A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a 'Tree of Life'. In this paper we use an approach based on discrete mathematics to address a basic question: could one delineate this hierarchical structure in… (More)
Various topological indices have been put forward in different studies from bio-chemistry to pure mathematics. Among them the Wiener index, the number of subtrees and the Randić index have received great attention from mathematicians. While studying the extremal problems regarding these indices among trees, one interesting phenomenon is that they share the… (More)
We investigate the computational complexity of finding an element of a permutation group H ⊆ S n with a minimal distance to a given π ∈ S n , for different metrics on S n. We assume that H is given by a set of generators, such that the problem cannot be solved in polynomial time by exhaustive enumeration. For the case of the Cayley Distance, this problem… (More)
INTRODUCTION A gene tree for a gene family is often discordant with the containing species tree because of its complex evolutionary course during which gene duplication, gene loss and incomplete lineage sorting events might occur. Hence, it is of great challenge to infer the containing species tree from a set of gene trees. One common approach to this… (More)
Given a metric d on a permutation group G, the corresponding weight problem is to decide whether there exists an element π ∈ G such that d(π, e) = k, for some given value k. Here we show that this problem is NP-complete for many well-known metrics. An analogous problem in matrix groups, eigenvalue-free problem, and two related problems in permutation… (More)
Evolutionary history of protein-protein interaction (PPI) networks provides valuable insight into molecular mechanisms of network growth. In this paper, we study how to infer the evolutionary history of a PPI network from its protein duplication relationship. We show that for a plausible evolutionary history of a PPI network, its relative quality, measured… (More)
Motivation: Millions of genes in the modern species belong to only thousands of gene families. Genes duplicate and are lost during evolution. A gene family includes instances of the same gene in different species and duplicate genes in the same species. Two genes in different species are ortholog if their common ancestor lies in the most recent common… (More)
Given a metric d on a permutation group G, the corresponding weight problem is to decide whether there exists an element g ∈ G such that d(g, e) = k for some k ∈ N. In this paper we show that this problem is NP-complete for many well known metrics.