IV. Ecosmomics: Independent Complex Network Systems, Computational Programs, Genetic Ecode Scripts

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

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)

Zhang, Yang, et al. Computational methods for analysing multiscale 3D genome organization.. Nature Reviews Genetics. 25/3, 2024. We note this report by Carnegie Mellon, NIH, and UCLA geneticists including Tom Misteli at the frontier of this amenable intersection of AI neural net methods with complex genomic forms and functions. Altogether it seems that a common nonlinear narrative, an original literacy from cerebral to ecosmic connectomes, is deftly being deciphered and translated.

Recent progress in whole-genome mapping and imaging technologies has illuminated the spatial organization and folding in of the nucleus. In parallel, advanced computations have revealed multiscale (3D) transcription features. Here, we discuss how machine-learning methods and integrative frameworks, have led to a systematic delineation of genomic and epigenomic features, nuclear components and connective function. However, approaches to scan a wide variety of genomic and imaging datasets are still needed to define cellular phenotypes in health and disease. (Excerpt)

Zhao, Xiangyi, et al. Irreversibility in Bacterial Regulatory Networks. arXiv:2409.04513. In a paper to appear in Science Advances, Northwestern University and University of Texas Southwestern Medical Center researchers including Adilson Motter take advantage of a widest compass to achieve an exemplary affinity for microbial and genetic phases with deep physical phenomena. In regard, here is another 2024 instance which roots living personal systems a whole scale encoded universality.

Irreversibility, in which a transient perturbation leaves a system in a new state, is an emergent property in systems of interacting entities. This feature has well-established implications in statistical physics but remains underexplored in biological phases. Focusing on the regulatory network of Escherichia coli, we examine responses to transient single-gene perturbations and find that irreversibility increases with the proximity of the perturbed gene to positive circuits. (Excerpt)

A common goal in both statistical physics and systems biology is to connect the attributes of microscopic entities with observable macroscopic properties. Of particular interest are macroscopic properties that are emergent—including pattern formation and synchronization because they arise from interactions between system entities and can therefore enable new system-level functionality. In statistical physics, an important property is the irreversibility of macroscopic processes, where entropy—a state function—can increase despite the time-reversibility of the microscopic dynamics. (1)

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