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Artificial Gene Regulatory Networks—A Review [PDF]
Artificial Life, 2019 In nature, gene regulatory networks are a key mediator between the information stored in the DNA of living organisms (their genotype) and the structural and behavioral expression this finds in their bodies, surviving in the world (their phenotype).
Sylvain Cussat-Blanc +2 more
semanticscholar +7 more sources
Evolution of evolvability in gene regulatory networks. [PDF]
PLoS Computational Biology, 2008 Gene regulatory networks are perhaps the most important organizational level in the cell where signals from the cell state and the outside environment are integrated in terms of activation and inhibition of genes.
Anton Crombach, Paulien Hogeweg
doaj +6 more sources
Quantum gene regulatory networks
npj Quantum Information, 2023 In this work, we present a quantum circuit model for inferring gene regulatory networks (GRNs) from single-cell transcriptomic data. The model employs qubit entanglement to simulate interactions between genes, resulting in competitive performance and ...
Cristhian Roman-Vicharra, James J. Cai
doaj +3 more sources
Fan-out in gene regulatory networks [PDF]
Journal of Biological Engineering, 2010 Background In synthetic biology, gene regulatory circuits are often constructed by combining smaller circuit components. Connections between components are achieved by transcription factors acting on promoters. If the individual components behave as true
Sauro Herbert M, Kim Kyung H
doaj +4 more sources
Dynamical Criticality in Gene Regulatory Networks [PDF]
Complexity, 2018 A well-known hypothesis, with far-reaching implications, is that biological evolution should preferentially lead to states that are dynamically critical.
Marco Villani +3 more
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Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues
Cell Reports, 2020 Sex differences manifest in many diseases and may drive sex-specific therapeutic responses. To understand the molecular basis of sex differences, we evaluated sex-biased gene regulation by constructing sample-specific gene regulatory networks in 29 human
Camila M Lopes-Ramos +2 more
exaly +2 more sources
Constructing gene regulatory networks using epigenetic data
npj Systems Biology and Applications, 2021 The biological processes that drive cellular function can be represented by a complex network of interactions between regulators (transcription factors) and their targets (genes).
Abhijeet Rajendra Sonawane +3 more
doaj +2 more sources
Chaotic motifs in gene regulatory networks. [PDF]
PLoS ONE, 2012 Chaos should occur often in gene regulatory networks (GRNs) which have been widely described by nonlinear coupled ordinary differential equations, if their dimensions are no less than 3. It is therefore puzzling that chaos has never been reported in GRNs
Zhaoyang Zhang +5 more
doaj +4 more sources
Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data
Nature BiotechnologyExisting methods for gene regulatory network (GRN) inference rely on gene expression data alone or on lower resolution bulk data. Despite the recent integration of chromatin accessibility and RNA sequencing data, learning complex mechanisms from limited ...
Qiuyue Yuan, Zhana Duren, Duren Zhana
exaly +2 more sources
Computational and Structural Biotechnology Journal, 2020 Discovering gene regulatory relationships and reconstructing gene regulatory networks (GRN) based on gene expression data is a classical, long-standing computational challenge in bioinformatics.
Juexin Wang, Anjun Ma, Qin Ma
exaly +2 more sources