2016
DOI: 10.1016/j.biosystems.2016.03.012
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Automated Synthesis and Analysis of Switching Gene Regulatory Networks

Abstract: Studying the gene regulatory networks (GRNs) that govern how cells change into specific cell types with unique roles throughout development is an active area of experimental research. The fate specification process can be viewed as a biological program prescribing the system dynamics, governed by a network of genetic interactions. To investigate the possibility that GRNs are not fixed but rather change their topology, for example as cells progress through commitment, we introduce the concept of Switching Gene … Show more

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Cited by 14 publications
(12 citation statements)
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“…We sought to confirm that the network topologies at each timepoint (Fig. 4a) were consistent with experimental observations of gene expression, by employing the automated reasoning approach encapsulated in the tool RE:SIN, as described by Shavit et al (2016). This approach allowed us to determine whether the inferred networks could recapitulate the dynamic changes in gene expression.…”
Section: Resultsmentioning
confidence: 86%
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“…We sought to confirm that the network topologies at each timepoint (Fig. 4a) were consistent with experimental observations of gene expression, by employing the automated reasoning approach encapsulated in the tool RE:SIN, as described by Shavit et al (2016). This approach allowed us to determine whether the inferred networks could recapitulate the dynamic changes in gene expression.…”
Section: Resultsmentioning
confidence: 86%
“…Therefore, we incorporated additional 'possible' interactions, to construct Abstract Boolean Networks (ABNs) for each stage. This formalism enables the investigation of putative interactions, as an ABN implicitly defines a set of concrete Boolean networks each with a unique topology (Yordanov et al, 2016). We included these possible interactions based on the effects of overexpressing DUSP6 and DUSP10, and by examining phosphatase protein levels (Extended Data Fig.…”
Section: Resultsmentioning
confidence: 99%
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“…There has been some work in applying synthesis technique in biology especially in gene regulatory networks [19,20]. A very recent work [20] synthesize executable gene regulatory networks from single-cell gene expression data.…”
Section: Related Workmentioning
confidence: 99%
“…Synthesis technique is also used in optimal synthesis for chemical reaction networks [21]. The [20] uses constraint (satisfiability) solving techniques for the synthesis whereas [19] uses SMT for synthesis. The paper [21] in addition to using SMT over ODE, uses a template-guided approach.…”
Section: Related Workmentioning
confidence: 99%