Graph theoretical approach to study molecular evolution

1.从蛋白质-蛋白质相互作用网络预测结构域间相互作用。 我们假设蛋白质之间的相互作用是以一种节俭的方式进化的。与简约假设一致，我们将相互作用区域确定为解释蛋白质相互作用网络所必需的最小(加权)对集合。这种方法已被证明优于以前预测域-域相互作用的方法(参考文献1)。 2.系统学性状稳定性研究的图论方法。 以前，我们研究了所谓的字符重叠图的性质。这种图形的节点是字符(其中字符是可以用于推断系统发育的任何属性)，如果两个字符一起出现在某些有机体中，则在两个字符之间有一条边。对这种图的属性的理解提供了对相应字符的可能演化模式的洞察。我们以前的研究主要集中在研究蛋白质结构域的重叠图。在过去的一年里，我们将这种方法扩展到对系统发育特征进化稳定性的一般研究。根据我们的图论结果，我们假设某些内含子是不稳定的，因此不应该用于推断系统发育(参考文献2)。 3.内含子保守性的定向研究。 利用图论研究内含子发展出的直觉，我们对内含子守恒进行了严格的分析。我们从对内含子保守模式的严格分析中证明了内含子保守的模式支持体腔动物分支(参考文献3)。

1. Predicting domain-domain interactions from protein-protein interaction network. We have postulated that protein-protein interactions evolved in a parsimonious way. Consistently with the parsimony postulate, we identified the interacting domain as the smallest (weighted) set of pairs that is necessary to explain the protein interaction network. This method has proven to outperform previous approaches to prediction of domain-domain interactions (ref 1). 2. Graph theoretical approaches to study stability of phylogentic characters. Previously, we studied the properties of the so called character overlap graph. The nodes of such graph are characters (where a character is any attribute that can by used in inferring phylogeny) and there is an edge between two characters if they occur together in some organism. Understanding of properties of such graph provides insights into possible modes of evolution of the corresponding characters. Our previous studies focused on studding the overlap graph of protein domains. In the last year we extended this approach to general study of evolutional stability of phylogenetic characters. Based on our graph-theoretical results, we postulated that some introns are unstable and therefore should not be used in inferring phylogeny (ref 2). 3. Directed studies of intron conservation. Using intuitions developed trough graph-theoretical studies of introns, we conducted a rigorous analysis of intron conservation. We demonstrated that the pattern of intron conservation support the Coelomata Clade of Animals From a Rigorous Analysis of the Pattern of Intron Conservation (ref 3).