Related papers: Network of tRNA Gene Sequences
The identification of disease-gene associations is instrumental in understanding the mechanisms of diseases and developing novel treatments. Besides identifying genes from RNA-Seq datasets, it is often necessary to identify gene clusters…
Motivation: Modules in gene coexpression networks (GCN) can be regarded as gene groups with individual relationships. No studies have optimized module detection methods to extract diverse gene groups from GCN, especially for data from…
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…
The mining and exploitation of graph structural information have been the focal points in the study of complex networks. Traditional structural measures in Network Science focus on the analysis and modelling of complex networks from the…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this work we investigate these properties within an artificial genome model originally…
Social networks exhibit strikingly systematic patterns across a wide range of human contexts. While genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric…
We study a recently introduced class of scale-free networks showing a high clustering coefficient and non-trivial connectivity correlations. We find that the connectivity probability distribution strongly depends on the fine details of the…
Network data sets are often constructed by some kind of thresholding procedure. The resulting networks frequently possess properties such as heavy-tailed degree distributions, clustering, large connected components and short average…
We consider complex clustered networks with a gradient structure, where sizes of the clusters are distributed unevenly. Such networks describe more closely actual networks in biophysical systems and in technological applications than…
Network topologies can be non-trivial, due to the complex underlying behaviors that form them. While past research has shown that some processes on networks may be characterized by low-order statistics describing nodes and their neighbors,…
Biological networks exhibit intricate architectures deemed to be crucial for their functionality. In particular, gene regulatory networks, which play a key role in information processing in the cell, display non-trivial architectural…
We derive the finite size dependence of the clustering coefficient of scale-free random graphs generated by the configuration model with degree distribution exponent $2<\gamma<3$. Degree heterogeneity increases the presence of triangles in…
Heterogeneous graph neural networks (HGNNs) have attracted increasing research interest in recent three years. Most existing HGNNs fall into two classes. One class is meta-path-based HGNNs which either require domain knowledge to handcraft…
Adaptive networks appear in many biological applications. They combine topological evolution of the network with dynamics in the network nodes. Recently, the dynamics of adaptive networks has been investigated in a number of parallel…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
Bistability plays a central role in the gene regulatory networks (GRNs) controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network topologies that can…
Connectivity networks have recently become widely used in biology due to increasing amounts of information on the physical and functional links between individual proteins. This connectivity data provides valuable material for expanding our…
Genes communicate with each other through different regulatory effects, which lead to the emergence of complex structures in cells, and such structures are expected to be different for normal and cancerous cells. To study breast cancer…
Complex networks as the World Wide Web, the web of human sexual contacts or criminal networks often do not have an engineered architecture but instead are self-organized by the actions of a large number of individuals. From these local…
We introduce a growing network model in which a new node attaches to a randomly-selected node, as well as to all ancestors of the target node. This mechanism produces a sparse, ultra-small network where the average node degree grows…