Computing Hierarchical Transition Graphs of Asynchronous Genetic Regulatory Networks

  • Marco Pedicini
  • Maria Concetta Palumbo
  • Filippo Castiglione
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 830)

Abstract

In the field of theoretical biology the study of the dynamics of the so-called gene regulatory networks is useful to follow the relationship between the expression of a gene and its dynamic regulatory effect on the cell fate. To date, most of the models developed for this purpose, applies the synchronous update schedule while reality is far from being so. On the other hand, the more realistic asynchronous update requires to compute all possible updates at each single instant, thus bearing a much greater computational load.

In the present work, we describe a novel method that addresses the problem of efficiently exploring the dynamics of a gene regulatory network with the asynchronous update.

Keywords

SAT solver Discrete dynamical systems Tarjan’s algorithm Gene regulatory networks Strongly connected components 

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Mathematics and PhysicsRoma Tre UniversityRomeItaly
  2. 2.CNR - Institute for Applied Computing “M. Picone”RomeItaly

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