Computational Systems Biology of Morphogenesis.
Computational Systems Biology of Morphogenesis.
复制标题
形态发生的计算系统生物学。
DOI：
10.1007/978-1-0716-1831-8_14
复制
发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Lobo,Daniel
中科院分区：
文献类型：
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作者：
Ko,JasonM;Mousavi,Reza;Lobo,Daniel
由于生物调控及其反馈回路的复杂性，从形态发生的空间和时间表型中提取机制知识是当前的挑战。此外，这些调节相互作用还与塑造发育组织的生物物理力量有关，从而产生负责紧急模式和形式的复杂相互作用。在这里，我们展示了如何计算系统生物学方法可以帮助从机械的角度理解形态发生。这种方法将组织和全胚胎的建模与动力系统、参数的逆向工程甚至整个方程与机器学习相结合，并生成可以在实验台上测试的精确计算预测。为了实现和执行的方法中的计算步骤，我们提出了用户友好的工具，计算机代码和准则。这种方法的原则是通用的，可以适用于其他模式生物，以提取其形态发生的机械知识。
Extracting mechanistic knowledge from the spatial and temporal phenotypes of morphogenesis is a current challenge due to the complexity of biological regulation and their feedback loops. Furthermore, these regulatory interactions are also linked to the biophysical forces that shape a developing tissue, creating complex interactions responsible for emergent patterns and forms. Here we show how a computational systems biology approach can aid in the understanding of morphogenesis from a mechanistic perspective. This methodology integrates the modeling of tissues and whole-embryos with dynamical systems, the reverse engineering of parameters or even whole equations with machine learning, and the generation of precise computational predictions that can be tested at the bench. To implement and perform the computational steps in the methodology, we present user-friendly tools, computer code, and guidelines. The principles of this methodology are general and can be adapted to other model organisms to extract mechanistic knowledge of their morphogenesis.