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Shaojie Zhang

Associate Professor
CS Graduate Program Coordinator
Department of Computer Science
University of Central Florida




CS Graduate Program Coordinator Office: HEC-437E
CS Graduate Program Secretary: Jeanine Clements, Email: Jeanine.Clements@ucf.edu, Phone: (407) 882-2313, Office: HEC-437B
CS Graduate Program Coordinator Office Hours: Appointment Only. Please come to see Ms. Clements before making an appointment by sending an email to cs-grad@cs.ucf.edu. Any other CS graduate program (CSMS or CSPhD) related inquires should be sent to cs-grad@cs.ucf.edu directly.

Prospective CS MS and PHD students: Graduate Admissions and FAQs


Office: HEC 311 (building 116)
Office Hours (Summer 2016): By Appointment Only. Please send request by email.

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

My research group: Computational Biology and Bioinformatics Group

Mailing Address:
Department of 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 (Advisor: Vineet Bafna)
M.Eng., Information Engineering, Nanyang Technological University, 2001
B.S., Computer Science, Peking University, 1997

Research Interests:
Computational Biology and Bioinformatics, particularly:

  • RNA structural motifs
  • Non-coding RNA discovery and RNA genomics
  • Comparative and computational genomics
  • Biological sequence analysis
  • Molecular and genomes evolution
  • computatiinal genomics
  • Metagenomics
  • Computational transcriptomics and epigenetics
  • Combinatorial algorithms and approximation algorithms
  • Bioinformatics Tools Developed:
    Software Packages


    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)
    19. Fall 2013: CAP6515 Algorithm in Computational Biology (Webcourses@UCF)
    20. Spring 2014: CAP6517 Computational Genomics (Webcourses@UCF)
    21. Fall 2014:CAP6515 Algorithm in Computational Biology (Webcourses@UCF)
    22. Fall 2014: COT3100C Introduction to Discrete Structures (Webcourses@UCF)
    23. Fall 2015:CAP6515 Algorithm in Computational Biology (Webcourses@UCF)
    24. Spring 2016: CAP6517 Computational Genomics (Webcourses@UCF) (T/Th 3:00 - 4:15 pm, ENG1-383)

    Students:

    Current Students:
    Ping Ge (Ph.D. student)
    Gene Sher (Ph.D. student)
    Ardalan Naseri (Ph.D. student)
    Shahidul Islam (Ph.D. student)
    Travis Meade (Ph.D. student)
    Erwin Holzhauser (Ph.D. student)
    Xiaoli Chen (Ph.D. student)

    Graduated Ph.D. Students:
    Yuan Li (2007-2012), Ph.D. 2012, Final Defence: Summer 2012, Dissertation Title: "Computational Methods For Analyzing RNA Folding Landscapes And Its Applications", From October 2012 Engineer II, Algorithms at Pacific BioSciences
    Cuncong Zhong (2007-2013), Ph.D. 2013, Final Defense: Summer 2013, Dissertation Title: "Computational methods for comparative non-coding RNA analysis: from structural motif identification to genome-wide functional classification" (2013-14 College Outstanding Dissertation Award), From September 2013 Post Doctoral Fellow at the J. Craig Venter Institute

    Graduated M.S. Students:
    Dan DeBlasio (2007-2010), M.S. 2009 by Thesis, Master's Thesis Title: "New Computational Approaches to Multiple RNA Alignment and RNA Search", Now at the University of Arizona Computer Science Ph.D. Program
    Matt Finch (M.S. 2010 by Courses)
    Erik Ladewig (M.S. 2010 by Courses, Now in Columbia University's Computational Biology Ph.D. Program)
    Albert Steppi (M.S. 2013 by Courses, Now at Florida State University Biostatistics Ph.D. Program)
    Joshua Burbridge (M.S. 2015 by Thesis, Master's Thesis Title: "Finding Consensus Energy Folding Landscapes Between RNA Sequences", now at the University of Arkansas Computer Science Ph.D. Program)

    Graduated B.S. Students:
    Peter Tonner (Undergraduate Researcher, RAMP Scholar, B.S. 2012, Now at Duke University Computational Biology & Bioinformatics Ph.D. Program)
    Jacob Martinek (B.S. 2015 Honors in the Major Thesis Title: "Improving fMRI Classification Through Network Deconvolution")

