Related papers: De Bruijn Graph Homomorphisms and Recursive De Bru…
The discrepancy of a binary string is the maximum (absolute) difference between the number of ones and the number of zeroes over all possible substrings of the given binary string. In this note we determine the minimal discrepancy that a…
The monography considers the problem of constructing a Hamiltonian cycle in a complete graph. A rule for constructing a Hamiltonian cycle based on isometric cycles of a graph is established. An algorithm for constructing a Hamiltonian cycle…
We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph…
We consider Hamilton cycles in the random digraph $D_{n,m}$ where the orientation of edges follows a pattern other than the trivial orientation in which the edges are oriented in the same direction as we traverse the cycle. We show that if…
In 1972 Mykkeltveit proved that the maximum number of vertex-disjoint cycles in the de Bruijn graphs of order $n$ is attained by the pure cycling register rule, as conjectured by Golomb. We generalize this result to the tensor product of…
Finding a Hamiltonian cycle in a given graph is computationally challenging, and in general remains so even when one is further given one Hamiltonian cycle in the graph and asked to find another. In fact, no significantly faster algorithms…
The enumeration of Hamiltonian cycles on 2n*2n grids of nodes is a longstanding problem in combinatorics. Previous work has concentrated on counting all cycles. The current work enumerates nonisomorphic cycles -- that is, the number of…
We first prove a one-to-one correspondence between finding Hamiltonian cycles in a cubic planar graphs and finding trees with specific properties in dual graphs. Using this information, we construct an exact algorithm for finding…
Searching for other participants is one of the most important operations in a distributed system. We are interested in topologies in which it is possible to route a packet in a fixed number of hops until it arrives at its destination. Given…
Hierarchical graph clustering is a common technique to reveal the multi-scale structure of complex networks. We propose a novel metric for assessing the quality of a hierarchical clustering. This metric reflects the ability to reconstruct…
In recent years many algorithms have been developed for finding patterns in graphs and networks. A disadvantage of these algorithms is that they use subgraph isomorphism to determine the support of a graph pattern; subgraph isomorphism is a…
Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…
Classic cycle-joining techniques have found widespread application in creating universal cycles for a diverse range of combinatorial objects, such as shorthand permutations, weak orders, orientable sequences, and various subsets of $k$-ary…
The graph of overlapping permutations is a directed graph that is an analogue to the De Bruijn graph. It consists of vertices that are permutations of length $n$ and edges that are permutations of length $n+1$ in which an edge $a_1\cdots…
A connected digraph in which the in-degree of any vertex equals its out-degree is Eulerian, this baseline result is used as the basis of existence proofs for universal cycles (also known as generalized deBruijn cycles or U-cycles) of…
In this paper we are interested in decomposing a dihypergraph $\mathcal{H} = (V, \mathcal{E})$ into simpler dihypergraphs, that can be handled more efficiently. We study the properties of dihypergraphs that can be hierarchically decomposed…
We establish necessary and sufficient conditions for the existence of a decomposition of a complete multigraph into edge-disjoint cycles of specified lengths, or into edge-disjoint cycles of specified lengths and a perfect matching.
Firstly, for a general graph, we find a recursion formula on the number of Hamiltonian cycles and one on cycles. By this result, we give some new polynomial invariants. Secondly, we give a condition to tell whether a polynomial defined by…
Pseudo-random arrays and perfect maps are the two-dimensional analogs of M-sequences and de Bruijn sequences, respectively. We modify the definitions to be applied to codes. These codes are also the two-dimensional analogs of certain…
The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…