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My research lab at Janelia Farm Research Campus, Howard Hughes Medical Institute focuses on understanding the structures and functioning mechanisms of biosystems using data mining techniques for bioinformatics and computational molecular biology, particularly, bioimage data mining and informatics. These bioimages include cellular and molecular images and related medical images. Several recent projects are listed below. Some further description of my ongoing research can be found here.
- 3D Digital Atlas Modeling of Animals at the Single Cell/Neuron Level: building a 3D digital Worm Atlas for every cell in C. elegans and a 3D digital Fly Brain Atlas for fruitfly;
- Analysis of Gene Expression Pattern Images: high-performance image analysis and mining for different model organisms, such as fruitfly, C. elegans, and mouse;
- Feature/Model Learning: developing algorithms and software to extract/select features and learn models from biological data (e.g. microarray data, neuronal gene expression patterns in microscopical images, etc.);
- Brain Morphometry and Neuronal Structure Analysis: developing computational tools to measure and analyze quantities of brain tissues and neurons.
- GPS for the Nematode: HHMI Bulletin, Feb 2010. Story about the recent Cell and Nature Methods papers about 3D digital worm atlas and its application in single-cell gene expression and fate analysis.
- 3D Single Cell Resolution Digital Atlas of C. elegans: Cover of Nature Methods, Vol.6, No.9, 2009. This art was generated using my V3D software.
- Google earthworm: Nature Methods News & Views (Sept 2009) article by Bill Mohler on the significance of the single-cell 3D digital worm atlas.
- 3D Fruit Fly Brain Atlas with Single Neuron Reconstructions: Cover of the conference proceedings, 2009 Bioimage Informatics Conference. This entire process of atlas building (3D neuron tracing, brain registration, and pattern mapping) and visualization were accomplished using my V3D software. This is also a proof-of-principle picture showing building single-neuron-resolution whole-brain 3D digital atlas of a fly's brain is feasible.
- Bioimaging's Proving Ground: Efforts to Build Brain Atlases: Genome Technology, Nov 2008. Highlighting my research on digital atlases and two software tools, V3D and VANO.
- 3D Brain Alignment of Multiple Fruit Fly GAL4 Lines: Cover of conference proceedings, 2008 Conference on Functional Anatomy of the Arthropod Central Complex & Motor System. The raw image data was generated by Phuong Chung, I produced the alignment, the picture was generated by Julie Simpson.
- Why I am doing what I am doing: HHMI's interview story about my research, 2007.
Many of the above projects are only possible through the joint efforts of multiple research labs. Currently I am collaborating most with Gene Myers lab, Julie Simpson lab, Gerry Rubin lab, Eric Betzig lab, Stuart Kim lab (Stanford), as well as many other labs and colleagues.
I have also worked in the more traditional pattern recognition and artificial intelligence field. I do have continuous interest in many theoretical problems there. |
