ArticleJournal of integrative bioinformatics2025
Petri net modeling and simulation of post-transcriptional regulatory networks of human embryonic stem cell (hESC) differentiation to cardiomyocytes.
Article in Journal of integrative bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Stem cells are capable of self-renewal and differentiation into various cell types, showing significant potential for cellular therapies and regenerative medicine, particularly in cardiovascular diseases. The differentiation to cardiomyocytes replicates the embryonic heart development, potentially supporting cardiac regeneration. Cardiomyogenesis is controlled by complex post-transcriptional regulation that affects the construction of gene regulatory networks (GRNs), such as: alternative polyadenylation (APA), length changes in untranslated regulatory regions (3'UTRs), and microRNA (miRNA) regulation. To deepen our understanding of the cardiomyogenesis process, we have modeled a GRN for each day of cardiomyocyte differentiation. Then, each GRN was automatically transformed by four transformation rules to a Petri net and simulated using the software VANESA. The Petri nets highlighted the relationship between genes and alternative isoforms, emphasizing the inhibition of miRNA on APA isoforms with varying 3'UTR lengths. Moreover,
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