Related papers: Modules of human micro-RNA co-target network
Analogous to biological sequence comparison, comparing cellular networks is an important problem that could provide insight into biological understanding and therapeutics. For technical reasons, comparing large networks is computationally…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…
Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…
The genetic regulatory network (GRN) plays a key role in controlling the response of the cell to changes in the environment. Although the structure of GRNs has been the subject of many studies, their large scale structure in the light of…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…
Biological network alignment (NA) aims to identify similar regions between molecular networks of different species. NA can be local or global. Just as the recent trend in the NA field, we also focus on global NA, which can be pairwise (PNA)…
For most networks, the connection between two nodes is the result of their mutual affinity and attachment. In this paper, we propose a mutual selection model to characterize the weighted networks. By introducing a general mechanism of…
Capsule networks are biologically inspired neural networks that group neurons into vectors called capsules, each explicitly representing an object or one of its parts. The routing mechanism connects capsules in consecutive layers, forming a…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
Wireless Mesh Networks (WMNs) consist of radio nodes organized in a mesh topology for serving wireless mesh clients to communicate with one another or to connect to the Internet. Nodes in a mesh network can communicate with each other…
We study the structure of loops in networks using the notion of modulus of loop families. We introduce a new measure of network clustering by quantifying the richness of families of (simple) loops. Modulus tries to minimize the expected…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…
MicroRNAs are small non-coding nucleotide sequences that regulate target protein expression at post-transcriptional levels. Biogenesis of microRNA is a highly regulated multi-step pathway. Regulation of miRNA biogenesis can be caused…
In neural networks with identical neurons, the matrix of connection weights completely describes the network structure and thereby determines how it is processing information. However, due to the non-linearity of these systems, it is not…
Most cellular phenotypes are genetically complex. Identifying the set of genes that are most closely associated with a specific cellular state is still an open question in many cases. Here we study the transcriptional profile of cellular…
In cheminformatics, network representations of the space of compounds have been suggested extensively. Among these, the threshold-network consists of nodes representing molecules. In this network representation, two molecules are connected…
One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
The study of neuronal morphology is important not only for its potential relationship with neuronal dynamics, but also as a means to classify diverse types of cells and compare than among species, organs, and conditions. In the present…