Boolean factor graph modeling and analysis of gene graphs: Budding yeast cell-cycle

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Authors
Kotiang, Stephen
Eslami, Ali
Issue Date
2023-03-24
Type
Conference paper
Language
en_US
Keywords
Boolean networks , Factor graph , Network perturbation , Systems biology
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Abstract

The desire to understand genomic functions and the behavior of complex gene regulatory networks has recently been a major research focus in systems biology. As a result, a plethora of computational and modeling tools have been proposed to identify and infer interactions among biological entities. Here, we consider the general question of the effect of perturbation on the global dynamical network behavior as well as error propagation in biological networks to incite research pertaining to intervention strategies. This paper introduces a computational framework that combines the formulation of Boolean networks (BNs) and factor graphs to explore the global dynamical features of biological systems. A message-passing algorithm is proposed for this formalism to evolve network states as messages in the graph. The model is applied to assess the network state progression and the impact of gene deletion in the budding yeast cell cycle. Simulation results show that our model predictions match published experimental data.

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S. Kotiang and A. Eslami, "Boolean Factor Graph Modeling and Analysis of Gene Graphs: Budding Yeast Cell-Cycle," 2023 57th Annual Conference on Information Sciences and Systems (CISS), Baltimore, MD, USA, 2023, pp. 1-6, doi: 10.1109/CISS56502.2023.10089697.
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IEEE
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