Related papers: Optimal Constructions for DNA Self-Assembly of $k$…
The reassembling of a simple connected graph G = (V,E) is an abstraction of a problem arising in earlier studies of network analysis. Its simplest formulation is in two steps: (1) We cut every edge of G into two halves, thus obtaining a…
Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…
The bidimensionality of a set of vertices $X$ in a graph $G$ is the maximum $k$ for which $G$ contains as a $X$-rooted minor the $(k \times k)$-grid. This notion allows for the following version of the Graph Minors Structure Theorem (GMST)…
Biological processes underlying the basic functions of a cell involve complex interactions between genes. From a technical point of view, these interactions can be represented through a graph where genes and their connections are,…
A graph $G$ is called self-ordered (a.k.a asymmetric) if the identity permutation is its only automorphism. Equivalently, there is a unique isomorphism from $G$ to any graph that is isomorphic to $G$. We say that $G=(V,E)$ is robustly…
Motivated by the question of how macromolecules assemble, the notion of an {\it assembly tree} of a graph is introduced. Given a graph $G$, the paper is concerned with enumerating the number of assembly trees of $G$, a problem that applies…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Designing well-connected graphs is a fundamental problem that frequently arises in various contexts across science and engineering. The weighted number of spanning trees, as a connectivity measure, emerges in numerous problems and plays a…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
Desirable random graph models (RGMs) should (i) reproduce common patterns in real-world graphs (e.g., power-law degrees, small diameters, and high clustering), (ii) generate variable (i.e., not overly similar) graphs, and (iii) remain…
Semi-random processes involve an adaptive decision-maker, whose goal is to achieve some predetermined objective in an online randomized environment. They have algorithmic implications in various areas of computer science, as well as…
A $k$-defective clique of an undirected graph $G$ is a subset of its vertices that induces a nearly complete graph with a maximum of $k$ missing edges. The maximum $k$-defective clique problem, which asks for the largest $k$-defective…
Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…
The notions of $r$-robustness and $(r,s)$-robustness of a network have been earlier introduced in the literature to achieve resilient consensus in the presence of misbehaving agents. However, while higher robustness levels enable networks…
The monography examines the problem of constructing a group of automorphisms of a graph. A graph automorphism is a mapping of a set of vertices onto itself that preserves adjacency. The set of such automorphisms forms a vertex group of a…
We consider additive spanners of unweighted undirected graphs. Let $G$ be a graph and $H$ a subgraph of $G$. The most na\"ive way to construct an additive $k$-spanner of $G$ is the following: As long as $H$ is not an additive $k$-spanner…
There has been significant recent interest in graph-based nearest neighbor search methods, many of which are centered on the construction of navigable graphs over high-dimensional point sets. A graph is navigable if we can successfully move…
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
The optimal design of DNA origami systems that assemble rapidly and robustly is hampered by the lack of a model for self-assembly that is sufficiently detailed yet computationally tractable. Here, we propose a model for DNA origami that…