A Novel Shape Matching Method using Biological-Sequence Dynamic Alignment. - Shaojie Zhang 001; Kai-Kuang Ma (IEEE International Conference on Multimedia and Expo (I), 2000)

FastR: Fast Database Search Tool for Non-Coding RNA. - Vineet Bafna; Shaojie Zhang 001 (CSB, 2004)

Searching Genomes for Noncoding RNA Using FastR. - Shaojie Zhang 001; Brian Haas; Eleazar Eskin; Vineet Bafna (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. - Shaojie Zhang 001; Ilya Borovok; Yair Aharonowitz; Roded Sharan; Vineet Bafna (ISMB (Supplement of Bioinformatics), 2006)

Consensus Folding of Unaligned RNA Sequences Revisited. - Vineet Bafna; Haixu Tang; Shaojie Zhang 001 (J. Comput. Biol., 2006)

Computational methods for genome-wide non-coding RNA discovery and analysis. - Shaojie Zhang 001 (2007)

Structural Alignment of Pseudoknotted RNA. - Buhm Han; Banu Dost; Vineet Bafna; Shaojie Zhang 001 (J. Comput. Biol., 2008)

PMFastR: A New Approach to Multiple RNA Structure Alignment. - Daniel DeBlasio; Jocelyne Bruand; Shaojie Zhang 001 (WABI, 2009)

TreeLign: simultaneous stepwise alignment and phylogenetic positioning, with its application to automatic phylogenetic assignment of 16S rRNAs. - Yuan Li; Aaron L. Halpern; Shaojie Zhang 001 (BCB, 2011)

Finding stable local optimal RNA secondary structures. - Yuan Li; Shaojie Zhang 001 (Bioinform., 2011)

Finding consensus stable local optimal structures for aligned RNA sequences. - Yuan Li; Shaojie Zhang 001 (ICCABS, 2012)

Predicting folding pathways between RNA conformational structures guided by RNA stacks. - Yuan Li; Shaojie Zhang 001 (BMC Bioinform., 2012)

A Memory Efficient Method for Structure-Based RNA Multiple Alignment. - Daniel DeBlasio; Jocelyne Bruand; Shaojie Zhang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction. - Ping Ge; Shaojie Zhang 001 (BMC Bioinform., 2013)

Efficient alignment of RNA secondary structures using sparse dynamic programming. - Cuncong Zhong; Shaojie Zhang 001 (BMC Bioinform., 2013)

FIGHT-Metric: Functional Identification of Gate-Level Hardware Trustworthiness. - Dean Sullivan; Jeff Biggers; Guidong Zhu; Shaojie Zhang 001; Yier Jin (DAC, 2014)

ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search. - Ping Ge; Cuncong Zhong; Shaojie Zhang 001 (BMC Bioinform., 2014)

Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements. - Yuan Li; Cuncong Zhong; Shaojie Zhang 001 (Int. J. Bioinform. Res. Appl., 2014)

Discovering non-coding RNA elements in Drosophila 3' untranslated regions. - Cuncong Zhong; Justen Andrews; Shaojie Zhang 001 (Int. J. Bioinform. Res. Appl., 2014)

Simultaneous Folding of Alternative RNA Structures with Mutual Constraints: An Application to Next-Generation Sequencing-based RNA Structure Probing. - Cuncong Zhong; Shaojie Zhang 001 (J. Comput. Biol., 2014)

A domain ontology for the Non-Coding RNA field. - Jingshan Huang; Karen Eilbeck; Judith A. Blake; Dejing Dou; Darren A. Natale; Alan Ruttenberg; Barry Smith 001; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; Bin Wu 008; Yongqun He; et al. (BIBM, 2015)

Netlist reverse engineering for high-level functionality reconstruction. - Travis Meade; Shaojie Zhang 001; Yier Jin (ASP-DAC, 2016)

Gate-level netlist reverse engineering for hardware security: Control logic register identification. - Travis Meade; Yier Jin; Mark Tehranipoor; Shaojie Zhang 001 (ISCAS, 2016)

WebSTAR3D: a web server for RNA 3D structural alignment. - Erwin Holzhauser; Ping Ge; Shaojie Zhang 001 (Bioinform., 2016)

