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Assistant Professor

Computer Science

National Center for Behavioral Genomics


Volen Center for Complex Systems 135

MS 018, Brandeis


Waltham, MA 02454

Phone: 781-736-2729

Fax: 781-736-2741


Research Highlights:

Computational Systems Biology: Animal organogenesis is a complicate process controlled by a network of intercellular signaling, intracellular signal transduction, and transcriptional regulation. The construction of quantitative models for this network can provide insights into the underlying biological mechanisms. We have developed a mathematical model to model the biological network that governs C. elegans vulval induction. The model was automatically learned from heterogeneous biological data and is capable of simulating vulval induction under various different genetic conditions. (details). In another ongoing project, we inferred a large-scale multi-cellular regulatory network that contains 2000+ cells and governs the development of Drosophila eye (details) from high-content images and other biological data. At the same time, we are generating a comprehensive signaling network in Drosophila by using tandem affinity purification/mass spectrometry protein-protein interaction mapping (details).

High-Content Image Analysis: Cell-based High-Content Screening (HCS) has recently led to high-throughput image-based studies of cellular phenotypes under various external treatments such as chemical compound or or RNA interference (RNAi). Such studies will significantly advance our understanding of gene functions, shed new light on the underlying biological networks, and have direct impact on cancer research and drug discovery/development. We have developed a robust method for quantifying the complex morphology of neuronal cells in HCS images (details). We are also developing a novel computing paradigm that integrates unsupervised pattern mining techniques, visual data exploration interfaces and interactive image analysis techniques to facilitate the application of the HCS technology to biomedical research. A prototype, called imCellPhen -- interactive mining of cellular phenotypes, has been realized (details).