My major interests are in the visualization of diverse biological data in ways that can communicate important properties about underlying properties. The major vehicle for that visualization has been Cytoscape, an open source platform for integration and visualization of biological data -- particularly biological data that can be mapped onto networks of various different kinds. Some examples of our work in this area include:
structureViz, which provides a linkage between the network view commonly used for visualization of pathways, protein-protein interaction networks, or protein similarity networks and the structural view commonly used by structural biologists to manipulate, analyze, and compare macromolecular structures. structureViz is a plugin for Cytoscape and is available from the Cytoscape web site or through the plugin manager.
clusterMaker, which unifies a number of different clustering techniques commonly used by biologists for segregating proteins into groups, performing expression profiling, and more recently epistatic mini-array profiles (EMAPs). clusterMaker provides the algorithms as well as familiar visualizations for the cluster results. clusterMaker is a Cytoscape plugin, allowing the nodes and edges in a Cytoscape network to interact with the visualizations provided by clusterMaker. clusterMaker is a plugin for Cytoscape and is available from the Cytoscape web site or through the plugin manager.
chemViz, extends the capabilities of Cytoscape into the domain of cheminformatics. chemViz displays 2D diagrams of compounds specified by InCHI or SMILES strings. chemViz can also calculate Tanimoto similarities of compounds and use the values to create chemical similarity networks. chemViz is a plugin for Cytoscape and is available from the Cytoscape web site or through the plugin manager.
In addition to the plugins mentioned above, I participate in the ongoing development of Cytoscape as a member of the core development team, contributing a number of plugins and extensions to Cytoscape to improve the general functionality as well as usability.