Dr. Xiaoyu Zhang
Dr. Xiaoyu Zhang
Computer Science

Office: SCI2 239A
Phone: 760-750-4187
HomeResearchCoursesPublications

Dr. Xiaoyu Zhang

Computer graphics and visualization, Bioinformatics, Parallel and distributed computing

I welcome interested students to work with me on projects / theses.

For more information please visit my personal site.


Research

Bioinformatics

Bioinformatics (computational biology) applies computational techniques to study biological problems. It has become one of the most exciting application fields of computer science and is central to biological research. I am currently working on several topics in bioinformatics.

  • Construction of databases and computational tools for sequence and microarray data of Coccolithophorids (link)
  • Analysis of genomic data, e.g. core promoters and Micro RNA
  • Gene and protein prediction
  • Construction of databases and tools to study HIV proteases
Publications

P. Quinn, R. M. Bowers, X. Zhang, T. M. Wahlund, M. A. Fanelli, D. Olszova, and B. A. Read. “cDNA Microarrays as a Tool for Identification of Biomineralization Proteins in the Coccolithophorid Emiliania huxleyi (Haptophyta)”, Applied and Environmental Microbiology, Aug. 2006, p. 5512–5526

X. Zhang and B. Read. “On the Prediction of Biomineralization Proteins in the Absence of Sequence Homologies”, Computational System Bioinformatics Conference, Stanford, CA 2006

D. Sun and X. Zhang. “Grid-based Secure Web Service Framework for Bioinformatics”, Computational System Bioinformatics Conference, Stanford, CA 2006

T.M. Wahlund , X. Zhang, and B.A. Read. “EST Expression Profiles from Calcifying and Non-Calcifying Cultures of Emiliania huxleyi”. Journal of Micropaleontology, v. 50, p 145-155, Dec 2004

A. K. Dhar, K. S. Licon, R. Robles-Sikisaka, X. Zhang, R. A. Bullis and B. Read. " Differential Gene Expression Profiling in Healthy and White Spot Syndrome (WSSV) Virus- Infected Shrimp (Penaeus stylirostris) by EST Analysis Isolated by Suppression Subtractive Hybridization (abstract)", Plant and Animal Genomics 2006

M. Ebert, A. Hadaegh, X. Zhang, and B. Read. “Predicting the Gene Prediction in the Eukaryote Emiliana huxleyi”. International Conference of Computer Science and its Applications (ICCSA-2003)

Publications

Journal Papers
  1. X. Zhang, C. L. Bajaj, B. Kwon, T. J. Dolinsky, J. E. Nielsen, and N. A. Baker. “Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity” SIAM journal on multiscale modeling & simulation, volume 5 issue 4, p. 1196-1213, 2006 - http://link.aip.org/link/?MMSUBT/5/1196/1 (PDF)
  2. P. Quinn, R. M. Bowers, X. Zhang, T. M. Wahlund, M. A. Fanelli, D. Olszova, and B. A. Read. “cDNA Microarrays as a Tool for Identification of Biomineralization Proteins in the Coccolithophorid Emiliania huxleyi (Haptophyta)”, Applied and Environmental Microbiology, vol. 72, No. 8, pp. 5512–5526, Aug. 2006
    http://aem.asm.org/cgi/content/abstract/72/8/5512 (PDF)
  3. T.M. Wahlund, X. Zhang, and B.A. Read. “EST Expression Profiles from Calcifying and Non-Calcifying Cultures of Emiliania huxleyi”. Journal of Micropaleontology, v. 50, pp. 145-155, Dec 2004  (PDF)
  4. X. Zhang and C.L. Bajaj, “Scalable Isosurface Visualization of Massive Datasets on Commodity off-the-shelf Clusters” (submitted)
  5. X. Zhang and C. L. Bajaj, “Extraction, Quantification and Visualization of Protein Pockets, with application to the Structural Comparison of Proteins” (submitted)
  6. X. Zhang and G. Guo, “Quantum Cryptography Using Coherent State” Chinese Physics Letter, Vol.13, No. 4, 1996

