based on list-decoding and iterative model refinement algorithms. The crux of our approach is to describe the update functions for gene expressions in terms of polynomials over finite fields, or more precisely, codewords of Reed-Muller (RM) codes. In this setting, errors, missing data points, and small sample sizes of the measurements are accounted for via list-decoding of RM codes. We test the performance of the new method both on synthetic data and a regulatory sub-net of the E. coli gene control network responsible for DNA repair. The expression profiles used in the study are obtained through data fusion techniques over the Many Microbe Microarray Database. The list-decoding approach offers significant performance improvements over previously known algebraic methods, such as those based on Grobner bases techniques.

Original languageEnglish (US)
Title of host publicationProceedings - 2008 IEEE International Symposium on Information Theory, ISIT 2008
Pages2282-2286
Number of pages5
DOIs
StatePublished - Sep 29 2008
Event2008 IEEE International Symposium on Information Theory, ISIT 2008 - Toronto, ON, Canada
Duration: Jul 6 2008Jul 11 2008

Publication series

NameIEEE International Symposium on Information Theory - Proceedings
ISSN (Print)2157-8101

Other

Other2008 IEEE International Symposium on Information Theory, ISIT 2008
CountryCanada
CityToronto, ON
Period7/6/087/11/08

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Information Systems
  • Modeling and Simulation
  • Applied Mathematics

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