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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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IV. Ecosmomics: An Independent, UniVersal, Source Code-Script of Generative Complex Network Systems

3. Whole Genome Regulatory Systems: DNA + AND = ANN/DAN

Verd, Berta, et al. Modularity, Criticality, and Evolvability of a Developmental Gene Regulatory Network. eLife. 8/e43832, 2019. In a highly technical, well referenced, 38 page entry, Barcelona Institute of Science and Technology systems biologists BV, Nick Monk, and Johannes Jaeger (search) identify and describe how these title features are prime functions of dynamic genetic nucleotides and networks. In regard, the presence of genome community modules, along with critically poised responses, offers another instantiation of nature’s archetypal complex cosmome to connectome system.

The existence of discrete phenotypic traits suggests that the complex regulatory processes which produce them are functionally modular and are usually represented by networks. Only modular networks can be partitioned into intelligible subcircuits able to evolve independently. Here we partition an experimentally tractable regulatory network—the gap gene system of dipteran insects. We show that this system, although not structurally modular, is composed of dynamical modules driving different aspects of whole-network behaviour. All these subcircuits share the same regulatory structure, but differ in components and sensitivity to regulatory interactions. Some subcircuits are in a state of criticality, which explains the differential evolvability of the various features in the system. (Abstract excerpt)

Waxman, David and Nina Stoletzki. Scaling and Fractal Behaviour Underlying Meitotic Recombination. BioSystems. Online in Press, 2009. University of Sussex, Center for the Study of Evolution, biologists find inherent mathematical regularities that span in a self-similar way the nested networks of genome systems.

Decreasing the length scale of a geometric object is found to be directly analogous, in a genetics problem, to specifying a multilocus haplotype at a larger number of loci, and it is here that the fractal dimension reveals itself. (1) Overall, the results obtained in this work indicate a general property of the transmission of genes in meiotic recombination, and are independent of essentially all details of: recombination, the distribution of parental genotypes in a population, and the distribution of gamete numbers produced. (7)

Yan, Koon-Kiu, et al. MrTADFinder: A Network Modularity based Approach to Identify Topologically Associating Domains in Multiple Resolutions. PLoS Computational Biology. Online July, 2017. Yan, Shaoke Lou and Mark Gerstein, Program in Bioinformatics, Yale University, advance a better method for parsing genetic topology and content. We note as an example of how whole genomes are being also treated by way of common network properties.

The accommodation of the roughly 2m of DNA in the nuclei of mammalian cells results in an intricate structure, in which the topologically associating domains (TADs) formed by densely interacting genomic regions emerge as a fundamental structural unit. Identification of TADs is essential for understanding the role of 3D genome organization in gene regulation. By viewing the chromosomal contact map as a network, TADs correspond to the densely connected regions in the network. Motivated by this mapping, we propose a novel method, MrTADFinder, to identify TADs based on the concept of modularity in network science. Using MrTADFinder, we identify domains at various resolutions, and further explore the interplay between domains and other chromatin features like transcription factors binding and histone modifications at different resolutions. (Summary)

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