Browsing by Author "Gao, J."
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Item Integrating Hi-C and FISH Data for Modeling of the 3D Organization of Chromosomes(Nature Publishing Group, 2019-05-03) Abbas, A.; He, X.; Niu, J.; Zhou, B.; Zhu, G.; Ma, T.; Song, J.; Gao, J.; Zhang, Michael Q.; Zeng, J.; Zhang, Michael Q.The new advances in various experimental techniques that provide complementary information about the spatial conformations of chromosomes have inspired researchers to develop computational methods to fully exploit the merits of individual data sources and combine them to improve the modeling of chromosome structure. Here we propose GEM-FISH, a method for reconstructing the 3D models of chromosomes through systematically integrating both Hi-C and FISH data with the prior biophysical knowledge of a polymer model. Comprehensive tests on a set of chromosomes, for which both Hi-C and FISH data are available, demonstrate that GEM-FISH can outperform previous chromosome structure modeling methods and accurately capture the higher order spatial features of chromosome conformations. Moreover, our reconstructed 3D models of chromosomes revealed interesting patterns of spatial distributions of super-enhancers which can provide useful insights into understanding the functional roles of these super-enhancers in gene regulation. © 2019, The Author(s).Item Web3DMol: Interactive Protein Structure Visualization Based on WebGL(Oxford University Press, 2017-05-08) Shi, M.; Gao, J.; Zhang, Michael Q.; Zhang, Michael Q.A growing number of web-based databases and tools for protein research are being developed. There is now a widespread need for visualization tools to present the three-dimensional (3D) structure of proteins in web browsers. Here, we introduce our 3D modeling program--Web3DMol--a web application focusing on protein structure visualization in modern web browsers. Users submit a PDB identification code or select a PDB archive from their local disk, and Web3DMol will display and allow interactive manipulation of the 3D structure. Featured functions, such as sequence plot, fragment segmentation, measure tool and meta-information display, are offered for users to gain a better understanding of protein structure. Easy-to-use APIs are available for developers to reuse and extend Web3DMol. Web3DMol can be freely accessed at http://web3dmol.duapp.com/, and the source code is distributed under the MIT license.