    Other Former Group Members:
    Joshua Keller (Undergraduate researcher, EXCEL URE program, Jan 2013 - May 2014)
    Erwin Holzhauser (Undergraduate researcher, EXCEL URE program, Jan 2013 - May 2014)
    Ryan Villaflores (EXCEL URE program, Jan-May 2014)
    Brook Stacy (Undergraduate researcher)


    Publications:

    1. Travis Meade, Shaojie Zhang, and Yier Jin, "Netlist Reverse Engineering for High-Level Functionality Reconstruction," in 21st Asia and South Pacific Design Automation Conference (ASP-DAC 2016), 2016. (to appear)
    2. Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei Wang, He Zhang, Zixing Liu, Ming Tan, "A domain ontology for the Non-Coding RNA field", in 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-2015), pp. 621-624, 2015. Full text
    3. Ping Ge and Shaojie Zhang*, "STAR3D: a stack-based RNA 3D structural alignment tool", Nucleic Acids Research, July 15, 2015. Full text
    4. Ping Ge and Shaojie Zhang*, "Computational analysis of RNA structures with chemical probing data". Methods, June 2015, Vol 79-80, Pages 60-66. Full text
    5. Hanhui Ma, Ardalan Naseri, Pablo Reyes-Gutierrez, Scot A. Wolfe, Shaojie Zhang, and Thoru Pederson, "Multicolor CRISPR labeling of chromosomal loci in human cells". Proc Natl Acad Sci USA, 2015 Feb 23. Full text
    6. Cuncong Zhong and Shaojie Zhang*, "RNAMotifScanX: a graph alignment approach for RNA structural motif identification" RNA, 2015 0: rna.044891.114v1-14. Full text
    7. Dean Sullivan, Jeff Biggers, Guidong Zhu, Shaojie Zhang, and Yier Jin. "FIGHT-Metric: Functional Identification of Gate-Level Hardware Trustworthiness". In Proceedings of the The 51st Annual Design Automation Conference on Design Automation Conference (DAC '14), June 2014. Full text
    8. Ping Ge, Cuncong Zhong, and Shaojie Zhang*, "ProbeAlign: incorporating high-throughput sequencing based structure probing information into ncRNA homology search". In Proceedings of 4th Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-SEQ), March 31 - April 1, 2014, and BMC Bioinformatics. 2014, 15 Suppl 9:S15. Full text
    9. Cuncong Zhong and Shaojie Zhang*, "Simultaneous Folding of Alternative RNA Structures with Mutual Constraints: An Application to Next-Generation Sequencing-based RNA Structure Probing", Journal of Computational Biology, Online Ahead of Print: April 1, 2014. Full text
    10. Jian-Liang Li, Joseph Mazar, Cuncong Zhong, Geoffrey J. Faulkner, Subramaniam S. Govindarajan, Zhan Zhang, Marcel E. Dinger, Gavin Meredith, Christopher Adams, Shaojie Zhang, John S. Mattick, Animesh Ray & Ranjan J. Perera, "Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network", Scientific Reports, 3:2962, 2013. Full text
    11. Cuncong Zhong and Shaojie Zhang*, "Efficient alignment of RNA secondary structures using sparse dynamic programming", BMC Bioinformatics, 14:269, 2013. Full text (Highly Accssed)
    12. 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)
    13. Yuan Li, Cuncong Zhong, and Shaojie Zhang*, "Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements", Accepted on January 21, 2013, Int J Bioinform Res Appl. 2014: 10(4):498-518. Full text
    14. 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).
    15. Cuncong Zhong, Justen Andrews and Shaojie Zhang*, "Discovering non-coding RNA elements in Drosophila 3' untranslated regions", Accepted on August 6, 2012, Int J Bioinform Res Appl. 2014: 10(4): 479-497. Full text
    16. 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)
    17. 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
    18. 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
    19. 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
    20. 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
    21. 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
    22. 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
    23. 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
    24. 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
    25. 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
    26. 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).
    27. 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
    28. 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
    29. 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
    30. 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
    31. 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
    32. 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
    33. 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
    34. 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
    35. 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
    36. 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.