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Shaojie Zhang

Professor
Department of Computer Science
University of Central Florida



Office: HEC 311 (building 116)
Office Hours (Summer 2022): by appointments

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

My research group: Computational Biology and Bioinformatics Group

Street Address (UPS, FedEx delivery):
4328 Scorpius Street
Building 116 - Room 346
Orlando, FL 32816-2362

Postal Address:
Department of Computer Science
University of Central Florida
4000 Central Florida Blvd
PO Box 162362
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, bioinformatics, and algorithms, particularly:

  • RNA structural motifs
  • Non-coding RNA discovery and RNA genomics
  • RNA biology
  • Comparative and computational genomics
  • Biological sequence analysis
  • Molecular and genome evolution
  • Computational genetics
  • Metagenomics
  • Computational transcriptomics and epigenetics
  • Combinatorial algorithms and approximation algorithms
  • Netlist analysis

    Bioinformatics Tools Developed:
    Software Packages

    Teaching:

  • CAP5510 Introduction of Bioinformatics
  • COT5405 Design and Analysis of Algorithms
  • COT3100 Intro to Discrete Structures
  • CAP6515 Algorithms in Computational Biology
  • CAP6517 Computational Genomics
  • CAP4932 Introduction to Bioinformatics Algorithms


    Current Students:

    1. Erwin Holzhauser (Ph.D. student)
    2. Xiaoli Chen (Ph.D. student)
    3. Mahfuzur Rahaman (Ph.D. student)
    4. Kecong Tang (Ph.D. student)
    5. Yuan Wei (Ph.D. student)
    6. Ahsan Sanaullah (Ph.D. student)
    7. Nabila Khan (Ph.D. student)
    8. Pramesh Shakya (Ph.D. student)
    9. James Geist (Ph.D. student)

    Graduated Ph.D. Students:
    1. 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
    2. 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, Now an Assistant Professor at the Universtiy of Kansas.
    3. Ping Ge (2012-2016), Ph.D. 2016, Final Defense: Spring 2016, Dissertation Title: "Computational Methods for Comparative Non-coding RNA Analysis: from Secondary Structures to Tertiary Structures"; First Job: Scientist at Advanced Cell Diagnostics.
    4. Gene Sher (2013-2017), Ph.D. 2017 (Co-Chair: Damian Dechev), Final Defense: Summer 2017, Dissertation Title: "Data Representation in Machine Learning Methods with its Application to Compilation Optimization and Epitope Prediction"; First Job: SMART Fellowship.
    5. Travis Meade (2014-2017), Ph.D. 2017 (Co-Chair: Yier Jin), Final Defense: Fall 2017, Dissertation Title: "Novel Computational Methods for Integrated Circuit Reverse Engineering"; First Job: UCF, Lecturer.
    6. Ardalan Naseri (2013-2018), Ph.D. 2018, Final Defense: Fall 2018, Dissertation Title: "Analysis of large-scale population genetic data using efficient algorithms and data structures"; First Job: UTHealth, Postdoc/Scientist
    7. Shahidul Islam (2013-2020), Ph.D. 2020, Final Defense: Summer 2020, Dissertation Title: " Computational methods for discovery and analysis of RNA structure motifs"; First Job: Assistant Professor, California State University, Monterey Bay

    Graduated M.S. Students:
    1. 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
    2. Matt Finch (M.S. 2010 by Courses)
    3. Erik Ladewig (M.S. 2010 by Courses, Now in Columbia University's Computational Biology Ph.D. Program)
    4. 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)
    5. Brook Stacy (M.S. 2017 by Courses, Research Assistant Oct 2014 - Aug 2015, Aug 2016 - May 2017, Starting Fall 2017 join in the University of Maryland College Park Computer Science Ph.D. Program)
    6. Michael Kirsche M.S. 2016 by Courses, Research Assitant Aug 2016 - May 2017, Starting Fall 2017 join in Johns Hopkins Universtiy Computer Science Ph.D. Program)

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

    Other Former Group Members at UCF:
    1. Joshua Keller (Undergraduate researcher, EXCEL URE program, Jan 2013 - May 2014)
    2. Erwin Holzhauser (Undergraduate researcher, EXCEL URE program, Jan 2013 - May 2014)
    3. Ryan Villaflores (EXCEL URE program, Jan-May 2014)
    4. Brook Stacy (Undergraduate researcher, Summer 2014)
    5. Jason Portillo (Undergradute student, Fall 2018 - Spring 2019)
    6. John Hacker (Undergradute student, Fall 2018 - Spring 2019)

    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 apply for admission first and indicate you are interested in my research in your statement. Please get in touch by sending email to shzhang at cs.ucf.edu after getting admitted by the UCF CS PhD program.

    Selected Publications (Google Scholar, ORCID):

