Related papers: Statistics of genome architecture
Structural properties of evolving random graphs are investigated. Treating linking as a dynamic aggregation process, rate equations for the distribution of node to node distances (paths) and of cycles are formulated and solved analytically.…
Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
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…
Graph embedding provides a feasible methodology to conduct pattern classification for graph-structured data by mapping each data into the vectorial space. Various pioneering works are essentially coding method that concentrates on a…
Periodic patterns play the important regulatory and structural roles in genomic DNA sequences. Commonly, the underlying periodicities should be understood in a broad statistical sense, since the corresponding periodic patterns have been…
Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
Graph-level representations are crucial tools for characterising structural differences between graphs. However, comparing graphs with different cardinalities, even when sampled from the same underlying distribution, remains challenging.…
In order to accommodate the empirical fact that population structures are rarely simple, modern studies of evolutionary dynamics allow for complicated and highly-heterogeneous spatial structures. As a result, one of the most difficult…
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…
A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the…
Many biomolecules have flexible structures, requiring distributional estimates of their conformations. Experiments to acquire distributional data typically measure pairs of labels separately, losing information on the joint distribution.…
In this article, we review the different models and methods to understand and estimate correlated evolution within the same genome, individual or species. We describe correlated evolution among traits, among genetic components and finally…
We study the growth of random networks under a constraint that the diameter, defined as the average shortest path length between all nodes, remains approximately constant. We show that if the graph maintains the form of its degree…
Population structure can be modelled by evolutionary graphs, which can have a substantial, but very subtle influence on the fate of the arising mutants. Individuals are located on the nodes of these graphs, competing with each other to…
The burst approximation is a widely used technique to simplify stochastic gene expression models. However, the dynamics and analytical properties of the protein number distribution in gene expression models under the burst approximation are…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
We briefly recall the main physical features of the parton distributions in the quantum statistical picture of the nucleon. Some predictions from a next-to-leading order QCD analysis are compared to recent experimental results.
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…