Related papers: A Gibbs approach to Chargaff's second parity rule
Chargaff's second parity rule for short oligonucleotides states that the frequency of any short nucleotide sequence on a strand is approximately equal to the frequency of its reverse complement on the same strand. Recent studies have shown…
Chargaff's second parity rule holds empirically for most types of DNA that along single strands of DNA the base contents are equal for complimentary bases, A = T, G = C. A Markov chain model is constructed to track the evolution of any…
This paper presents the study of a DNA replication model grounded in the biochemical kinetics of DNA polymerases, which copy each DNA strand into a complementary strand, except for rare point-like mutations caused by nucleotide substitution…
This work presents a mathematical model that establishes an interesting connection between nucleotide frequencies in human single-stranded DNA and the famous Fibonacci's numbers. The model relies on two assumptions. First, Chargaff's second…
In this work we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance…
We analyze the convergence rate of a simplified version of a popular Gibbs sampling method used for statistical discovery of gene regulatory binding motifs in DNA sequences. This sampler satisfies a very strong form of ergodicity (uniform).…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
The Gibbs sampler (GS) is a crucial algorithm for approximating complex calculations, and it is justified by Markov chain theory, the alternating projection theorem, and $I$-projection, separately. We explore the equivalence between these…
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
We derive precise asymptotic expressions for the expectations, variances, covariance, and quite a few further mixed moments for the number of hairpins and the number of basepairs in RNA secondary structures, and give convincing evidence…
We study plane trees as a model for RNA secondary structure, assigning energy to each tree based on the Nearest Neighbor Thermodynamic Model, and defining a corresponding Gibbs distribution on the trees. Through a bijection between plane…
We investigate a model where superconducting electrons are coupled to a frequency dependent charge-density wave (CDW) order parameter Delta(w). Our approach can reconcile the simultaneous existence of low energy Bogoljubov quasiparticles…
Genomes in living organisms consist of the nucleotides adenine (A), guanine (G), cytosine (C) and thymine (T). All prokaryotes have genomes consisting of double-stranded DNA, where the A's and G's (purines) of one strand bind respectively…
Motivation: The reconstruction of gene networks from gene expression microarrays is gaining popularity as methods improve and as more data become available. The reliability of such networks could be judged by the probability that a…
Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of anti-viral immune system in these organisms. We here study the diversity of spacers in CRISPR…
We study the evidence for and possible origins of parity doubling among the baryons. First we explore the experimental evidence, finding a significant signal for parity doubling in the non-strange baryons, but little evidence among strange…
Bayesian analysis of data from the general linear mixed model is challenging because any nontrivial prior leads to an intractable posterior density. However, if a conditionally conjugate prior density is adopted, then there is a simple…
The basic facts of charge symmetry breaking (CSB) phenomena are reviewed. The relevance of CSB to parity-violating electron-proton scattering experiments that seek to extract strange elastic form factors is discussed. Experimentalists have…
Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…
Consider two independent random strings having same length and taking values uniformly in a common finite alphabet. We study the order of the variance of the length of the longest common subsequences (LCS) of these strings when long blocks,…