P-Simrank: Extending Simrank to Scale-Free Bipartite Networks

Author(s):  
Prasenjit Dey ◽  
Kunal Goel ◽  
Rahul Agrawal
Author(s):  
Ankush Bansal ◽  
Pulkit Anupam Srivastava

A lot of omics data is generated in a recent decade which flooded the internet with transcriptomic, genomics, proteomics and metabolomics data. A number of software, tools, and web-servers have developed to analyze the big data omics. This review integrates the various methods that have been employed over the years to interpret the gene regulatory and metabolic networks. It illustrates random networks, scale-free networks, small world network, bipartite networks and other topological analysis which fits in biological networks. Transcriptome to metabolome network is of interest because of key enzymes identification and regulatory hub genes prediction. It also provides an insight into the understanding of omics technologies, generation of data and impact of in-silico analysis on the scientific community.


Biotechnology ◽  
2019 ◽  
pp. 361-379
Author(s):  
Ankush Bansal ◽  
Pulkit Anupam Srivastava

A lot of omics data is generated in a recent decade which flooded the internet with transcriptomic, genomics, proteomics and metabolomics data. A number of software, tools, and web-servers have developed to analyze the big data omics. This review integrates the various methods that have been employed over the years to interpret the gene regulatory and metabolic networks. It illustrates random networks, scale-free networks, small world network, bipartite networks and other topological analysis which fits in biological networks. Transcriptome to metabolome network is of interest because of key enzymes identification and regulatory hub genes prediction. It also provides an insight into the understanding of omics technologies, generation of data and impact of in-silico analysis on the scientific community.


2020 ◽  
Vol 43 ◽  
Author(s):  
Chris Fields ◽  
James F. Glazebrook

Abstract Gilead et al. propose an ontology of abstract representations based on folk-psychological conceptions of cognitive architecture. There is, however, no evidence that the experience of cognition reveals the architecture of cognition. Scale-free architectural models propose that cognition has the same computational architecture from sub-cellular to whole-organism scales. This scale-free architecture supports representations with diverse functions and levels of abstraction.


2010 ◽  
Author(s):  
Takuma Takehara ◽  
Tumio Ochiai ◽  
Kosuke Tamiguchi ◽  
Naoto Suzuki
Keyword(s):  

2009 ◽  
Vol 29 (5) ◽  
pp. 1230-1232
Author(s):  
Hao RAO ◽  
Chun YANG ◽  
Shao-hua TAO

Author(s):  
Mark Newman

A discussion of the most fundamental of network models, the configuration model, which is a random graph model of a network with a specified degree sequence. Following a definition of the model a number of basic properties are derived, including the probability of an edge, the expected number of multiedges, the excess degree distribution, the friendship paradox, and the clustering coefficient. This is followed by derivations of some more advanced properties including the condition for the existence of a giant component, the size of the giant component, the average size of a small component, and the expected diameter. Generating function methods for network models are also introduced and used to perform some more advanced calculations, such as the calculation of the distribution of the number of second neighbors of a node and the complete distribution of sizes of small components. The chapter ends with a brief discussion of extensions of the configuration model to directed networks, bipartite networks, networks with degree correlations, networks with high clustering, and networks with community structure, among other possibilities.


Sign in / Sign up

Export Citation Format

Share Document