Switching gene regulatory networks

Yoli Shavit, Boyan Yordanov, Sara Jane Dunn, Christoph M. Wintersteiger, Youssef Hamadi, Hillel Kugler

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

3 Scopus citations

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.

Original languageEnglish
Title of host publicationInformation Processing in Cells and Tissues - 10th International Conference, IPCAT 2015, Proceedings
EditorsStephen Smith, Andy Tyrrell, Michael Lones, Gary Fogel
PublisherSpringer Verlag
Pages131-144
Number of pages14
ISBN (Print)9783319231075
DOIs
StatePublished - 2015
Event10th International Conference on Information Processing in Cells and Tissues, IPCAT 2015 - San Diego, United States
Duration: 14 Sep 201516 Sep 2015

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9303
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference10th International Conference on Information Processing in Cells and Tissues, IPCAT 2015
Country/TerritoryUnited States
CitySan Diego
Period14/09/1516/09/15

Bibliographical note

Publisher Copyright:
© Springer International Publishing Switzerland 2015.

Keywords

  • Biological modeling
  • Boolean networks
  • Gene regulatory networks (GRNs)
  • Satisfiability modulo theories (SMT)
  • Self-modifying code
  • Synthesis

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