Automated Annotation of Drosophila Gene Expression Patterns Using a Controlled Vocabulary

Joint CS/GRAND Seminar
11:00am, Sep 11, Thursday, 2008, ST2, 330


Jieping Ye
Computer Science and Engineering Department
Arizona State University


Regulation of gene expression in space and time directs its localization to a specific subset of cells during development. Systematic determination of the spatiotemporal dynamics of gene expression plays an important role in understanding the regulatory networks driving development. An atlas for the gene expression patterns of fruit fly Drosophila melanogaster has been created by whole-mount in situ hybridization, and it documents the dynamic changes of gene expression pattern during Drosophila embryogenesis. The spatial and temporal patterns of gene expression are integrated by anatomical terms from a controlled vocabulary linking together intermediate tissues developed from one another. Currently, the terms are assigned to patterns manually. However, the number of patterns generated by high-throughput in situ hybridization is rapidly increasing. It is therefore tempting to approach this problem by employing computational methods. In this talk, I will present our recent work on the automated annotation of gene expression patterns using a controlled vocabulary.

Short Bio

Jieping Ye is an Assistant Professor of the Department of Computer Science and Engineering at the Arizona State University (ASU), and a core faculty member of the Center for Evolutionary Functional Genomics at the Bio-design Institute at ASU. He received his Ph.D. in Computer Science from University of Minnesota, Twin Cities in 2005. His research interests are concentrated in the areas of machine learning, data mining, and bioinformatics. He has published extensively in these areas in leading conferences and journals. He won the outstanding student paper award at the Twenty-First International Conference on Machine Learning in 2004 and the SCI Young Investigator of the Year award at ASU in 2007.