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Switching Gene Regulatory Networks

  • Yoli Shavit
  • Boyan Yordanov
  • Sara-Jane Dunn
  • Christoph M. Wintersteiger
  • Youssef  Hamadi
  • Hillel Kugler
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9303)

Abstract

A fundamental question in biology is how cells change into specific cell types with unique roles throughout development. This process can be viewed as a program prescribing the system dynamics, governed by a network of genetic interactions. Recent experimental evidence suggests that these networks are not fixed but rather change their topology as cells develop. Currently, there are limited tools for the construction and analysis of such self-modifying biological programs.We introduce Switching Gene Regulatory Networks to enable the modeling and analysis of network reconfiguration, and define the synthesis problem of constructing switching networks from observations of cell behavior. We solve the synthesis problem using Satisfiability Modulo Theories (SMT) based methods, and evaluate the feasibility of our method by considering a set of synthetic benchmarks exhibiting typical biological behavior of cell development.

Keywords

Gene regulatory networks (GRNs) Boolean networks Biological Modeling Satisfiability Modulo Theories (SMT) Synthesis Self-modifying code 

Notes

Acknowledgments.

Yoli Shavit is supported by the Cambridge International Scholarship Scheme (CISS). The research was carried out during her internship at Microsoft Research Cambridge, UK.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Yoli Shavit
    • 1
    • 2
  • Boyan Yordanov
    • 2
  • Sara-Jane Dunn
    • 2
  • Christoph M. Wintersteiger
    • 2
  • Youssef  Hamadi
    • 2
  • Hillel Kugler
    • 2
    • 3
  1. 1.University of CambridgeCambridgeUK
  2. 2.Microsoft ResearchCambridgeUK
  3. 3.Bar-Ilan UniversityRamat GanIsrael

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