Related papers: Modules of human micro-RNA co-target network
This paper introduces the notion of co-modularity, to co-cluster observations of bipartite networks into co-communities. The task of co-clustering is to group together nodes of one type with nodes of another type, according to the…
Complex systems are successfully reduced to interacting elements via the network concept. Transport plays a key role in the survival of networks. For example the specialized signaling cascades of cellular networks filter noise and…
Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network currently being complete. In this study, we analyzed…
Generative mechanisms which lead to empirically observed structure of networked systems from diverse fields like biology, technology and social sciences form a very important part of study of complex networks. The structure of many…
Cellular function is widely believed to be organized in a modular fashion. On all scales and at all levels of complexity, relatively independent sub-units perform relatively independent sub-tasks of biological function. This functional…
MicroRNAs (miRNAs) are non-coding RNAs with approximately 22 nucleotides (nt) that are derived from precursor molecules. These precursor molecules or pre-miRNAs often fold into stem-loop hairpin structures. However, a large number of…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
Non-conding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs through protein-mediated, sequence-specific binding, giving rise…
In the face of the stupefying complexity of the human brain, network analysis is a most useful tool that allows one to greatly simplify the problem, typically by approximating the billions of neurons comprising the brain by means of a…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
To comprehend the multipartite organization of large-scale biological and social systems, we introduce a new information theoretic approach that reveals community structure in weighted and directed networks. The method decomposes a network…
In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops…
Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated…
Biomedical sciences are increasingly recognising the relevance of gene co-expression-networks for analysing complex-systems, phenotypes or diseases. When the goal is investigating complex-phenotypes under varying conditions, it comes…
A typical complex system should be described by a supernetwork or a network of networks, in which the networks are coupled to some other networks. As the first step to understanding the complex systems on such more systematic level,…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
The Internet is composed of routing devices connected between them and organized into independent administrative entities: the Autonomous Systems. The existence of different types of Autonomous Systems (like large connectivity providers,…
In this study, an efficient method to immunize modular networks (i.e., networks with community structure) is proposed. The immunization of networks aims at fragmenting networks into small parts with a small number of removed nodes. Its…