    1. Ardalan Naseri, Xiaoming Liu, Kecong Tang, Shaojie Zhang*, and Degui Zhi*. "RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts". Genome biology, 20(1), 143, 2019. Full text
    2. Ardalan Naseri, Erwin Holzhauser, Degui Zhi*, and Shaojie Zhang*. "Efficient haplotype matching between a query and a panel for genealogical search". Bioinformatics, 35(14), i233-i241, 2019. (ISMB 2019)Full text
    3. Ardalan Naseri, Degui Zhi, and Shaojie Zhang*. "Multi-allelic positional Burrows-Wheeler transform". BMC bioinformatics, 20(11), 279, 2019. Full text
    4. Cuncong Zhong and Shaojie Zhang. "Accurate and Efficient Mapping of the Cross-Linked microRNA-mRNA Duplex Reads." iScience, 18, 11-19, 2019. (RECOMB-Seq 2019) Full text
    5. Hanhui Ma, Li-Chun Tu, Yu-Chieh Chung, Ardalan Naseri, David Grunwald, Shaojie Zhang, and Thoru Pederson. "Cell cycle - and genomic distance - dependent dynamics of a discrete chromosomal region." Journal of Cell Biology, jcb-201807162, 2019. Full text
    6. Xiaoli Chen, Sarah A. Castro, Qiuying Liu, Wenqian Hu, Shaojie Zhang*. "Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-Protein interactions." Methods, 155, 49-57, 2019. Full text
    7. Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Yu-Chieh Chung, David Grunwald, Shaojie Zhang, and Thoru Pederson. "CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging". Nature Methods, 15, 928--931, 2018. Full text
    8. Travis Meade, Kaveh Shamsi, Thao Le, Jia Di, Shaojie Zhang, and Yier Jin. "The Old Frontier of Reverse Engineering: Netlist Partitioning." Journal of hardware and Systems Security (HASS), 2(3), 201-213, 2018. Full text
    9. Ping Ge, Shahidul Islam, Cuncong Zhong, Shaojie Zhang*; "De novo discovery of structural motifs in RNA 3D structures through clustering", Nucleic Acids Research, 09 March 2018, gky139. Full text
    10. Ardalan Naseri, Degui Zhi and Shaojie Zhang*, "Multi-allelic positional burrows-wheeler transform", IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2017. Full text, Source Code
    11. Shahidul Islam, Ping Ge, and Shaojie Zhang*. "CompAnnotate: A comparative approach for RNA base-pair annotation". Nucleic Acids Research. 2017, 45(14):e136. Full text, Source Code
    12. Xu Zhang, Xiaoli Chen, Qiuying Liu, Shaojie Zhang, Wenqian Hu. "Translation repression via modulation of the cytoplasmic poly(A)-binding protein in the inflammatory response". eLife. 2017, 6:e27786. Full text
    13. Gene Sher, Degui Zhi, and Shaojie Zhang. "DRREP: deep ridge regressed epitope predictor". BMC Genomics. 2017, 18(Suppl 6):676. Full text, Source Code
    14. Bongyong Lee, Anupama Sahoo, John Marchica, Erwin Holzhauser, Xiaoli Chen, Jian-Liang Li,Tatsuya Seki, Subramaniam Shyamala Govindarajan, Fatu Badiane Markey, Mona Batish, Sonali J. Lokhande, Shaojie Zhang, Animesh Ray, and Ranjan J. Perera, "The long noncoding RNA SPRIGHTLY acts as an intranuclear organizing hub for pre-mRNA molecules", Science Advances, 03 May 2017, Vol. 3, no. 5, e1602505. Full text
    15. Ardalan Naseri, Xiaoming Liu, Shaojie Zhang* and Degui Zhi*, "Ultra-fast Identity by Descent Detection in Biobank-Scale Cohorts using Positional Burrows-Wheeler Transform", Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2017. Full text, Source Code
    16. Travis Meade, Zheng Zhao, Shaojie Zhang, David Pan, and Yier Jin, "Revisit Sequential Logic Obfuscation: Attacks and Defenses," IEEE International Symposium on Circuits and Systems (ISCAS), 2017. Full text
    17. Travis Meade, Shaojie Zhang, and Yier Jin, "IP protection through gate-level netlist security enhancement", Integration, the VLSI Journal, Available online 5 November 2016. Full text
    18. Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Maximiliaan Huisman, Shaojie Zhang, David Grunwald, and Thoru Pederson, "CRISPR-Cas9 nuclear dynamics and target recognition in living cells", Journal of Cell Biology, August 22, 2016. Full text
    19. Erwin Holzhauser, Ping Ge, and Shaojie Zhang*, "WebSTAR3D: a web server for RNA 3D structural alignment", Bioinformatics, August 6, 2016. Full text, WebSTAR3D Server
    20. Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Maximiliaan Huisman, Shaojie Zhang, David Grunwald & Thoru Pederson, "Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow", Nature Biotechnology, 34, 528-530, 2016. Full Text
    21. Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert and Ming Tan, "The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology", Journal of Biomedical Semantics, 7:24, 2016. Full text
    22. Travis Meade, Yier Jin, Mark Tehranipoor, and Shaojie Zhang, "Gate-Level Netlist Reverse Engineering for Hardware Security: Control Logic Register Identification," in IEEE International Symposium on Circuits and Systems (ISCAS 2016), pp. 1334-1337, 2016. Full text
    23. 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. Fall text
    24. 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
    25. Ping Ge and Shaojie Zhang*, "STAR3D: a stack-based RNA 3D structural alignment tool", Nucleic Acids Research, July 15, 2015. Full text, Source Code
    26. 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
    27. 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
    28. Cuncong Zhong and Shaojie Zhang*, "RNAMotifScanX: a graph alignment approach for RNA structural motif identification" RNA, 2015 0: rna.044891.114v1-14. Full text
    29. 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
    30. 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
    31. 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
    32. 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
    33. Cuncong Zhong and Shaojie Zhang*, "Efficient alignment of RNA secondary structures using sparse dynamic programming", BMC Bioinformatics, 14:269, 2013. Full text (Highly Accssed)
    34. 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)
    35. 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
    36. 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).
    37. 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
    38. 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)
    39. 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
    40. 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
    41. 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
    42. 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
    43. 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
    44. 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
    45. 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
    46. 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
    47. 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
    48. 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).
    49. 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
    50. 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
    51. 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
    52. 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
    53. 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
    54. 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
    55. 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
    56. 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
    57. 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
    58. 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.