Computer Science Seminar - University of Houston
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Computer Science Seminar

Visualizing Human Genome in 3-Dimension

When: Tuesday, February 25, 2014
Where: PGH 563
Time: 11:00 AM

Speaker: Prof. W. Jim Zheng, University of Texas Health Science Centre at Houston

Host: Prof. Zhigang Deng

More and more evidence indicates that the 3D conformation of eukaryotic genome is a critical part of genome function. However, this information is ignored by most of the genome study as most of these studies have used information systems that view the DNA in a linear structure.  In recent years, new technologies are enabling the measurement of 3D conformation of chromosome.   Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is an increasing need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation.

We have applied object-oriented technology to develop a visualization tool, Genome3D, for integrating and displaying epigenomic data within a prescribed three-dimensional physical model of the human genome.  In order to integrate and visualize large volume of data, novel statistical and mathematical approaches have been developed to reduce the size of the data.   To our knowledge, this is the first such tool developed that can visualize human genome in three-dimension.  Genome3D employs a multi-scale data framework using a representative basic physical model.  Genome3D software is a visualization tool that explores a wide range of structural genomic and epigenetic data.  Data from various sources of differing scales can be integrated within a hierarchical framework that is easily adapted to new developments concerning the structure of the physical genome. In addition, our tool has a simple annotation mechanism to incorporate non-structural information. Genome3D is unique is its ability to manipulate large amounts of multi-resolution data from diverse sources to uncover complex and new structural relationships within the genome.  The new version of Genome3D will use a game engine and sophisticated video game visualization techniques to construct a multi-platform real-time 3D genome viewer.  Combining this viewer with 3D genome models from experimental data could provide unprecedented opportunities to gain insight into the conformation-function relationships of a genome.

Bio:
Dr. W. Jim Zheng received a Ph.D. in Biochemistry & Molecular Biology from UT Southwestern, a MS in Computer Science from UT Dallas, a MS in Biophysics and a BS in Virology & Molecular Biology from Wuhan University.  His research focuses on large-scale data integration and analysis, systems biology, ontology, literature mining, genome structure modeling and visualization. Dr. Zheng has authored more than 25 peer-reviewed journal articles, reporting the novel concepts such as Ontology Fingerprints and the first model-view framework, Genome3D, that models, integrates and visualizes human genome in 3-dimension.  Dr. Zheng has over 25 US and International patents from his work in genomics and bioinformatics area. Dr. Zheng was a recipient of PhRMA Foundation Research Start Award, currently serves on the editorial board of three bioinformatics journals, and served on many study section panels at NIH and EPA.  Dr. Zheng’s research is currently funded by NIH, NSF and the Cancer Prevention & Research Institute of Texas.