Related papers: Minimum de Bruijn Sequence in a Language with Forb…
A forbidden transition graph is a graph defined together with a set of permitted transitions i.e. unordered pair of adjacent edges that one may use consecutively in a walk in the graph. In this paper, we look for the smallest set of…
What is the length of the shortest sequence $S$ of reals so that the set of consecutive $n$-words in $S$ form a covering code for permutations on $\{1,2, >..., n\}$ of radius $R$ ? (The distance between two $n$-words is the number of…
De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well…
Motivated by generalizations of de Bruijn cycles to various combinatorial structures (Chung, Diaconis, and Graham), we study various Euler tours in set systems. Let $\mathcal{G}$ be a hypergraph whose corank and rank are $c\geq 3$ and $k$,…
A signed circuit is a minimal signed graph (with respect to inclusion) that admits a nowhere-zero flow. We show that each flow-admissible signed graph on $m$ edges can be covered by signed circuits of total length at most $(3+2/3)\cdot m$,…
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…
This paper introduces the de Bruijn graph edge minimization problem, which is related to the compression of de Bruijn graphs: find the order-k de Bruijn graph with minimum edge count among all orders. We describe an efficient algorithm that…
This paper initiates the study of shortening universal cycles (u-cycles) and universal words (u-words) for permutations either by using incomparable elements, or by using non-deterministic symbols. The latter approach is similar in nature…
Grammar inference deals with determining (preferable simple) models/grammars consistent with a set of observations. There is a large body of research on grammar inference within the theory of formal languages. However, there is surprisingly…
Free-space quantum key distribution requires to synchronize the transmitted and received signals. A timing and synchronization system for this purpose based on a de Bruijn sequence has been proposed and studied recently for a channel…
Lekkerkerker and Boland characterized the minimal forbidden induced subgraphs for the class of interval graphs. We give a linear-time algorithm to find one in any graph that is not an interval graph. Tucker characterized the minimal…
The minimum semi-degree of a digraph D is the minimum of its minimum outdegree and its minimum indegree. We show that every sufficiently large digraph D with minimum semi-degree at least n/2 +k-1 is k-linked. The bound on the minimum…
A minimum feedback arc set of a directed graph $G$ is a smallest set of arcs whose removal makes $G$ acyclic. Its cardinality is denoted by $\beta(G)$. We show that an Eulerian digraph with $n$ vertices and $m$ arcs has $\beta(G) \ge…
A labelled, undirected graph is a graph whose edges have assigned labels, from a specific set. Given a labelled, undirected graph, the well-known minimum labelling spanning tree problem is aimed at finding the spanning tree of the graph…
An $(m,n,R)$-de Bruijn covering array (dBCA) is a doubly periodic $M \times N$ array over an alphabet of size $q$ such that the set of all its $m \times n$ windows form a covering code with radius $R$. An upper bound of the smallest array…
A well known theorem in graph theory states that every graph $G$ on $n$ vertices and minimum degree at least $d$ contains a path of length at least $d$, and if $G$ is connected and $n\ge 2d+1$ then $G$ contains a path of length at least…
For any context-free grammar, we build a transition diagram, that is, a finite directed graph with labeled arcs, which describes the work of the grammar. This approach is new, and it is different from previously known graph models. We…
DNA labeling is a tool in molecular biology and biotechnology to visualize, detect, and study DNA at the molecular level. In this process, a DNA molecule is labeled by a set of specific patterns, referred to as labels, and is then imaged.…
Substantial efforts have been made to compute or estimate the minimum number $c(G)$ of cycles needed to partition the edges of an Eulerian graph. We give an equivalent characterization of Eulerian graphs of treewidth $2$ and with maximum…
Upper bounds on the maximum number of minimal codewords in a binary code follow from the theory of matroids. Random coding provide lower bounds. In this paper we compare these bounds with analogous bounds for the cycle code of graphs. This…