生物相互作用网络鲁棒稳定性的图形刻画
Graphical characterizations of robust stability in biological interaction networks
摘要：
以往的研究都是利用线性规划或迭代算法来推断反应网络的鲁棒稳定性。这样的算法对于大型网络变得冗长或计算上不可行。此外，它们像黑箱一样运作，无法提供维持稳定所需的结构的直觉。在这项工作中，我们提供了几个图形的标准，构造强大的稳定性证书，检查强大的非退化，{验证持久性}，并建立全局稳定性。通过描述一组包含酶修饰基序的保持稳定的图形修饰，我们证明了任意大的非线性网络的稳定性可以通过简单的视觉检查来检查。我们展示了这种技术在系统生物学中无处不在的基序，如翻译后修饰（PTM）循环，核糖体流动模型（RFM），T细胞动力学校对等方面的应用。
英文摘要：
Previous studies have inferred robust stability of reaction networks by utilizing linear programs or iterative algorithms. Such algorithms become tedious or computationally infeasible for large networks. In addition, they operate like black-boxes without offering intuition for the structures that are necessary to maintain stability. In this work, we provide several graphical criteria for constructing robust stability certificates, checking robust non-degeneracy, {verifying persistence}, and establishing global stability. By characterizing a set of stability-preserving graph modifications that includes the enzymatic modification motif, we show that the stability of arbitrarily large nonlinear networks can be examined by simple visual inspection. We show applications of this technique to ubiquitous motifs in systems biology such as Post-Translational Modification (PTM) cycles, the Ribosome Flow Model (RFM), T-cell kinetic proofreading and others.
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