Related papers: Network of tRNA Gene Sequences
Phylogenetic networks are rooted acyclic directed graphs in which the leaves are identified with members of a set X of species. The cluster of a vertex is the set of leaves that are descendants of the vertex. A network is "distinct-cluster"…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…
The linear preferential attachment hypothesis has been shown to be quite successful to explain the existence of networks with power-law degree distributions. It is then quite important to determine if this mechanism is the consequence of a…
Many of the structural characteristics of a network depend on the connectivity with and within the hubs. These dependencies can be related to the degree of a node and the number of links that a node shares with nodes of higher degree. In…
Real-world networks often exhibit strong transitivity with nontrivial local clustering spectra and degree correlations. Such features are not easily modeled in tractable network models, creating an obstacle to the theoretical understanding…
The degree distribution is an important characteristic of complex networks. In many data analysis applications, the networks should be represented as fixed-length feature vectors and therefore the feature extraction from the degree…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…
Many complex networks demonstrate a phenomenon of striking degree correlations, i.e., a node tends to link to other nodes with similar (or dissimilar) degrees. From the perspective of degree correlations, this paper attempts to characterize…
Higher-order connectivity patterns such as small induced sub-graphs called graphlets (network motifs) are vital to understand the important components (modules/functional units) governing the configuration and behavior of complex networks.…
Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple operations on a set of sequences called orthology relations may be employed. In addition to being…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
We use a generalised version of the individual-based Tangled Nature model of evolutionary ecology to study the relationship between ecosystem structure and evolutionary history. Our evolved model ecosystems typically exhibit interaction…
This paper describes characteristic features of networks reconstructed from gene expression time series data. Several null models are considered in order to discriminate between informations embedded in the network that are related to real…
We propose the n-clique network as a powerful tool for understanding global structures of combined highly-interconnected subgraphs, and provide theoretical predictions for statistical properties of the n-clique networks embedded in a…
RNA velocity is an important model that combines cellular spliced and unspliced RNA counts to infer dynamical properties of various regulatory functions. Despite its wide applicability and many variants used in practice, the model has not…
Gene regulatory network (GRN) refers to the complex network formed by regulatory interactions between genes in living cells. In this paper, we consider inferring GRNs in single cells based on single cell RNA sequencing (scRNA-seq) data. In…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
Networks are a fundamental tool for understanding and modeling complex systems in physics, biology, neuroscience, engineering, and social science. Many networks are known to exhibit rich, lower-order connectivity patterns that can be…
The deep Convolutional Neural Network (CNN) is the state-of-the-art solution for large-scale visual recognition. Following basic principles such as increasing the depth and constructing highway connections, researchers have manually…