Department of Mathematics, North Carolina State University, Raleigh, North Carolina, United States of America.
Mathematical Institute, University of Oxford, Oxford, United Kingdom.
PLoS Comput Biol. 2021 Jun 28;17(6):e1009094. doi: 10.1371/journal.pcbi.1009094. eCollection 2021 Jun.
Angiogenesis is the process by which blood vessels form from pre-existing vessels. It plays a key role in many biological processes, including embryonic development and wound healing, and contributes to many diseases including cancer and rheumatoid arthritis. The structure of the resulting vessel networks determines their ability to deliver nutrients and remove waste products from biological tissues. Here we simulate the Anderson-Chaplain model of angiogenesis at different parameter values and quantify the vessel architectures of the resulting synthetic data. Specifically, we propose a topological data analysis (TDA) pipeline for systematic analysis of the model. TDA is a vibrant and relatively new field of computational mathematics for studying the shape of data. We compute topological and standard descriptors of model simulations generated by different parameter values. We show that TDA of model simulation data stratifies parameter space into regions with similar vessel morphology. The methodologies proposed here are widely applicable to other synthetic and experimental data including wound healing, development, and plant biology.
血管生成是指血管从预先存在的血管中形成的过程。它在许多生物学过程中起着关键作用,包括胚胎发育和伤口愈合,并导致许多疾病,如癌症和类风湿性关节炎。由此产生的血管网络的结构决定了它们从生物组织中输送营养物质和清除废物的能力。在这里,我们在不同的参数值下模拟安德森-查普林(Anderson-Chaplain)的血管生成模型,并量化由此产生的合成数据的血管结构。具体来说,我们为模型提出了一个拓扑数据分析(TDA)管道,用于系统地分析模型。TDA 是计算数学中一个充满活力且相对较新的领域,用于研究数据的形状。我们计算了不同参数值生成的模型模拟的拓扑和标准描述符。我们表明,TDA 可将模型模拟数据的参数空间划分为具有相似血管形态的区域。这里提出的方法广泛适用于其他合成和实验数据,包括伤口愈合、发育和植物生物学。
Bioinformatics. 2022-4-28
Math Biosci. 1996-8
Nat Med. 2003-6
PLoS Comput Biol. 2008-9-19
Phys Rev E. 2017-1-25
Curr Pharm Des. 2009
PLoS Comput Biol. 2013-3-21
PLoS Comput Biol. 2015-8-6
J Math Biol. 2025-8-5
Bull Math Biol. 2024-9-17
PLoS Comput Biol. 2024-2
Sci Adv. 2022-6-10
PLoS Comput Biol. 2021-1
Cancers (Basel). 2020-5-6
Proc Natl Acad Sci U S A. 2020-2-25
EPJ Data Sci. 2017
Cell Mol Life Sci. 2019-11-6