Tao Ju, Ph.D.

Associate Professor
Computer Science and Engineering

Biochemistry, Biophysics, and Structural Biology Program

  • 314-935-6648

  • 314-935-7302

  • 1045

  • Lopata Hall 517

  • taoju@cse.wustl.edu

  • http://www.cs.wustl.edu/~taoju/

  • molecular imaging, geometric algorithms, anatomical modeling, computer graphics, biomedicine

  • Developing geometric algorithms for interpreting protein structures from low-resolution density maps produced by cryo-electron microscopy and X-ray crystallography

Research Abstract:

My research involves developing novel geometric algorithms and exploring their applications to various problems in computational biomedicine. In the realm of structural biology, I have been working on deciphering the 3-dimensional shape and architecture of macromolecular assemblies (such as viruses and ribosomes), which hold the very key to the understanding of basic cellular processes, using volumetric density maps produced by cryo-electron microscopy (cryo-EM) and X-ray crystallography. Inherent limitations in these imaging techniques result in insufficient resolutions in the maps (typically much worse than 4 Angstrom), which in turn creates significant computational challenges for automatic structure discovery. The objective of my research is to maximally automate the currently labor-intensive process of structure mining in these density maps by adapting existing, and developing new geometric and image analysis algorithms.

Selected Publications:

Baker M, Abeysinghe S, Schuh S, Coleman R, Abrams A, Marsh M, Hryc C, Ruths T, Chiu W, Ju T.  Modeling protein structure at near atomic resolutions with Gorgon. Journal of Structural Biology 2011 174(2):360-373
 
Abeysinghe S, Baker M, Chiu W, Ju T.  Semi-isometric registration of line features for flexible fitting of protein structures. Computer Graphics Forum 2010 29(7):2243-2252.
 
Abeysinghe S, Ju T, Baker ML, Chiu W.  Shape modeling and matching in identifying 3D protein structures. Computer-Aided Design 2008 40:708-720.
 
Ju T, Baker M, Chiu W.  Computing a family of skeletons of volumetric models for shape description. Computer-Aided Design 2007 39(5):352-260.
 
Baker MM, Ju T, Chiu W.  Identification of Secondary Structure Elements in Intermediate Resolution Density Maps. Structure 2007 15(1):7-19.
 
Wong J, Rice R, Baker N, Ju T, and Lohman T.  Probing 3`-ssDNA Loop Formation in E. coli RecBCD/RecBC-DNA Complexes using Non-natural DNA: A Model for "Chi" Recognition Complexes. Journal of Molecular Biology 2006 362(1):26-43.

Last Updated: 11/14/2011 11:41:23 AM

Gorgon: an interactive environment for protein modeling from density maps
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