Related papers: Statistics of genome architecture
The mean length and the variability of coding sequences for 48 genomes of bacteria and archaea were analyzed. It was found that the plotted data can be described by an angular area. This suggests the followings: a) The variability of a…
The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards…
We propose a principle of consistency between different hierarchical levels of biological systems. Given a consistency between molecule replication and cell reproduction, universal statistical laws on cellular chemical abundances are…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
We investigate number count statistics as measures for transition to homogeneity of the matter distribution in the Universe and analyse how such statistics might be `dressed' by the assumed survey selection function. Since the estimated…
Epidemic disease spreading is conventionally often modelled and analyzed by means of rate and diffusion equations, following the paradigms of well-controlled chemical reactions and diffusive dynamics in a test tube. Yet, serious worries…
Computing the embedding distribution of a given graph is a fundamental question in topological graph theory. In this article, we extend our viewpoint to a sequence of graphs and consider their asymptotic embedding distributions, which are…
In this paper we study the component structure of random graphs with independence between the edges. Under mild assumptions, we determine whether there is a giant component, and find its asymptotic size when it exists. We assume that the…
A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a 'Tree of Life.' In this paper we use an…
A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing…
The statistics of meander and related problems are studied as particular realizations of compact polymer chain foldings. This paper presents a general discussion of these topics, with a particular emphasis on three points: (i) the use of a…
Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
A comprehensive investigation of logN-logS distributions of gamma-ray sources discovered by EGRET has been performed for subsequent use in population studies. Existing models explaining the spatial arrangement of unidentified sources do not…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
Pattern-forming nonequilibrium systems are ubiquitous in nature, from driven quantum matter and biological life forms to atmospheric and interstellar gases. Identifying universal aspects of their far-from-equilibrium dynamics and statistics…
Breakpoint graphs are ubiquitous structures in the field of genome rearrangements. Their cycle decomposition has proved useful in computing and bounding many measures of (dis)similarity between genomes, and studying the distribution of…
Degree distributions of graph representations for compact urban patterns are scale-dependent. Therefore, the degree statistics alone does not give us the enough information to reach a qualified conclusion on the structure of urban spatial…
Computational topology has recently known an important development toward data analysis, giving birth to the field of topological data analysis. Topological persistence, or persistent homology, appears as a fundamental tool in this field.…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…