Microsoft Research
Computational User Experiences

Bioinformatics Visualization

We are exploring the design, development, and evaluation of visualization methods for the bioinformatics domain. We are applying the principles of Information Visualization to develop tools that can be used to interactively analyze the large datasets resulting from high-throughput technology in bioinformatics.

 

Project Team

PhyloDet

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.

GeneShelf

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.

GOTreePlus

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.

ConSet

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.

 

Publications

GeneShelf: A Web-based Visual Interface for Large Gene Expression Time-Series Data Repositories

Bohyoung Kim, Bongshin Lee, Susan Knoblach, Eric Hoffman, Jinwook Seo

IEEE TVCG (InfoVis 2009), Vol. 15, No. 6, pp. 905-912

PhyloDet: A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees

Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman

To appear in Bioinformatics

Det. (Distance Encoded Tree): A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees

Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan Carlson, David Heckerman

MSR Tech Report (MSR-TR-2008-97), Microsoft Research, 2008

Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-na´ve patients

Thomas Kuntzen, Joerg Timm, Andrew Berical, Niall Lennon, Aaron M. Berlin, Sarah K. Young, Bongshin Lee, David Heckerman, Jonathan Carlson, Laura L. Reyor, Marianna Kleyman, Cory M. McMahon, Christopher Birch, Julian Schulze zur Wiesch, Timothy Ledlie, Michael Koehrsen, Chinnappa Kodira, Andrew D. Roberts, Georg M. Lauer, Hugo R. Rosen, Florian Bihl, Andreas Cerny, Ulrich Spengler, Zhimin Liu, Arthur Y. Kim, Yanming Xing, Arne Schneidewind, Margaret A. Madey, Jaquelyn F. Fleckenstein, Vicki M. Park, James E. Galagan, Chad Nusbaum, Bruce D. Walker, Gerond V. Lake-Bakaar, Eric S. Daar, Ira M. Jacobson, Edward D. Gomperts, Brian R. Edlin, Sharyne M. Donfield, Raymond T. Chung, Andrew H. Talal, Tony Marion, Bruce W. Birren, Matthew R. Henn, Todd M. Allen

Hepatology, Vol. 48, No. 6, 2008, pp.1769-1778

GOTreePlus: An Interactive Gene Ontology Browser

Bongshin Lee, Kristy Brown, Yetrib Hathout, Jinwook Seo

Bioinformatics, Vol. 24, No. 7, 2008, pp.1026-1028

Visualizing Set Concordance with Permutation Matrices and Fan Diagrams

Bohyoung Kim, Bongshin Lee, Jinwook Seo

Interacting with Computers, Vol. 19, Issues 5-6, 2007, pp.630-643

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