Related papers: Quantifying Local Randomness in Human DNA and RNA …
A sequence $S=s_{1}s_{2}..._{n}$ is \emph{nonrepetitive} if no two adjacent blocks of $S$ are identical. In 1906 Thue proved that there exist arbitrarily long nonrepetitive sequences over 3-element set of symbols. We study a generalization…
In the past decade, the use of ordinal patterns in the analysis of time series and dynamical systems has become an important and rich tool. Ordinal patterns (otherwise known as a permutation patterns) are found in time series by taking $n$…
The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen…
High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…
Reachability questions are one of the most fundamental algorithmic primitives in temporal graphs -- graphs whose edge set changes over discrete time steps. A core problem here is the NP-hard Short Restless Temporal Path: given a temporal…
Single particle tracking allows probing how biomolecules interact physically with their natural environments. A fundamental challenge when analysing recorded single particle trajectories is the inverse problem of inferring the physical…
We study arithmetic properties of short uniform random walks in arbitrary dimensions, with a focus on explicit (hypergeometric) evaluations of the moment functions and probability densities in the case of up to five steps. Somewhat to our…
We consider the Erdos-Renyi random graph G(n,p) inside the critical window, where p = 1/n + lambda * n^{-4/3} for some lambda in R. We proved in a previous paper (arXiv:0903.4730) that considering the connected components of G(n,p) as a…
The well known Erdos-Turan law states that the logarithm of an order of a random permutation is asymptotically normally distributed. The aim of this work is to estimate convergence rate in this theorem and also to prove analogous result for…
The random walk with choice is a well known variation to the random walk that first selects a subset of $d$ neighbours nodes and then decides to move to the node which maximizes the value of a certain metric; this metric captures the number…
Shannon entropy is widely used to measure the complexity of DNA sequences but suffers from saturation effects that limit its discriminative power for long uniform segments. We introduce a novel metric, the entropy rank ratio R, which…
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,…
We study the distribution of the number of (non-backtracking) periodic walks on large regular graphs. We propose a formula for the ratio between the variance of the number of $t$-periodic walks and its mean, when the cardinality of the…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
A famous theorem of Erdos and Szekeres states that any sequence of $n$ distinct real numbers contains a monotone subsequence of length at least $\sqrt{n}$. Here, we prove a positive fraction version of this theorem. For $n > (k-1)^2$, any…
We study the phenomenon of weak ergodicity breaking for a class of globally correlated random walk dynamics defined over a finite set of states. The persistence in a given state or the transition to another one depends on the whole previous…
Consider a sequence of independent random isometries of Euclidean space with a previously fixed probability law. Apply these isometries successively to the origin and consider the sequence of random points that we obtain this way. We prove…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information…
Cellular phones are now offering an ubiquitous means for scientists to observe life: how people act, move and respond to external influences. They can be utilized as measurement devices of individual persons and for groups of people of the…