Home Address
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3400 Morningside Drive, #14
Houston, Texas 77098
Work Address
Human Genome Sequencing Center, N1619
Baylor College of Medicine
One Baylor Plaza
Houston, Texas 77030
713/798-7453
zzhang1@bcm.tmc.edu
prion.bchs.uh.edu/~zzhang
Objective
Seeking a challenging postdoctoral position in a cutting-edge institution to apply my knowledge of computer science and molecular biology to current problems in the field of Bioinformatics.
Qualifications
Strong background in both computer science and molecular biology. Excellent organizational, communication, and interpersonal skills.
Education
2002 Ph.D. in Biochemistry, University of Houston, USA
2000 M.S. in Computer Science, University of Houston, USA
1996 B.S. in Biochemistry, Nanjing University, China
Competencies
- Computer skills
* Platforms: Windows, MacOS, Unix, and Linux. Working experience as a Linux system administrator.
* Programming languages: Perl/CGI/DBI, Java, C, C++, Visual Basic, SQL, PL/SQL, HTML
* Database: Mysql, Oracle, Access; database design, database system administration, data retrieval and analysis, data mining
* Applications: web server administration, web page design; image processing; evolutionary programming, machine learning; Internet computing, standalone software development; knowledge and practice of rapid software development
* Software/Tools: GDE, GCG; Jbuilder, Visual Studio; Photoshop, Illustrator, Golive; Microsoft Office Suite
- Laboratory techniques
* PCR, DNA/RNA/protein purification, recombinant DNA techinques, automated DNA sequencing, mutagenesis, western blotting, RNA hybridization
Experience
- 2002 to Present, Baylor College of Medicine
- 1996 to 2002, University of Houston
Conducted the study of common Vibrio 5S ribosomal RNA sequence variants and developed a new methodology to identify the phenotypes of Vibro proteolyticus 5S rRNA variants.
Independently developed a software package to identify characteristic oligonucleotides in the 16S rRNA sequence dataset. The identification result is not only of theoretical significance but also can be utilized to design oligonucleotide microarrays to quickly identify unknown bacteria. The article which describes the algorithm and the system implementation has been accepted by Bioinformatics. For more information, please visit the web site at prion.bchs.uh.edu/16S_signatures/.
Independently designed a relational database for the non-canonical base pairs found in known RNA structures. Designed the web-side front end of the database. Implemented the online database search functionality using Perl/CGI/DBI. The related papers were published in the Database Issue of Nucleic Acid Research in 2000 and 2002. Please visit the web site at prion.bchs.uh.edu/bp_typefor complete information.
Web server (Apache) setup, configuration and administration. Set up the web site and designed the web pages for the Fox lab (prion.bchs.uh.edu). This lab web site is under active update and maintenance.
Linux and Solaris 8 server administration. Operating systems and software installation, network configuration, user accounts management and general troubleshooting.
Creative Products
- Thesis
Zhang, Zhengdong, "Identification of characteristic oligonucleotides in the 16S ribosomal RNA sequence dataset." Master's thesis, University of Houston, Houston, Texas, 2000.
Advisors: Dr. G.E. Fox and Dr. S.-H. Huang.
- Dissertation
Zhang, Zhengdong, "Study of common Vibrio 5S ribosomal RNA sequence variants and development of a new methodology to identify the phenotypes of Vibrio proteolyticus 5S rRNA variants." Doctoral dissertation, University of Houston, Houston, Texas, 2002.
Advisor: Dr. G.E. Fox.
- Publications
1. Zhang, Zhengdong, Willson RC, Fox GE (2002) "Identification of characteristic oligonucleotides in the 16S ribosomal RNA sequence dataset." Bioinformatics 18:244-250
2. Nagaswamy U, Larios-Sanz M, Hury J, Collins S, Zhang, Zhengdong, Zhao Q, Fox GE (2002) "NCIR: a database of non-canonical interactions in known RNA structures." Nucleic Acids Research 30:395-397.
3. Zhang, Zhengdong, D'sauza LM, Lee Y-H, Yang Y, Fox GE "Variable positions may be evolutionarily unconstrained over a large range of sequence contexts." Journal of Molecular Evolution. (In press)
4. Zhang, Zhengdong, Ammons D, Rampersad J, Fox GE "A novel method for screening 5S rRNA sequence variants in vivo." (In preparation)
5. Zhang, Zhengdong, Fox GE, Willson RC "Microbial identification based on the overall composition of characteristic oligonucleotides." (In preparation)
6. Nagaswamy, Uma, Voss N, Zhang, Zhengdong, Fox GE (2000) "Database of non-canonical base pairs found in known RNA structures." Nucleic Acid Research 28:375-376.
- Presentation
Zhang, Zhengdong, D'sauza LM, Lee Y-H, Yang Y, Fox GE "Variable positions may be evolutionarily unconstrained over a large range of sequence contexts." The Third Annual Meeting of the RNA Society. Madison, Wisconsin, 1998.
Awards and Honors
People's Scholarship for Academic Achievement, Nanjing University, 1995
Memberships in Professional Associations
American Association for the Advancement of Science (AAAS) - Current
American Society for Microbiology (ASM) - Current
Association for Computing Machinery (ACM) - Current
Languages
Bilingual, fluent in English and Chinese.
Personal Information
Health: Good
Physical Limitations: None
References
Dr. George E. Fox, Professor
Department of Biology and Biochemistry
University of Houston
Houston, Texas 77204-5001
713/743-8384
fox@uh.edu
Dr. Richard C. Willson, Associate Professor
Department of Chemical Engineering
University of Houston
Houston, Texas 77204-4004
713/743-4308
willson@uh.edu
Dr. S.-H. Stephen Huang, Professor and Department Chairman
Department of Computer Science
University of Houston
Houston, Texas 77204-3010
713/743-3338
shuang@cs.uh.edu
Dr. Christoph F. Eick, Associate Professor
Department of Computer Science
University of Houston
Houston, Texas 77204-3010
713/743-3345
ceick@cs.uh.edu
Zhengdong Zhang 
