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Constructing gene regulatory networks is a critical step in revealing disease mechanisms from transcriptomic data. In this work, we present NO-BEARS, a novel algorithm for estimating gene regulatory networks. The NO-BEARS algorithm is built…
Identifying the importance of nodes of complex networks is of interest to the research of Social Networks, Biological Networks etc.. Current researchers have proposed several measures or algorithms, such as betweenness, PageRank and HITS…
Deciphering complex gene-gene interactions remains challenging in transcriptomics as traditional methods often miss higher-order and nonlinear dependencies. This study introduces a quantum-inspired framework leveraging tensor networks (TNs)…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…
Emergence, where complex behaviors develop from the interactions of simpler components within a network, plays a crucial role in enhancing neural network capabilities. We introduce a quantitative framework to measure emergence during the…
Nowadays there is a multitude of measures designed to capture different aspects of network structure. To be able to say if the structure of certain network is expected or not, one needs a reference model (null model). One frequently used…
In recent years, the theory and application of complex networks have been quickly developing in a markable way due to the increasing amount of data from real systems and to the fruitful application of powerful methods used in statistical…
Relevance and importance are the main factors when humans build network connections. We propose an evolutionary network model based on preferential attachment(PA) considering these factors. We analyze and compute several important features…
Regulatory gene networks contain generic modules like those involving feedback loops, which are essential for the regulation of many biological functions. We consider a class of self-regulated genes which are the building blocks of many…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
In this work, we propose a novel centrality metric, referred to as star centrality, which incorporates information from the closed neighborhood of a node, rather than solely from the node itself, when calculating its topological importance.…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
Mutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants plays a key role in the…
When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several…
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…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
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…
For many networks of scientific interest we know both the connections of the network and information about the network nodes, such as the age or gender of individuals in a social network, geographic location of nodes in the Internet, or…