Researcher:
Çoban, Hamza

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Master Student

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Hamza

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Çoban

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Çoban, Hamza

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20222

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Researcher Of Publications: search.filters.isAuthorOfPublication.48ea1a00-3871-466b-9a78-a21bbd14c74f

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    Critical dynamics in biological Boolean networks follows from symmetric response to input genes
    (Scientific and Technological Research Council Turkey, 2022) N/A; Department of Physics; Çoban, Hamza; Kabakçıoğlu, Alkan; Master Student; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; N/A; 49854
    a recent observation on an extensive collection of biological gene regulatory networks suggests that the regulatory dynamics is tuned to remain close to the order-chaos boundary in the Lyapunov sense [1]. We here investigate, from a mathematical perspective, the structural/functional constraints which give rise to such accumulation around criticality in these systems. While the role of canalizing functions in this respect is well established, we find that critical sensitivity to small input variations also follows from an over-abundance of symmetrical inputs, i.e. regulatory genes invoking identical or complementary responses on their common target. a random network ensemble constructed to have the same distribution of symmetric inputs as in the above collection of biological networks captures the dependence of the sensitivity on mean activity bias, A nontrivial characteristic which the canalizing ensemble fails to fully reproduce.
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    Proof for minimum sensitivity of nested canalizing functions, a fractal bound, and implications for biology
    (American Physical Society (APS), 2022) Department of Physics; Kabakçıoğlu, Alkan; Çoban, Hamza; Faculty Member; Department of Physics; College of Sciences; 49854; N/A
    We prove that nested canalizing functions are the minimum-sensitivity Boolean functions for any activity ratio and we determine the functional form of this boundary which has a nontrivial fractal structure. We further observe that the majority of the gene regulatory functions found in known biological networks (submitted to the Cell Collective database) lie on the line of minimum sensitivity which paradoxically remains largely in the unstable regime. Our results provide a quantitative basis for the argument that an evolutionary preference for nested canalizing functions in gene regulation (e.g., for higher robustness) and for plasticity of gene activity are sufficient for concentration of such systems near the ""edge of chaos.""