Graph theoretical approach to study molecular evolution

1.从蛋白质相互作用网络预测结构域相互作用。 我们假设蛋白质-蛋白质相互作用是以一种简约的方式进化的。与简约假设一致，我们确定了相互作用域作为解释蛋白质相互作用网络所必需的最小（加权）对集。这种方法已被证明优于以前的方法来预测域-域相互作用（参考文献1）。 2.研究遗传特征标稳定性的图论方法。 以前，我们研究了所谓的字符重叠图的性质。这种图的节点是字符（字符是可以用于推断遗传的任何属性），如果两个字符在某些生物体中一起出现，则它们之间存在边。理解这种图的属性提供了对相应字符的可能演化模式的见解。我们以前的研究主要集中在蛋白质结构域重叠图的研究上。去年，我们将这种方法推广到系统发育性状进化稳定性的一般研究。基于我们的图论结果，我们假设某些内含子是不稳定的，因此不应该用于推断染色体发生（参考文献2）。 3.指导内含子保守性的研究。 利用通过对内含子的图论研究所得到的直觉，我们对内含子的保守性进行了严格的分析。我们通过对内含子保守模式的严格分析，证明了内含子保守模式支持动物的腔肠动物分支。

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).