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We consider random sub-graphs of a fixed graph $G=(V,E)$ with large minimum degree. We fix a positive integer $k$ and let $G_k$ be the random sub-graph where each $v\in V$ independently chooses $k$ random neighbors, making $kn$ edges in…
In the generalized truncation construction, one replaces each vertex of a $k$-regular graph $\Gamma$ with a copy of a graph $\Upsilon$ of order $k$. We investigate the symmetry properties of the graphs constructed in this way, especially in…
The growth in number and nature of dynamical attractors in Kauffman NK network models are still not well understood properties of these important random boolean networks. Structural circuits in the underpinning graph give insights into the…
We study multiple simultaneous cut events for k-out-of-n:F and linear consecutive k-out-of-n:F systems in which each component has a constant failure probability. We list the multicuts of these systems and describe the structural…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
Chromosomes in the nucleus assemble into hierarchies of 3D domains that, during interphase, share essential features with a knot-free condensed polymer known as the fractal globule (FG). The FG-like chromosome likely affects macromolecular…
Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end…
We consider the algorithmic problem of generating each subset of $[n]:=\{1,2,\ldots,n\}$ whose size is in some interval $[k,l]$, $0\leq k\leq l\leq n$, exactly once (cyclically) by repeatedly adding or removing a single element, or by…
For the random interval partition of $[0,1]$ generated by the uniform stick-breaking scheme known as GEM$(1)$, let $u_k$ be the probability that the first $k$ intervals created by the stick-breaking scheme are also the first $k$ intervals…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
Consider the process of random transpositions on the complete graph. We use representation theory to give an exact, simple formula for the expected number of cycles of size k at time t, in terms of an incomplete Beta function. Using this we…
This article considers the problem of 3-dimensional genome reconstruction for single-cell data, and the uniqueness of such reconstructions in the setting of haploid organisms. We consider multiple graph models as representations of this…
Various specifiable combinatorial structures, with d extensive parameters, can be exactly sampled both by the recursive method, with linear arithmetic complexity if a heavy preprocessing is performed, or by the Boltzmann method, with…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
Several orders of magnitude typically separate the contour length of eukaryotic chromosomes and the size of the nucleus where they are confined. The ensuing topological constraints can slow down the relaxation dynamics of genomic filaments…
In a graph $G$, a subset of vertices $S \subseteq V(G)$ is said to be cyclable if there is a cycle containing the vertices in some order. $G$ is said to be $k$-cyclable if any subset of $k \geq 2$ vertices is cyclable. If any $k$…
The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k-mers, which are short fixed-length strings present in a…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
We consider a model of fragmentation of sheet by cracks that move with a velocity in preferred direction, but undergo random transverse displacements as they move. There is a non-zero probability of crack-splitting, and the split cracks…
Redistricting is the problem of partitioning a set of geographical units into a fixed number of districts, subject to a list of often-vague rules and priorities. In recent years, the use of randomized methods to sample from the vast space…