Ye Min, Zhang Xiuwei, Racz Gabriela C, Jiang Qijia, Moret Bernard M E
IEEE Trans Nanobioscience. 2017 Mar;16(2):131-139. doi: 10.1109/TNB.2017.2656058. Epub 2017 Jan 19.
Modeling the evolution of biological networks is a major challenge. Biological networks are usually represented as graphs; evolutionary events not only include addition and removal of vertices and edges but also duplication of vertices and their associated edges. Since duplication is viewed as a primary driver of genomic evolution, recent work has focused on duplication-based models. Missing from these models is any embodiment of modularity, a widely accepted attribute of biological networks. Some models spontaneously generate modular structures, but none is known to maintain and evolve them. We describe network evolution with modularity (NEMo), a new model that embodies modularity. NEMo allows modules to appear and disappear and to fission and to merge, all driven by the underlying edge-level events using a duplication-based process. We also introduce measures to compare biological networks in terms of their modular structure; we present comparisons between NEMo and existing duplication-based models and run our measuring tools on both generated and published networks.
对生物网络的进化进行建模是一项重大挑战。生物网络通常用图来表示；进化事件不仅包括顶点和边的添加与删除，还包括顶点及其相关边的复制。由于复制被视为基因组进化的主要驱动力，最近的研究工作主要集中在基于复制的模型上。这些模型中缺少模块化这一生物网络广泛认可的属性的任何体现。一些模型会自发产生模块化结构，但尚无已知模型能维持并进化这些结构。我们描述了带模块化的网络进化（NEMo），这是一种体现模块化的新模型。NEMo允许模块出现、消失、分裂和合并，所有这些都由基于复制过程的底层边级事件驱动。我们还引入了根据模块化结构比较生物网络的方法；我们展示了NEMo与现有基于复制模型之间的比较，并在生成的网络和已发表的网络上运行我们的测量工具。
