Network visualization and analysis of gene expression data using BioLayout Express3D

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Embedding Networks with Edge Attributes (2018, background): “Similarly, in biology, interactions of proteins can be modeled as a network and the connections in the network can be used to identify genes [28].”
Using MCL to extract clusters from networks. (2012, methodology): “Regarding Protocol 2, BioLayout Express3D is a comprehensive tool for analyzing expression data [10,15], integrating large scale data analysis and network visualisation with the ability to use mcl.”
InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation (2012, background): “2 (23), an application designed for the visualization, clustering and analysis of large networks in 2D and 3D space.”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, methodology): “…Chung et al., 2005 AVIS http://actin.pharm.mssm.edu/AVIS2 Berger et al., 2007 BioLayout Express 3D http://www.biolayout.org Freeman et al., 2007; Theocharidis et al., 2009 BiologicalNetworks http://biologicalnetworks.net Kozhenkov & Baitaluk, 2012 BioTapestry http://www.biotapestry.org…”
An expression atlas of human primary cells: inference of gene function from coexpression networks (2013, methodology): “The method used in this study employed the network tool BioLayout Express which was specifically developed to allow the visualisation and analysis of coexpression relationships in large datasets [26,27].”