Related papers: Information-theoretic View of Sequence Organizatio…
Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct…
With the number of fully-sequenced genomes now well over a hundred it has become possible to start investigating if there are any quantitative regularities in the genetic make-up of genomes. In (physics/0307001), I originally showed that…
The use of statistical methods for the description of complex quantum systems was primarily motivated by the failure of a line-by-line interpretation of atomic spectra. Such methods reveal regularities and trends in the distributions of…
We show, that the specific distribution of gene's length, which is observed in natural genomes, might be a result of a growth process, in which a single length scale $L(t)$ develops that grows with time as $t^{1/3}$. This length scale could…
Using a population dynamics inspired by an ensemble of growing cells, a set of fluctuation theorems linking observables measured at the lineage and population levels are derived. One of these relations implies specific inequalities…
Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing, expression profiles, proteomics, and electronic health records are…
Statistical analysis of distributions of occurrence frequencies of short words in 108 microbial complete genomes reveals the existence of a set of universal "root-sequence lengths" shared by all microbial genomes. These lengths and their…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
The dynamics of adaptation is difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from number fluctuations, called genetic drift, arising in the small number of particularly fit…
Nucleosome organization in eukaryotic genomes has a deep impact on gene function. Although progress has been recently made in the identification of various concurring factors influencing nucleosome positioning, it is still unclear whether…
The problem of the order of the fluctuation of the Longest Common Subsequence (LCS) of two independent sequences has been open for decades. There exist contradicting conjectures on the topic, due to Chvatal - Sankoff in 1975 and Waterman in…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. While the biochemical details of this code were unraveled long ago, its origin is still obscure. We review information-theoretic approaches to the…
In this article we consider the cycle structure of compositions of pairs of involutions in the symmetric group S_n chosen uniformly at random. These can be modeled as modified 2-regular graphs, giving rise to exponential generating…
With the number of sequenced genomes now over one hundred, and the availability of rough functional annotations for a substantial proportion of their genes, it has become possible to study the statistics of gene content across genomes. Here…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
The problem of the fluctuation of the Longest Common Subsequence (LCS) of two i.i.d. sequences of length $n>0$ has been open for decades. There exist contradicting conjectures on the topic. Chvatal and Sankoff conjectured in 1975 that…
In a quantum system coupled with a non-Markovian environment, quantum information may flow out of or in to the system. Measuring quantum information flow and its sensitivity to perturbations is important for a better understanding of open…
We investigate a model protein interaction network whose links represent interactions between individual proteins. This network evolves by the functional duplication of proteins, supplemented by random link addition to account for…
The concept of k-spectrum for genomes is here investigated as a basic tool to analyze genomes. Related spectral notions based on k-mers are introduced with some related mathematical properties which are relevant for informational analysis…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…