Related papers: Modules of human micro-RNA co-target network
Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes…
Molecular signaling networks are believed to determine cancer robustness. Although cancer patient survivability was reported to correlate with the heterogeneous connectivity of the signaling networks inspired by theoretical studies on the…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
The inclusion of link weights into the analysis of network properties allows a deeper insight into the (often overlapping) modular structure of real-world webs. We introduce a clustering algorithm (CPMw, Clique Percolation Method with…
Network motifs are small building blocks of complex networks. Statistically significant motifs often perform network-specific functions. However, the precise nature of the connection between motifs and the global structure and function of…
MicroRNAs play important roles in many biological processes. Their aberrant expression can have oncogenic or tumor suppressor function directly participating to carcinogenesis, malignant transformation, invasiveness and metastasis. Indeed,…
Many complex systems present an intrinsic bipartite nature and are often described and modeled in terms of networks [1-5]. Examples include movies and actors [1, 2, 4], authors and scientific papers [6-9], email accounts and emails [10],…
Background: If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological…
"Module networks" are a framework to learn gene regulatory networks from expression data using a probabilistic model in which coregulated genes share the same parameters and conditional distributions. We present a method to infer ensembles…
The connectome, or the entire connectivity of a neural system represented by network, ranges various scales from synaptic connections between individual neurons to fibre tract connections between brain regions. Although the modularity they…
The human brain is a complex network of interconnected brain regions organized into functional modules with distinct roles in cognition and behavior. An important question concerns the persistence and stability of these modules over the…
Myriad viruses use positive-strand RNA molecules as their genomes. Far from being only a repository of genetic material, viral RNA performs numerous other functions mediated by its physical structure and chemical properties. In this…
Background: MicroRNAs, post-transcriptional repressors of gene expression, play a pivotal role in gene regulatory networks. They are involved in core cellular processes and their dysregulation is associated to a broad range of human…
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…
Given a graph of interactions, a module (also called a community or cluster) is a subset of nodes whose fitness is a function of the statistical significance of the pairwise interactions of nodes in the module. The topic of this paper is a…
We introduce a network growth model based on complete redirection: a new node randomly selects an existing target node, but attaches to a random neighbor of this target. For undirected networks, this simple growth rule generates unusual,…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
Network motifs can capture basic interaction patterns and inform the functional properties of networks. However, real-world complex systems often have multiple types of relationships, which cannot be represented by a monolayer network. The…
In this paper, a new multi-hop weighted clustering procedure is proposed for homogeneous Mobile Ad hoc networks. The algorithm generates double star embedded non-overlapping cluster structures, where each cluster is managed by a leader node…
The information regarding the structure of a single protein is encoded in the network of interacting amino acids. Considering each protein as a weighted and unweighted network of amino acids we have analyzed a total of forty nine protein…