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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). They integrate environmental signals, steer development, buffer stochasticity, and allow evolution to ...
Cussat-Blanc, Sylvain +2 more
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Wheat leaf senescence and its regulatory gene network
Crop Journal, 2021 Wheat leaf senescence is a developmental process that involves expressional changes in thousands of genes that ultimately impact grain protein content (GPC), grain yield (GY), and nitrogen use efficiency.
Nigarin Sultana +3 more
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Current approaches to gene regulatory network modelling
BMC Bioinformatics, 2007 Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic
Brazma Alvis, Schlitt Thomas
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A boolean model of the cardiac gene regulatory network determining first and second heart field identity. [PDF]
PLoS ONE, 2012 Two types of distinct cardiac progenitor cell populations can be identified during early heart development: the first heart field (FHF) and second heart field (SHF) lineage that later form the mature heart.
Franziska Herrmann +4 more
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Gene regulatory network reconfiguration in direct lineage reprogramming
Stem Cell Reports, 2023 Summary: In direct lineage conversion, transcription factor (TF) overexpression reconfigures gene regulatory networks (GRNs) to reprogram cell identity.
Kenji Kamimoto +6 more
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Single-cell transcriptomics unveils gene regulatory network plasticity
Genome Biology, 2019 Background Single-cell RNA sequencing (scRNA-seq) plays a pivotal role in our understanding of cellular heterogeneity. Current analytical workflows are driven by categorizing principles that consider cells as individual entities and classify them into ...
Giovanni Iacono +2 more
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Fan-out in gene regulatory networks [PDF]
Journal of Biological Engineering, 2010 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 modules and certain module interface conditions are satisfied, the function of the composite circuits can in ...
Sauro Herbert M, Kim Kyung H
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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. In previous papers, we showed that a well‐known model of genetic regulatory networks, namely, that of random Boolean networks, allows one to study in depth the relationship between the dynamical ...
Villani, Marco +3 more
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PLoS ONE, 2023 Biological condition-responsive gene network analysis has attracted considerable research attention because of its ability to identify pathways or gene modules involved in the underlying mechanisms of diseases.
Heewon Park, Seiya Imoto, Satoru Miyano
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GeRNet: a gene regulatory network tool [PDF]
Biosystems, 2017 Gene regulatory networks (GRNs) are crucial in every process of life since they govern the majority of the molecular processes. Therefore, the task of assembling these networks is highly important. In particular, the so called model-free approaches have an advantage modeling the complexities of dynamic molecular networks, since most of the gene ...
Julieta Sol Dussaut +5 more
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