Shaojie Zhang's
Personal Home Page
|
Contact Info Research Interests Resume Personal Interests |
CSE Department
UCSD
Curriculum Vitae
Shaojie Zhang
Ph.D. student in Bioinformatics
Department of Computer Science and Engineering,
University of California at San Diego
La Jolla, CA 92093-0114
E-mail: shzhang at cs.ucsd.edu
Phone: (858) 822-5004
FAX: (858) 534-7029
Education
M.Eng. in Information Enginnering, School of EEE, Nanyang Technological University, Singapore.
Gradute Program in Computational Molecular Biology, Shanghai Institute of Biochemistry, Chinese Academy of Sciences, China.
B.S. in Computer Science, Peking University, China.
Professional Experience
2001- Present: Research Assitant at Bioinformatics Lab of Computer Science and Engineering Department, UCSD, with Prof. Pavel Pevzner and with Prof. Vinnet Bafna.
1999-2001: Research Assitant and Project Officer at the school of EEE and Network Technology Research Centre of Nanyang Technological University, Singapore, with Prof. Kai-Kuang Ma.
1997-1999: Graduate Research Assistant at Computational Molecular biology Lab, in Shanghai Institute of Biochemistry, Chinese Academy of Sciences, Shanghai, China, with Prof. Dafu Ding and Dr. Haixu Tang.
1997: Undergraduate Research Assistant at Computer Graphics Lab, in the Institute of Software, Chinese Academy of Sciences, Beijing, China, whith Prof. Enghua Wu.
Teaching Experience
Winter 2006: Teaching Assistant for CSE101, UCSD.
Fall, 2002: Teaching Assistant for CSE141, UCSD.
Fall, 2000: Digital Logic Lab Instructor, NTU.
Publications
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)
Banu Dost, Buhm Han, Shaojie Zhang and Vineet Bafna, "Structural alignment of pseudoknotted RNA", RECOMB 2006
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.
Vineet Bafna, Haixu Tang and Shaojie Zhang, "Consensus folding of unaligned RNA sequences revisited", RECOMB 2005
Vineet Bafna and Shaojie Zhang, "FastR: Fast Database Search Tool for Non-Coding RNA", CSB2004 page:52-61.
Shaojie Zhang, Brian Haas, Eleazar Eskin and Vineet Bafna, "Searching Genomes for non-coding RNA using FastR", IEEE TCBB , 2005 2(4).
Zhang Wen, Zhang Shaojie, Tang Haixu and Ding Dafu, "Reverse-Translated Alignment of EST Sequence with Protein Sequence", Acta. Biophysica Sinica , Vol. 16, No. 2, 2000.
Shaojie Zhang and Kai-Kuang Ma, "A novel shape matching method using biological-sequence dynamic alignment", IEEE International Conference on Multimedia and Expo, New York City, USA, July 30 - August 2, 2000.
Shaojie Zhang and Kai-Kuang Ma, "A New Proposal for Shape Description and Matching", ISO/IEC JTC1/SC29/WG11 MPEG99/M5507, Dec. 1999, Maui, USA.
Rewards & Scholarships
1994 - 1995 : Peking University Special Scholarships.
1997 - 1999 : Chinese Academy of Sciences Graduate Student fellowship.
1999 - 2001 : Nanyang Technological University Postgraduate fellowship.
2001 - 2002 : CAL IT2 Fellowship
