Bioinformatics, CSE, UCSD

Shaojie Zhang's

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Shaojie Zhang

I completed my Ph.D. in Computer Science (Bioinformatics) at UCSD in 2007 under Dr. Vineet Bafna. As of fall 2007, I am an assistant professor at University of Central Florida.
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E-mail: shzhang at
Phone: (858) 822-5004
FAX:     (858) 534-7029
Office: CSE 4254

Mailing address:
Department of Computer Science & Engineering,
University of California, San Diego
La Jolla, CA 92093-0404

Research Interests:
Computational Molecular Biology and Bioinformatics.

Current Project:

Currently, I am working on the non-coding RNA gene finding problem. One goal of the Human Genome Project is to detect protein coding genes. It seems that the number of protein coding genes is far lower than the initial estimates. Where are the genes? One assumption is that there are a large number of genes that produce functional noncoding RNAs. Therefore, we have many interesting questions to ask: Could it be possible that a large class of genes has gone undetected because they do not make proteins? How many ncRNA genes are there? How can we find them from the whole genome? How important are they in the whole biological system? To answer these questions, new gene discovery methods are needed to be developed which are aimed at ncRNAs.

One problem I am working on is quickly finding homologs of an RNA sequence in a genome based on the structure information. Since noncoding RNA evolution is constrained by its secondary structure, we hope that we can find a lot ncRNA genes based on the RNA secondary structure information.

Recent Publications:

6) Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan and Vineet Bafna, "A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements", Bioinformatics Vol. 22, No. 14, page e557-e565, 2006 (ISMB 2006). Supplementary data (all searching results) updated, PDF version

5) Banu Dost, Buhm Han, Shaojie Zhang and Vineet Bafna, "Structural alignment of pseudoknotted RNA", RECOMB 2006. PDF version

4) Vineet Bafna, Haixu Tang and Shaojie Zhang, "Consensus folding of unaligned RNA sequences revisited", Journal of Computational Biology, Vol. 13, No. 2, page 283-295, 2006. PDF version

3) Vineet Bafna, Haixu Tang and Shaojie Zhang, "Consensus folding of unaligned RNA sequences revisited", RECOMB 2005. updated version

2) Vineet Bafna and Shaojie Zhang, "FastR: Fast Database Search Tool for Non-Co ding RNA", CSB 2004 page:52-61. Link

1) Shaojie Zhang, Brian Haas, Eleazar Eskin and Vineet Bafna, "Searching Genomes for non-coding RNA using FastR", IEEE TCBB , 2005 2(4). Link, PDF version

Short Bio:

Ph.D., Computer Science, University of California San Diego. (2001 - 2007)
M.S. Information Enigneering, Nanyang Technological Unviersity. (1999 - 2001)
Graduate Program in Computational Molecular Biology,
Shanghai Institute of Biochemistry, Chinese Academy of Sciences. (1997 - 1999)
B.S. Computer Science, Peking University. (1993 - 1997)

ucsd UCSD CSE Bioinformatics Lab