Full-length Conference Proceeding Papers
  1. X. Zhang and C. Bajaj, “Extraction, Visualization and Quantification of Protein Pockets”, Proceeding of 6th annual International Conference on Computational System Bioinformatics Conference (CSB 2007), p. 275-286, San Diego, CA, 2007.  - http://www.lifesciencessociety.org/CSB2007/toc/ (PDF)
  2. X. Zhang. “Complementary Shape Comparison with Additional Properties”, Eurographics/IEEE Proceedings of Volume Graphics 2006, p. 79-86, Boston, MA 2006. - http://vg.swan.ac.uk/vg06/program.html (PDF)
  3. X. Zhang, C. Bajaj and V. Ramachandran, “Parallel and Out-of-core View-dependent Isocontouring with Random Data Distribution” Proceedings of the Joint Eurographics - IEEE TCVG Symposium on Visualization (VisSym 2002), p. 9-18, IEEE Computer Society Press, 2002 (PDF)
  4. X. Zhang, C. Bajaj, W. Blanke, “Scalable Isosurface Visualization of Massive Datasets on COTS Clusters”. Proceeding of IEEE Symposium on Parallel and Large-data Visualization and Graphics 2001,  p. 51-58, 2001 (PDF)
  5. C. Bajaj, V. Pascucci, D. Thompson and X. Zhang, “Parallel Accelerated Isocontouring for Out-of-Core Visualization”, Proceedings of Parallel Visualization and Graphics Symposium, page 97-104, 1999 (PDF)
  6. X. Zhang and G. Guo, “Secure Key Distribution Based on Coherent States” Proc. Of 4th International Conference on Quantum Mechanics and Uncertainty Relations, 1996

Other Conference Publications
  1. J. Dailey, X. Zhang and B. Read, “Genome-wide Analysis of Core Promoter Regions in Emiliania Huxleyi”,  6th Annual International Conference on Computational System Bioinformatics, San Diego, CA, August 2007 (extended abstract and poster presentation) (PDF, Poster)
  2. X. Zhang and B. Read, “On the Prediction of Biomineralization Proteins in the Absence of Sequence Homologies”, Computational System Bioinformatics Conference, Stanford, CA 2006 (extended abstract and poster presentation) - http://www.lifesciencessociety.org/CSB2006/posters.html (PDF, Poster)
  3. D. Sun and X. Zhang. “Grid-based Secure Web Service Framework for Bioinformatics”, Computational System Bioinformatics Conference, Stanford, CA 2006 (extended abstract and poster presentation) - http://www.lifesciencessociety.org/CSB2006/posters.html (PDF, Poster)
  4. A. K. Dhar, K. S. Licon, R. Robles-Sikisaka1, X. Zhang, R. A. Bullis and B. Read, “Differential Gene Expression Profiling in Healthy and White Spot Syndrome (WSSV) Virus- Infected Shrimp (Penaeus stylirostris) by EST Analysis Isolated by Suppression Subtractive Hybridization”,  Plant & Animal Genomes XIV Conferencee, San Diego, CA, January 14-18, 2006 (abstract and poster presentation) - http://www.intl-pag.org/14/abstracts/PAG14_P608.html
  5. N.A. Baker, X. Zhang, Z. Xu, Zaiqing, and C.L. Bajaj. “Electrostatic Comparison of Biomolecular Structures” Biomedical Information Science and Technology Initiative (BISTI) 2003 Symposium, National Institutes of Health, Bethesda, Maryland, Nov 6-7, 2003 (abstract and poster presentation) http://www.bisti.nih.gov/2003meeting/Abstracts/I44.pdf
  6. M. Ebert, A. Hadaegh, X. Zhang, and B. Read. “Gene Prediction in the Eukaryote Emiliana huxleyi”. International Conference of Computer Science and its Applications (ICCSA-2003), San Diego, CA, pp. 320-322, July 2003, ISBN:0-9742-4480-5.

Technical Reports
  1. X. Zhang, C. Bajaj, N. Baker. “Affine Invariant Comparison of Molecular Shapes with Properties”, ICES Tech Report, University of Texas at Austin, 2005 (PDF)
  2. W. Blanke, C. Bajaj, X. Zhang and D. Fussell, “Foveated Rendering of Large Datastreams using a Multi-display, Multi-resolution Parallel Image Compositing System”. TICAM Tech Report, University of Texas at Austin, 2002
  3. W. Blanke, C. Bajaj, X. Zhang and D. Fussell. “A Cluster Based Emulator for Multi-display, Multi-resolution Parallel Image Compositing”. TICAM Tech Report, University of Texas at Austin, 2001
  4. W. Blanke, D. Fussell, C. Bajaj and X. Zhang. “The Metabuffer: A Scalable Multi-resolution Multi-display 3-D Graphics System Using Commodity Rendering Engines”. TR2000-16, Computer Science Department, University of Texas at Austin, February 2000

Dissertation
  1. X. Zhang. “Scalable Isocontour Visualization for Large Datasets”. Ph.D. Dissertation, Department of Computer Sciences, University of Texas at Austin, December 2001