The notion of graph which is most useful in computer science is that of a directed graph or
just a graph. A graph is a combinatorial structure consisting of a finite nonempty set of …

Motivation: In systematic biology, one is often faced with the task of comparing different
phylogenetic trees, in particular in multi-gene analysis or cospeciation studies. One …

Many methods have been proposed for RNA secondary structure comparison, and new
ones are still being developed. In this chapter, we first consider structure representations …

Many discrete mathematics problems in phylogenetics are defined in terms of the relative
labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as …

We consider the following problem (and variants thereof) that has important applications in
the construction and evaluation of phylogenetic trees: Two rooted unordered binary trees …

Tree identification is the problem of determining whether two trees are isomorphic, and it is a
fundamental problem with a variety of interesting applications in diverse scientific and …

We present two enhancements to Jiang's tree alignment algorithm, motivated by experience
with its use for RNA structure alignment. One enhancement is the introduction of an affine …

In this article we address two pattern matching problems which have important applications
to bioinformatics. First we address the topology-free network query problem: Given a set of …

We present two enhancements to Jiang's tree alignment algorithm, motivated by experience
with its use for RNA structure alignment. One enhancement is the introduction of an affine …

In this thesis we are interested in optimization problems on caterpillar trees. A caterpillar is a
tree with this property that if one removes its leaves only a path is left. The majority of this …