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. - Jingshan Huang; Karen Eilbeck; Barry Smith 001; Judith A. Blake; Dejing Dou; Weili Huang; Darren A. Natale; Alan Ruttenberg; Jun Huan; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; et al. (J. Biomed. Semant., 2016)

The development of non-coding RNA ontology. - Jingshan Huang; Karen Eilbeck; Barry Smith 001; Judith A. Blake; Dejing Dou; Weili Huang; Darren A. Natale; Alan Ruttenberg; Jun Huan; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; et al. (Int. J. Data Min. Bioinform., 2016)

Revisit sequential logic obfuscation: Attacks and defenses. - Travis Meade; Zheng Zhao 003; Shaojie Zhang 001; David Z. Pan; Yier Jin (ISCAS, 2017)

Ultra-Fast Identity by Descent Detection in Biobank-Scale Cohorts Using Positional Burrows-Wheeler Transform. - Ardalan Naseri; Xiaoming Liu; Shaojie Zhang 001; Degui Zhi (RECOMB, 2017)

IP protection through gate-level netlist security enhancement. - Travis Meade; Shaojie Zhang 001; Yier Jin (Integr., 2017)

Hardware Trojan Detection and Functionality Determination for Soft IPs. - Thao Le 001; Lucas Weaver; Jia Di; Shaojie Zhang 001; Yier Jin (IVSW, 2018)

The Old Frontier of Reverse Engineering: Netlist Partitioning. - Travis Meade; Kaveh Shamsi; Thao Le 001; Jia Di; Shaojie Zhang 001; Yier Jin (J. Hardw. Syst. Secur., 2018)

RERTL: Finite State Transducer Logic Recovery at Register Transfer Level. - Jason Portillo; Travis Meade; John Hacker; Shaojie Zhang 001; Yier Jin (AsianHOST, 2019)

NETA: when IP fails, secrets leak. - Travis Meade; Jason Portillo; Shaojie Zhang 001; Yier Jin (ASP-DAC, 2019)

Efficient haplotype matching between a query and a panel for genealogical search. - Ardalan Naseri; Erwin Holzhauser; Degui Zhi; Shaojie Zhang 001 (Bioinform., 2019)

Multi-allelic positional Burrows-Wheeler transform. - Ardalan Naseri; Degui Zhi; Shaojie Zhang 001 (BMC Bioinform., 2019)

RELIC-FUN: Logic Identification through Functional Signal Comparisons. - James Geist; Travis Meade; Shaojie Zhang 001; Yier Jin (DAC, 2020)

mcPBWT: Space-Efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching. - Pramesh Shakya; Ardalan Naseri; Degui Zhi; Shaojie Zhang 001 (ICCABS, 2021)

Efficient Haplotype Block Matching in Bi-Directional PBWT. - Ardalan Naseri; William Yue; Shaojie Zhang 001; Degui Zhi (WABI, 2021)

d-PBWT: dynamic positional Burrows-Wheeler transform. - Ahsan Sanaullah; Degui Zhi; Shaojie Zhang 001 (Bioinform., 2021)

A Structural and SAT Analysis of SANSCrypt. - James Geist; Shaojie Zhang 001; Yier Jin; Travis Meade (AsianHOST, 2022)

NetViz: A Tool for Netlist Security Visualization. - James Geist; Travis Meade; Shaojie Zhang 001; Yier Jin (ISQED, 2023)

RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families. - Md. Mahfuzur Rahaman; Nabila Shahnaz Khan; Shaojie Zhang 001 (Bioinform., 2023)

Improving FSM State Enumeration Performance for Hardware Security with RECUT and REFSM-SAT. - Jim Geist; Travis Meade; Shaojie Zhang 001; Yier Jin (CoRR, 2023)

Syllable-PBWT for space-efficient haplotype long-match query. - Victor Wang; Ardalan Naseri; Shaojie Zhang 001; Degui Zhi (Bioinform., 2023)

Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data. - Pramesh Shakya; Ahsan Sanaullah; Degui Zhi; Shaojie Zhang 001 (RECOMB, 2025)

An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT. - Ahsan Sanaullah; Degui Zhi; Shaojie Zhang 001 (WABI, 2025)