Shaojie Zhang

Contact

Research

My research interests include computational biology, bioinformatics, and algorithms, particularly:

• Computational genomics and pangenomics
• Population genetics and haplotype analysis
• Scalable algorithms and data structures for genomic data
• RNA structural motifs and RNA structural analysis
• Biological sequence analysis
• Computational biology and bioinformatics
• Hardware security and netlist analysis

Bioinformatics Tools Developed

Software Packages  |  GitHub

Research Group

Current Group Members

1. Yuan Wei (Postdoc)
2. Khanh Duong (Ph.D. student, Computer Science)
3. Christopher Blessing (M.S. student, Computer Science)
4. JD Byers (Undergraduate student, Computer Science)

Former Postdocs

1. Ahsan Sanaullah — Next position: Scientist, Dana-Farber Cancer Institute and Harvard Medical School.
2. Kecong Tang — Next position: 23andMe.

Graduated Ph.D. Students

1. Yuan Li (2007–2012), Ph.D. 2012, Final Defense: Summer 2012. Dissertation: “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: “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: Postdoctoral Fellow at the J. Craig Venter Institute; now an Assistant Professor at the University of Kansas.
3. Ping Ge (2012–2016), Ph.D. 2016, Final Defense: Spring 2016. Dissertation: “Computational Methods for Comparative Non-coding RNA Analysis: from Secondary Structures to Tertiary Structures.” Employment: Director of Bioinformatics, Novogene.
4. Gene Sher (2013–2017), Ph.D. 2017 (Co-Chair: Damian Dechev), Final Defense: Summer 2017. Dissertation: “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: “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: “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: “Computational methods for discovery and analysis of RNA structure motifs.” First job: Assistant Professor, California State University, Monterey Bay.
8. Xiaoli Chen, Ph.D., Computer Science, Fall 2021. Dissertation: “Computational methods for RNA 3D structural alignment and sgRNA design for CRISPR-based imaging.” First employment: Amazon.com, Inc.
9. Ahsan Sanaullah, Ph.D., Computer Science, Spring 2023. Dissertation: “Algorithms and variations on the positional Burrows-Wheeler transform and their applications.” First employment: Postdoc, UCF. Second employment: Scientist, Dana-Farber Cancer Institute/Harvard Medical School.
10. James Geist, Ph.D., Computer Science, Spring 2023. Dissertation: “Discovery and evaluation of finite state machines in hardware security.” First employment: Sandia National Laboratories.
11. Md Mahfuzur Rahaman, Ph.D., Computer Science, Summer 2025. Dissertation: “Computational Approaches for RNA Structural Motif Analysis: Similarities, Variations, and Spatial Relationships.” First employment: Lecturer, UCF.
12. Kecong Tang, Ph.D., Computer Science, Summer 2025. Dissertation: “Parallel Algorithms and Benchmarking for Identity-by-Descent Segment Detection in Biobank-Scale Data.” First employment: Postdoc, UCF. Second employment: 23andMe.
13. Yuan Wei, Ph.D., Computer Science, Summer 2025. Dissertation: “Computational Methods for Population Genetic Inference Using Identity by Descent and Local Ancestry.” First employment: Postdoc, UCF.
14. Pramesh Shakya, Ph.D., Computer Science, Fall 2025. Dissertation: “PBWT-based Methods for Biobank-Scale Haplotype Data Analysis.” First employment: Postdoc, St. Jude Children's Research Hospital.
15. Nabila Shahnaz Khan, Ph.D., Computer Science, Spring 2026. Dissertation: “Computational Methods for RNA 3D Structure Classification and Structural Motif Discovery.” First employment: Illumina, Inc.

Selected Recent Publications

A representative selection of peer-reviewed publications from 2023–2026. For the complete publication list, see Google Scholar or ORCID.

1. Ahsan Sanaullah, Nathaniel K. Brown, Pramesh Shakya, Arun Deegutla, Ardalan Naseri, Ben Langmead, Degui Zhi, and Shaojie Zhang. “RLBWT-based LCP computation in compressed space for terabase-scale pangenome analysis.” Bioinformatics, 42(Supplement 1), btag268, 2026. Full text
2. Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang. “An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT.” 25th International Conference on Algorithms for Bioinformatics (WABI 2025), LIPIcs 344, Article 17, 2025. Full text
3. Yuan Wei, Degui Zhi, and Shaojie Zhang. “Recomb-Mix: fast and accurate local ancestry inference.” Bioinformatics, 41(Supplement 1), i180–i188, 2025. Full text
4. Xiaoli Chen, Md Mahfuzur Rahaman, Ardalan Naseri, and Shaojie Zhang. “CRIBAR: a fast and flexible sgRNA design tool for CRISPR imaging.” Bioinformatics Advances, 5(1), vbaf022, 2025. Full text
5. Md Mahfuzur Rahaman and Shaojie Zhang. “RNAMotifProfile: a graph-based approach to build RNA structural motif profiles.” NAR Genomics and Bioinformatics, 6(3), lqae128, 2024. Full text
6. Ardalan Naseri, Degui Zhi, and Shaojie Zhang. “Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank.” eLife, 13:e81698, 2024. Full text
7. Ardalan Naseri, William Yue, Shaojie Zhang, and Degui Zhi. “Fast inference of genetic recombination rates in biobank scale data.” Genome Research, 33(7), 1015–1022, 2023. Full text
8. Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang. “Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model.” Genome Research, 33(7), 1007–1014, 2023. Full text
9. Md Mahfuzur Rahaman, Nabila Shahnaz Khan, and Shaojie Zhang. “RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families.” Bioinformatics, 39(Supplement 1), i337–i346, 2023. Full text
10. Xiaoli Chen and Shaojie Zhang. “CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching.” Nucleic Acids Research, 51(9), e53, 2023. Full text

Teaching

• CAP 5510 — Introduction to Bioinformatics
• COT 5405 — Design and Analysis of Algorithms
• COT 3100 — Introduction to Discrete Structures
• CAP 6515 — Algorithms in Computational Biology
• CAP 6517 — Computational Genomics
• CAP 4543 — Introduction to Bioinformatics Algorithms

Education

• 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