Duhong Chen

Duhong Chen is a PhD Student in Computer Science at Iowa State University.

His research interests are focused on the following fields:

Computational Biology. Development of software algorithms and visualization tools in bioinformatics. He is currently working with David Fernández-Baca on algorithmic phylogenetic tree and supertree inference.

Graph partition, decomposition, and data mining. He is interested in mining tree-species relations in TreeBASE, discovering trees that are perfect for phylogenetic supertree inference; He is also interested in molecular sequences partition: clustering sites with different evolutionary signals in phylogenetic data sets (a spectral clustering method is available here), finding fast sites without assumptions of the phylogeny, model of evolution, or characteristics of the data (using network flow).

Information integration, retrieval, and visualization. He is currently working on PhyloFinder: an intelligent search engine for phylogenetic tree databases. PhyloFinder using trees from TreeBASE is available now. It used information from TreeBASE, TBMap, and NCBI taxonomy databases. PhyloFinder provides many useful features such as subtree mining, tree similarity search, automatic translation of different names for the same species, spelling suggestions for misspelling species names, visualization of query results, and ontology/classification guides to enhance the user query etc. A search engine for gene trees is also under development.