Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Reaction Centric Layout for Metabolic Networks
ISVC '09 Proceedings of the 5th International Symposium on Advances in Visual Computing: Part II
Protein-to-protein interactions: Technologies, databases, and algorithms
ACM Computing Surveys (CSUR)
Visual Exploration across Biomedical Databases
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
CompIMAGE'10 Proceedings of the Second international conference on Computational Modeling of Objects Represented in Images
On open problems in biological network visualization
GD'09 Proceedings of the 17th international conference on Graph Drawing
Transforming semi-structured life science diagrams into meaningful domain ontologies with DiDOn
Journal of Biomedical Informatics
Proceedings of the 30th ACM international conference on Design of communication
Visualizing genome expression and regulatory network dynamics in genomic and metabolic context
EuroVis'08 Proceedings of the 10th Joint Eurographics / IEEE - VGTC conference on Visualization
Semi-automatic drawing of metabolic networks
Information Visualization - Special issue on Best Papers of Visual Analytics Science and Technology (VAST) 2010
Protein Interactions for Functional Genomics
International Journal of Knowledge Discovery in Bioinformatics
Prioritizing Disease Genes and Understanding Disease Pathways
International Journal of Knowledge Discovery in Bioinformatics
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Many tools exist for visually exploring biological networks including well-known examples such as Cytoscape, VisANT, Pathway Studio and Patika. These systems play a key role in the development of integrative biology, systems biology and integrative bioinformatics. The trend in the development of these tools is to go beyond ‘static’ representations of cellular state, towards a more dynamic model of cellular processes through the incorporation of gene expression data, subcellular localization information and time-dependent behavior. We provide a comprehensive review of the relative advantages and disadvantages of existing systems with two goals in mind: to aid researchers in efficiently identifying the appropriate existing tools for data visualization; to describe the necessary and realistic goals for the next generation of visualization tools. In view of the first goal, we provide in the Supplementary Material a systematic comparison of more than 35 existing tools in terms of over 25 different features. Contact: msuder@mcb.mcgill.ca Supplementary information: Supplementary data are available at Bioinformatics online.