Related papers: Statistics of genome architecture
Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…
This work gives a mathematical foundation for bifurcation from a stable equilibrium in the genome. We construct idealized dynamics associated with the genome. For this dynamics we investigate the two main bifurcations from a stable…
Random graph models are used to describe the complex structure of real-world networks in diverse fields of knowledge. Studying their behavior and fitting properties are still critical challenges, that in general, require model specific…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
A new method for analyzing the morphological features of point patterns is presented. The method is taken from the study of molecular liquids, where it has been introduced for making a statistical description of anisotropic distributions.…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
Exploration of structure-property relationships as a function of dopant concentration is commonly based on mean field theories for solid solutions. However, such theories that work well for semiconductors tend to fail in materials with…
In several recent papers new gene-detection algorithms were proposed for detecting protein-coding regions without requiring learning dataset of already known genes. The fact that unsupervised gene-detection is possible closely connected to…
Stochastic models play an essential role in accounting for the variability and unpredictability seen in real-world. This paper focuses on the application of the gamma distribution to analysis of the stationary distributions of populations…
We study the efficiency of genus statistics in differentiating between different models of structure formation. Simple models which reproduce the salient features of the structure seeded by topological defects are examined. We consider…
Networks of genetic expression can be modelled by hypergraphs with the additional structure that real coefficients are given to each vertex-edge incidence. The spectra, i.e. the multiset of the eigenvalues, of such hypergraphs, are known to…
In systems biology, it is becoming increasingly common to measure biochemical entities at different levels of the same biological system. Hence, data fusion problems are abundant in the life sciences. With the availability of a multitude of…
In this paper, we consider the problem of exploring structural regularities of networks by dividing the nodes of a network into groups such that the members of each group have similar patterns of connections to other groups. Specifically,…
Biological processes underlying the basic functions of a cell involve complex interactions between genes. From a technical point of view, these interactions can be represented through a graph where genes and their connections are,…
The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study and of two algorithms for determining the presence of a particular (known) genome in this medium.…
Subgraphs and cycles are often used to characterize the local properties of complex networks. Here we show that the subgraph structure of real networks is highly time dependent: as the network grows, the density of some subgraphs remains…
By analyzing the spacing of genes on chromosomes, we find that transcriptional and RNA-processing regulatory sequences outside coding regions leave footprints on the distribution of intergenic distances. Using analogies between genes on…
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…
Recent theoretical and empirical studies have focused on the structural properties of complex relational networks in social, biological and technological systems. Here we study the basic properties of twenty 1-square-mile samples of street…
The state of chromatin in individual cells is directly related to the state of the whole organism and may be used for assessment of the state of the whole organism. Many hereditary diseases are connected with chromatin rearrangements.…