Shaojie Zhang

Office: HEC 311 (building 116)
Office Hours (Summer 2013): by appointments

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
M.Eng., Information Engineering, Nanyang Technological University, 2001
B.S., Computer Science, Peking University, 1997

Research Interests:
Computational Biology and Bioinformatics, particularly:

Bioinformatics Tools Developed:
Software Packages

Current Grants:
NIH NIGMS R01: "Identification, Discovery, and Public Archiving of RNA Structural Motifs" (Sept 2012 -- Aug 2015)
UCF I.H. Award: "Computational Methods for Discovering Post-Transcriptional Control Elements in Drosophila 3'UTR" (May 2012 -- Oct 2013)

Teaching:

1. Fall 2007: CAP5510 Introduction to Bioinformatics
2. Spring 2008: CAP6938 Special Topic on Computational Genomics
3. Fall 2008: CAP6938 Special Topic on Algorithms in Computational Molecular Biology
4. Spring 2009: CAP6938 Computational Genomics
5. Fall 2009: CAP6938 Algorithms in Computational Molecular Biology
6. Fall 2009: COT3100C Introduction to Discrete Structures (Webcourses@UCF)
7. Spring 2010: CAP6938 Computational Genomics (Spring 2010)
8. Fall 2010: CAP6938 Algorithms in Computational Molecular Biology (Fall 2010)
9. Fall 2010: COT3100C Introduction to Discrete Structures (Webcourses@UCF)
10. Spring 2011: CAP6938 Computational Genomics
11. Summer 2011: COT3100C Introduction to Discrete Structures (Webcourses@UCF)
12. Fall 2011: CAP6515 Algorithms in Computational Biology
13. Fall 2011: COT3100C Introduction to Discrete Structures (Webcourses@UCF)
14. Spring 2012: CAP6517 Computational Genomics
15. Summer 2012: COT3100C Introduction to Discrete Structures (Webcourses@UCF)
16. Fall 2012: CAP6515 Algorithms in Computational Biology (Webcourses@UCF)
17. Fall 2012: COT3100C Introduction to Discrete Structures , (Webcourses@UCF)
18. Spring 2013: COT5405 Design and Analysis of Algorithms (Webcourses2@UCF)

Students:

Current Students:
Cuncong Zhong (Ph.D. student)
Ping Ge (Ph.D. student)
Albert Steppi (M.S. student)
Joshua Keller (Undergraduate researcher, EXCEL URE program)
Erwin Holzhauser (Undergraduate researcher, EXCEL URE program)

Graduated Students:
Dan DeBlasio (M.S. 2009 by Thesis, Now at the University of Arizona Computer Science Ph.D. Program)
Matt Finch (M.S. 2010 by Courses)
Peter Tonner (Undergraduate Researcher, RAMP Scholar, B.S. 2012, Now at Duke University Computational Biology & Bioinformatics Ph.D. Program)
Yuan Li (Ph.D. 2012, Final Defence: Summer 2012, From October 2012 at Pacific BioSciences)

UCF CS PhD applicants to my group should have strong algorithm development and programming skills (C/C++/Java and Perl/Python) and strong interest in biology. But no biology knowledge is required. We are interested in solving biological problems through algorithmic approaches. Please get in touch by sending email to shzhang at eecs.ucf.edu. If applying for admission, please indicate you are interested in my research in your statement.

Recent Publications:

1. Ping Ge and Shaojie Zhang*, "Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction", BMC Bioinformatics, 14:142, 2013. Full text (Highly Accessed).
2. Yuan Li, Cuncong Zhong, and Shaojie Zhang*, "Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements", BMC Genomics, Accepted on January 21, 2013.
3. Peter Tonner, Vinodh Srinivasasainagendra, Shaojie Zhang* and Degui Zhi*, "Detecting transcription of ribosomal protein pseudogenes in diverse human tissues in RNA-seq data", BMC Genomics, 13:412, 2012. Full text, (Highly Accessed).
4. Cuncong Zhong, Justen Andrews and Shaojie Zhang*, "Discovering non-coding RNA elements in Drosophila 3' untranslated regions", BMC Genomics, Accepted on August 6, 2012.
5. 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. Full text (Best Paper Award)
6. 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. Full text
7. Yuan Li and Shaojie Zhang*, "Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks", BMC Bioinformatics,Volume 13 (Supplement 3): S5, 2012. Full text
8. Joseph Mazar, Divya Khaitan, Dan DeBlasio, Cuncong Zhong, Subramaniam S. Govindarajan, Sharmila Kopanathi, Shaojie Zhang, Animesh Ray, Ranjan J. Perera*, "Epigenetic Regulation of Micro-RNA Genes and the Role of miR-34b in Cell Invasion and Motility in Human Melanoma", PLoS ONE, 6(9): e24922, 2011. Pubmed, Full text
9. Cuncong Zhong and Shaojie Zhang*, "Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment", Nucleic Acids Research, first published online: October 5, 2011. Pubmed, Full text, NAR Cover Story, Genome Technology Story
10. Yuan Li and Shaojie Zhang*, "Finding Stable Local Optimal RNA Secondary Structures", Bioinformatics, 27(21) 2994-3001, 2011. (Epub 2011 Sep 8). Pubmed, Full text
11. 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. Full text
12. 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. Full text
13. 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
14. Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang*, "A Memory Efficient Method for Structure-Based RNA Multiple Alignment," IEEE/ACM Transactions on Computational Biology and Bioinformatics, Accepted on 29 Apr. 2011. Pubmed, Full-text at IEEEXplore
15. 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).
16. 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
17. Daniel DeBlasio, Jocelyne Bruand, and Shaojie Zhang*, "PMFastR: A new approach to multiple 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
18. 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

    Publications before coming to UCF:

19. 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
20. 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
21. 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
22. 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
23. 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
24. 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
25. 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.