Literature DB >> 21828085

NetDS: a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks.

Duc-Hau Le1, Yung-Keun Kwon.   

Abstract

SUMMARY: NetDS is a novel Cytoscape plugin that conveniently simulates dynamics related to robustness, and examines structural properties with respect to feedforward/feedback loops. It can evaluate how robustly a network sustains a stable state against mutations by employing a Boolean network model. In addition, the plugin can examine all feedforward/feedback loops appearing in a network and determine whether or not a pair of loops is coupled. Random networks can also be generated to evaluate whether or not an interesting finding in real biological networks is significantly random. AVAILABILITY: NetDS is freely available for non-commercial purposes at http://netds.sourceforge.net/. CONTACT: kwonyk@ulsan.ac.kr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Mesh：

Year:  2011        PMID： 21828085     DOI： 10.1093/bioinformatics/btr466

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  14 in total

1.  MORO: a Cytoscape app for relationship analysis between modularity and robustness in large-scale biological networks.

Authors:  Cong-Doan Truong; Tien-Dzung Tran; Yung-Keun Kwon
Journal:  BMC Syst Biol       Date:  2016-12-23

Review 2.  Boolean modelling as a logic-based dynamic approach in systems medicine.

Authors:  Ahmed Abdelmonem Hemedan; Anna Niarakis; Reinhard Schneider; Marek Ostaszewski
Journal:  Comput Struct Biotechnol J       Date:  2022-06-17       Impact factor: 6.155

3.  PANET: a GPU-based tool for fast parallel analysis of robustness dynamics and feed-forward/feedback loop structures in large-scale biological networks.

Authors:  Hung-Cuong Trinh; Duc-Hau Le; Yung-Keun Kwon
Journal:  PLoS One       Date:  2014-07-24       Impact factor: 3.240

4.  A systems' biology approach to study microRNA-mediated gene regulatory networks.

Authors:  Xin Lai; Animesh Bhattacharya; Ulf Schmitz; Manfred Kunz; Julio Vera; Olaf Wolkenhauer
Journal:  Biomed Res Int       Date:  2013-11-17       Impact factor: 3.411

5.  Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures.

Authors:  Faiz M Khan; Stephan Marquardt; Shailendra K Gupta; Susanne Knoll; Ulf Schmitz; Alf Spitschak; David Engelmann; Julio Vera; Olaf Wolkenhauer; Brigitte M Pützer
Journal:  Nat Commun       Date:  2017-08-04       Impact factor: 14.919

6.  Identification of miRNA-mRNA Modules in Colorectal Cancer Using Rough Hypercuboid Based Supervised Clustering.

Authors:  Sushmita Paul; Petra Lakatos; Arndt Hartmann; Regine Schneider-Stock; Julio Vera
Journal:  Sci Rep       Date:  2017-02-21       Impact factor: 4.379

7.  Simulation of the Dynamics of Primary Immunodeficiencies in B Cells.

Authors:  Gabriel Ndipagbornchi Teku; Mauno Vihinen
Journal:  Front Immunol       Date:  2018-08-02       Impact factor: 7.561

8.  RMOD: a tool for regulatory motif detection in signaling network.

Authors:  Jinki Kim; Gwan-Su Yi
Journal:  PLoS One       Date:  2013-07-12       Impact factor: 3.240

9.  CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks.

Authors:  Andrea Paroni; Alex Graudenzi; Giulio Caravagna; Chiara Damiani; Giancarlo Mauri; Marco Antoniotti
Journal:  BMC Bioinformatics       Date:  2016-02-04       Impact factor: 3.169

10.  Analysis of microRNA and Gene Expression Profiles in Multiple Sclerosis: Integrating Interaction Data to Uncover Regulatory Mechanisms.

Authors:  Sherry Freiesleben; Michael Hecker; Uwe Klaus Zettl; Georg Fuellen; Leila Taher
Journal:  Sci Rep       Date:  2016-10-03       Impact factor: 4.379
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