相关论文: On a chain of fragmentation equations for duplicat…
We study the continuous-time evolution of the recombination equation of population genetics. This evolution is given by a differential equation that acts on a product probability space, and its solution can be described by a Markov chain on…
We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and…
This work is devoted to the study of the scaling, and the consequent power-law behavior, of the correlation function in a mutation-replication model known as the expansion-modification system. The latter is a biology inspired random…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
Many applications in genetic analyses utilize sampling distributions, which describe the probability of observing a sample of DNA sequences randomly drawn from a population. In the one-locus case with special models of mutation such as the…
Heavy-tailed or power-law distributions are becoming increasingly common in biological literature. A wide range of biological data has been fitted to distributions with heavy tails. Many of these studies use simple fitting methods to find…
Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations, hence there is considerable interest…
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of…
We propose a new mechanism for generating power laws. Starting from a random walk, we first outline a simple derivation of the Fokker-Planck equation. By analogy, starting from a certain Markov chain, we derive a master equation for power…
We study the large population limit of the Moran process, assuming weak-selection, and for different scalings. Depending on the particular choice of scalings, we obtain a continuous model that may highlight the genetic-drift (neutral…
Genetic feedback loops in cells break detailed balance and involve bimolecular reactions; hence exact solutions revealing the nature of the stochastic fluctuations in these loops are lacking. We here consider the master equation for a gene…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
In this paper we study the tightness of solutions for a family of recursion equations. These equations arise naturally in the study of random walks on tree-like structures. Examples include the maximal displacement of a branching random…
We analytically and numerically study the probabilistic properties of inverted and mirror repeats in model sequences of nucleic acids. We consider both perfect and non-perfect repeats, i.e. repeats with mismatches and gaps. The considered…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
We analyze the fragmentation behavior of random clusters on the lattice under a process where bonds between neighboring sites are successively broken. Modeling such structures by configurations of a generalized Potts or random-cluster model…