Related papers: On NP-Hardness of the Paired de Bruijn Sound Cycle…

A generalized de Bruijn digraph generalizes a de Bruijn digraph to the case where the number of vertices need not be a pure power of an integer. Hamiltonian cycles in these digraphs thus generalize regular de~Bruijn cycles, and we will thus…

Testing if a given graph $G$ contains the $k$-vertex path $P_k$ as a minor or as an induced minor is trivial for every fixed integer $k\geq 1$. However, the situation changes for the problem of checking if a graph can be modified into $P_k$…

We study the following generalization of the Hamiltonian cycle problem: Given integers $a,b$ and graph $G$, does there exist a closed walk in $G$ that visits every vertex at least $a$ times and at most $b$ times? Equivalently, does there…

We introduce the notion of unavoidable (complete) sets of word patterns, which is a refinement for that of words, and study certain numerical characteristics for unavoidable sets of patterns. In some cases we employ the graph of pattern…

For a graph (undirected, directed, or mixed), a cycle-factor is a collection of vertex-disjoint cycles covering the entire vertex set. Cycle-factors subject to parity constraints arise naturally in the study of structural graph theory and…

Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…

The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph…

Motivated by a relaxed notion of the celebrated Hamiltonian cycle, this paper investigates its variant, parity Hamiltonian cycle (PHC): A PHC of a graph is a closed walk which visits every vertex an odd number of times, where we remark that…

Properties of graphs that can be characterized by the spectrum of the adjacency matrix of the graph have been studied systematically recently. Motivated by the complexity of these properties, we show that there are such properties for which…

A de Bruijn cycle is a cyclic listing of length A, of a collection of A combinatorial objects, so that each object appears exactly once as a set of consecutive elements in the cycle. In this paper, we show the power of de Bruijn's original…

We study the Telephone Broadcasting problem in graphs with restricted structure. Given a designated source in an undirected graph, the goal is to disseminate a message to all vertices in the minimum number of rounds, where in each round…

We study homomorphism problems of signed graphs. A signed graph is an undirected graph where each edge is given a sign, positive or negative. An important concept for signed graphs is the operation of switching at a vertex, which is to…

Pangenomes serve as a framework for joint analysis of genomes of related organisms. Several pangenome models were proposed, offering different functionalities, applications provided by available tools, their efficiency etc. Among them, two…

Universal cycles, such as De Bruijn cycles, are cyclic sequences of symbols that represent every combinatorial object from some family exactly once as a consecutive subsequence. Graph universal cycles are a graph analogue of universal…

Motivation: Working with a large number of genomes simultaneously is of great interest in genetic population and comparative genomics research. Bubbles discovery in multi-genomes coloured de bruijn graph for de novo genome assembly is a…

This paper presents a method to find new De Bruijn cycles based on ones of lesser order. This is done by mapping a De Bruijn cycle to several vertex disjoint cycles in a De Bruijn digraph of higher order and connecting these cycles into one…

Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an $O(n \log g)$…

A chord of a cycle $C$ is an edge joining two non-consecutive vertices of $C$. A cycle $C$ in a graph $G$ is chorded if the vertex set of $C$ induces at least one chord. In this paper, we prove that if $G$ is a graph with order $n\geq 6$…

Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig…

A special case of a combinatorial theorem of De Bruijn and Erdos asserts that every noncollinear set of n points in the plane determines at least n distinct lines. Chen and Chvatal suggested a possible generalization of this assertion in…