HIV/AIDS researchers are using machine learning techniques to identify how the human immune system influences the evolution of HIV within a human host. To do so, they need to take the evolutionary tree of HIV into account. PhyloDet is a scalable Phylogeny Tree Browser to allow biologists to visualize multiple traits mapped to the tree.

Responding to the growing need for better interfaces to improve the utility of the public datasets, we have designed and developed a new web-based visual interface entitled GeneShelf. It builds upon a zoomable grid display to represent two categorical dimensions. It also incorporates an augmented timeline with expandable time points that better shows multiple data values for the focused time point by embedding bar charts. We applied GeneShelf to one of the largest microarray datasets generated to study the progression and recovery process of injuries at the spinal cord of mice and rats.

We developed an interactive gene ontology visualization tool named GOTreePlus that can superimpose annotation information over gene ontology structures. GOTreePlus can facilitate the identification of important GO terms while visualizing them in the gene ontology structure. The interactive pie chart summary for a selected gene ontology term provides users with a succinct overview of their experimental results.

We developed an interactive visualization tool called ConSet, where users can effectively examine relationships among multiple sets at once. ConSet provides an overview using an improved permutation matrix to enable users to easily identify relationships among sets with a large number of elements. Not only do we use a standard Venn diagram, we also introduce a new diagram called Fan diagram that allows users to compare two or three sets without any inconsistencies that may exist in Venn diagrams.