Literature DB >> 23101871

Building blocks of biological networks: a review on major network motif discovery algorithms.

A Masoudi-Nejad1, F Schreiber, Z R M Kashani.   

Abstract

In recent years, there has been a great interest in studying different aspects of complex networks in a range of fields. One important local property of networks is network motifs, recurrent and statistically significant sub-graphs or patterns, which assists researchers in the identification of functional units in the networks. Although network motifs may provide a deep insight into the network's functional abilities, their detection is computationally challenging. Therefore several algorithms have been introduced to resolve this computationally hard problem. These algorithms can be classified under various paradigms such as exact counting methods, sampling methods, pattern growth methods and so on. Here, the authors will give a review on computational aspects of major algorithms and enumerate their related benefits and drawbacks from an algorithmic perspective.

Mesh:

Substances:

Year:  2012        PMID: 23101871     DOI: 10.1049/iet-syb.2011.0011

Source DB:  PubMed          Journal:  IET Syst Biol        ISSN: 1751-8849            Impact factor:   1.615


  11 in total

1.  Probabilistic generation of random networks taking into account information on motifs occurrence.

Authors:  Frederic Y Bois; Ghislaine Gayraud
Journal:  J Comput Biol       Date:  2015-01       Impact factor: 1.479

2.  Social insect colony as a biological regulatory system: modelling information flow in dominance networks.

Authors:  Anjan K Nandi; Annagiri Sumana; Kunal Bhattacharya
Journal:  J R Soc Interface       Date:  2014-12-06       Impact factor: 4.118

3.  Elements of the cellular metabolic structure.

Authors:  Ildefonso M De la Fuente
Journal:  Front Mol Biosci       Date:  2015-04-28

4.  Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network.

Authors:  Yuji Zhang; Cui Tao; Guoqian Jiang; Asha A Nair; Jian Su; Christopher G Chute; Hongfang Liu
Journal:  J Biomed Semantics       Date:  2014-08-06

5.  Emergence of Network Motifs in Deep Neural Networks.

Authors:  Matteo Zambra; Amos Maritan; Alberto Testolin
Journal:  Entropy (Basel)       Date:  2020-02-11       Impact factor: 2.524

6.  Identification of large disjoint motifs in biological networks.

Authors:  Rasha Elhesha; Tamer Kahveci
Journal:  BMC Bioinformatics       Date:  2016-10-06       Impact factor: 3.169

7.  SuperNoder: a tool to discover over-represented modular structures in networks.

Authors:  Danilo Dessì; Jacopo Cirrone; Diego Reforgiato Recupero; Dennis Shasha
Journal:  BMC Bioinformatics       Date:  2018-09-10       Impact factor: 3.169

8.  Disjoint motif discovery in biological network using pattern join method.

Authors:  Sabyasachi Patra; Anjali Mohapatra
Journal:  IET Syst Biol       Date:  2019-10       Impact factor: 1.615

9.  Identification, visualization, statistical analysis and mathematical modeling of high-feedback loops in gene regulatory networks.

Authors:  Benjamin Nordick; Tian Hong
Journal:  BMC Bioinformatics       Date:  2021-10-04       Impact factor: 3.169

Review 10.  Review of tools and algorithms for network motif discovery in biological networks.

Authors:  Sabyasachi Patra; Anjali Mohapatra
Journal:  IET Syst Biol       Date:  2020-08       Impact factor: 1.615

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.