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Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
We introduce a new way to tabulate knots by representing knot diagrams using a pair of planar trees. This pair of trees have their edges labeled by integers, they have no valence 2 vertices, and they have the same number of valence 1…
A drawing of a graph is 1-planar if each edge participates in at most one crossing and adjacent edges do not cross. Up to symmetry, each crossing in a 1-planar drawing belongs to one out of six possible crossing types, where a type…
Network alignment has extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation…
We describe a linear-time algorithm that finds a planar drawing of every graph of a simple line or pseudoline arrangement within a grid of area O(n^{7/6}). No known input causes our algorithm to use area \Omega(n^{1+\epsilon}) for any…
The $k$-leaf power graph $G$ of a tree $T$ is a graph whose vertices are the leaves of $T$ and whose edges connect pairs of leaves at unweighted distance at most~$k$ in $T$. Recognition of the $k$-leaf power graphs for $k \geq 7$ is still…
We define some Schnyder-type combinatorial structures on a class of planar triangulations of the pentagon which are closely related to 5-connected triangulations. The combinatorial structures have three incarnations defined in terms of…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
We provide an $\Omega(n\log n) $ lower bound and an $O(n^2)$ upper bound for the smallest size of rooted binary trees (a.k.a. phylogenetic tree shapes), which are universal for rooted binary trees with $n$ leaves, i.e., contain all of them…
The construction of a dendogram on a set of individuals is a key component of a genomewide association study. However even with modern sequencing technologies the distances on the individuals required for the construction of such a…
In this paper, we introduce two families of planar and self-similar graphs which have small-world properties. The constructed models are based on an iterative process where each step of a certain formulation of modules results in a final…
While every rooted binary phylogenetic tree is determined by its set of displayed rooted triples, such a result does not hold for an arbitrary rooted binary phylogenetic network. In particular, there exist two non-isomorphic rooted binary…
Let G = (V, E) be a planar triangulated graph (PTG) having every face triangular. A rectilinear dual or an orthogonal floor plan (OFP) of G is obtained by partitioning a rectangle into \mid V \mid rectilinear regions (modules) where two…
Given a digraph $D$, the Minimum Leaf Out-Branching problem (MinLOB) is the problem of finding in $D$ an out-branching with the minimum possible number of leaves, i.e., vertices of out-degree 0. We prove that MinLOB is polynomial-time…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
We discuss the problem of embedding graphs in the plane with restrictions on the vertex mapping. In particular, we introduce a technique for drawing planar graphs with a fixed vertex mapping that bounds the number of times edges bend. An…
Automatic detection and segmentation of overlapping leaves in dense foliage can be a difficult task, particularly for leaves with strong textures and high occlusions. We present Dense-Leaves, an image dataset with ground truth segmentation…
We address the problem of computing a single linkage dendrogram. A possible approach is to: (i) Form an edge weighted graph $G$ over the data, with edge weights reflecting dissimilarities. (ii) Calculate the MST $T$ of $G$. (iii) Break the…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…