Shaojie Zhang

Office: HEC 311 (building 116)
Office Hours (Spring 2012): Tuesday/Thursday 2:00-3:00 and 4:30-5:30

Phone: (407) 823-6095
Fax: (407) 823-5835
E-mail: shzhang(at)eecs.ucf.edu

My research group:Computational Biology and Bioinformatics Group

Mailing Address:

Department of Electrical Engineering and Computer Science
University of Central Florida
4000 Central Florida Blvd
Orlando, FL 32816-2362

Educational Background:

Ph.D., Computer Science, University of California, San Diego, 2007

Research Interests:
Computational Biology and Bioinformatics, particularly:

Teaching:

CAP5510 Introduction to Bioinformatics (Fall 2007)
UCF Bioinformatics Seminar (Fall 2007)
CAP6938 Special Topic: Computational Genomics (Spring 2008)
CAP6938 Special Topic: Algorithms in Computational Molecular Biology (Fall 2008)
CAP6938 Computational Genomics (Spring 2009)
CAP6938 Algorithms in Computational Molecular Biology (Fall 2009)
COT3100C Introduction to Discrete Structures (Fall 2009)
CAP6938 Computational Genomics (Spring 2010)
CAP6938 Algorithms in Computational Molecular Biology (Fall 2010)
COT3100C Introduction to Discrete Structures (Fall 2010)
CAP6938 Computational Genomics (Spring 2011)
CAP6515 Algorithms in Computational Biology (Fall 2011)
COT3100C Introduction to Discrete Structures (Fall 2011)
CAP6517 Computational Genomics (Spring 2012)

Students:

Current Students:
Yuan Li (Ph.D. student)
Cuncong Zhong (Ph.D. student)
Peter Tonner (Undergraduate student)
Gene Sher (Ph.D. student)

Former Students:
Dan DeBlasio (M.S. 2009, Now at University of Arizona)
Matt Finch (M.S. 2010)

We are always looking for motivated undergraduate and graduate students currently at UCF. If you are looking for research projects, please get in touch.

Recent Publications:

1. Cuncong Zhong, Justen Andrews and Shaojie Zhang, "Discovering Non-coding RNA Elements in Drosophila 3' Untranslated Regions", IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) 2012, Feb. 23-25, 2012, Las Vegas, Nevada, USA (accepted).
2. Yuan Li and Shaojie Zhang, "Finding consensus stable local optimal structures for aligned RNA sequences", IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) 2012, Feb. 23-25, 2012, Las Vegas, Nevada, USA (accepted).
3. Yuan Li and Shaojie Zhang, "Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks", BMC Bioinformatics,Volume 13 Supplement, 2012
4. Joseph Mazar, Divya Khaitan, Dan DeBlasio, Cuncong Zhong, Subramaniam S. Govindarajan, Sharmila Kopanathi, Shaojie Zhang, Animesh Ray, Ranjan J. Perera, "Epigenetic Regulation of MicroRNA Genes and the Role of miR-34b in Cell Invasion and Motility in Human Melanoma", PLoS ONE, 6(9): e24922, 2011. Pubmed Fulltext
5. Cuncong Zhong and Shaojie Zhang, "Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment", Nucleic Acids Research, Sep. 12 2011.Pubmed Fulltext
6. Yuan Li and Shaojie Zhang, "Finding Stable Local Optimal RNA Secondary Structures", Bioinformatics, 27(21) 2994-3001, 2011. (Epub 2011 Sep 8.) Pubmed Fulltext
7. Yuan Li and Shaojie Zhang, "Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks", In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), 2011. Fulltext
8. Yuan Li, Aaron Halpern and Shaojie Zhang, "TreeLign: simultaneous stepwise alignment and phylogenetic positioning, with its application to automatic phylogenetic assignment of 16S rRNAs", In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), 2011. Fulltext
9. Joseph Mazar, Dan DeBlasio, Subramaniam Govindarajan, Shaojie Zhang, and Ranjan J. Perera, "Epigenetic regulation of microRNA-375 and its role in melanoma development in humans", FEBS Letters , 26 Jun 2011. Pubmed Full-text
10. Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang, "A Memory Efficient Method for Structure-Based RNA Multiple Alignment," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 29 Apr. 2011. Pubmed Full-text at IEEEXplore
11. Shaojie Zhang and Cuncong Zhong, "Computational tools for RNA structural motif identification", Biotech International, Vol 22, page 6-9, Nov. 2010. Full-text (featured article).
12. Cuncong Zhong, Haixu Tang, and Shaojie Zhang, "RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment", Nucleic Acids Research Aug. 8, 2010. Pubmed Full-text
13. Daniel DeBlasio, Jocelyne Bruand, and Shaojie Zhang, "PMFastR: A new approach to mulitiple RNA structure alignment", In: Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI 2009), Berlin: Springer-Verlag: LNBI Vol. 5724, pp. 49-61, 2009. ACM Digital Library
14. Buhm Han, Banu Dost, Vineet Bafna and Shaojie Zhang, "Structural alignment of pseudoknotted RNA", Journal of Computational Biology, 15(5) page 489-504, 2008. Pubmed
15. 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 (Proceedings of ISMB 2006) Vol. 22, No. 14, page e557-e565, 2006. Pubmed
16. Banu Dost, Buhm Han, Shaojie Zhang and Vineet Bafna, "Structural alignment of pseudoknotted RNA", In RECOMB 2006: Proceedings of the 10th annual international conference on research in computational molecular biology, 2006. SpringerLink
17. 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. Pubmed
18. Vineet Bafna, Haixu Tang and Shaojie Zhang, "Consensus folding of unaligned RNA sequences revisited", In RECOMB 2005: Proceedings of the 9th annual international conference on research in computational molecular biology, 2005. SpringerLink
19. Shaojie Zhang, Brian Haas, Eleazar Eskin and Vineet Bafna, "Searching Genomes for non-coding RNA using FastR", IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 2(4) 366-379, 2005. Pubmed ACM Digital Library
20. Vineet Bafna and Shaojie Zhang, "FastR: Fast Database Search Tool for Non-coding RNA", In Proceedings of IEEE Computational Systems Bioinformatics (CSB 2004) Conference, page:52-61, 2004.Pubmed
21. Wen Zhang, Shaojie Zhang, Haixu Tang and Dafu Ding, "Reverse-Translated Alignment of EST Sequence with Protein Sequence", Acta. Biophysica Sinica, 16(2) page 322-333, 2000.