Department of Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA.
Department of Computer Science, University of Bonn, Bonn 53113, Germany.
Biology (Basel). 2013 Dec 19;3(1):1-21. doi: 10.3390/biology3010001.
In this survey paper, we will present a number of core algorithmic questions concerning several transitive reduction problems on network that have applications in network synthesis and analysis involving cellular processes. Our starting point will be the so-called minimum equivalent digraph problem, a classic computational problem in combinatorial algorithms. We will subsequently consider a few non-trivial extensions or generalizations of this problem motivated by applications in systems biology. We will then discuss the applications of these algorithmic methodologies in the context of three major biological research questions: synthesizing and simplifying signal transduction networks, analyzing disease networks, and measuring redundancy of biological networks.
在这篇调查论文中，我们将提出一些关于网络中几个传递约简问题的核心算法问题，这些问题在涉及细胞过程的网络综合和分析中有应用。我们的出发点将是所谓的最小等价有向图问题，这是组合算法中的一个经典计算问题。随后，我们将考虑由系统生物学中的应用所激发的这个问题的几个非平凡扩展或推广。然后，我们将讨论这些算法方法在三个主要的生物学研究问题中的应用：信号转导网络的综合和简化、疾病网络的分析以及生物网络的冗余性测量。
