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ORCIDShaojie Zhang 0001
Person information
- affiliation: University of Central Florida (UCF), Department of Computer Science, Orlando, FL, USA
- affiliation (PhD 2007): University of California, San Diego, CA, USA
Other persons with the same name
- Shaojie Zhang (aka: Shao-Jie Zhang) — disambiguation page
- Shaojie Zhang 0002 — Anhui University, School of Computer Science and Technology, Hefei, China
- Shaojie Zhang 0003
![[0009-0004-5489-5134]](https://dblp.uni-trier.de/img/orcid-mark.12x12.png "0009-0004-5489-5134")
— Jilin University, Key Laboratory of Symbolic Computation and Knowledge Engineering, Jilin, China
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2020 – today
- 2025
[j24]Yuan Wei, Degui Zhi, Shaojie Zhang:
Recomb-Mix: fast and accurate local ancestry inference. Bioinform. 41(Supplement_1): i180-i188 (2025)- [c29]Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang:
Haplotype-Based Parallel PBWT for Biobank Scale Data. ICCABS 2025: 130-143 - [c28]Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang:
Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data. RECOMB 2025: 209-226 - [c27]Ahsan Sanaullah, Degui Zhi, Shaojie Zhang:
An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT. WABI 2025: 17:1-17:25 - [i2]Ahsan Sanaullah, Degui Zhi, Shaojie Zhang:
An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT. CoRR abs/2505.15698 (2025) - 2023
- [j23]Victor Wang, Ardalan Naseri, Shaojie Zhang, Degui Zhi:
Syllable-PBWT for space-efficient haplotype long-match query. Bioinform. 39(1) (2023) - [j22]Yuan Wei, Ardalan Naseri, Degui Zhi, Shaojie Zhang:
RaPID-Query for fast identity by descent search and genealogical analysis. Bioinform. 39(6) (2023) - [j21]Md. Mahfuzur Rahaman, Nabila Shahnaz Khan, Shaojie Zhang:
RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families. Bioinform. 39(Supplement-1): 337-346 (2023) - [c26]James Geist, Travis Meade, Shaojie Zhang, Yier Jin:
NetViz: A Tool for Netlist Security Visualization. ISQED 2023: 1-8 - [i1]Jim Geist, Travis Meade, Shaojie Zhang, Yier Jin:
Improving FSM State Enumeration Performance for Hardware Security with RECUT and REFSM-SAT. CoRR abs/2311.10273 (2023) - 2022
- [c25]James Geist, Shaojie Zhang, Yier Jin, Travis Meade:
A Structural and SAT Analysis of SANSCrypt. AsianHOST 2022: 1-6 - 2021
- [j20]Ahsan Sanaullah, Degui Zhi, Shaojie Zhang:
d-PBWT: dynamic positional Burrows-Wheeler transform. Bioinform. 37(16): 2390-2397 (2021) - [c24]Pramesh Shakya, Ardalan Naseri, Degui Zhi, Shaojie Zhang:
mcPBWT: Space-Efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching. ICCABS 2021: 115-130 - [c23]Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi:
Efficient Haplotype Block Matching in Bi-Directional PBWT. WABI 2021: 19:1-19:13 - 2020
- [c22]James Geist, Travis Meade, Shaojie Zhang, Yier Jin:
RELIC-FUN: Logic Identification through Functional Signal Comparisons. DAC 2020: 1-6 - [c21]Ahsan Sanaullah, Degui Zhi, Shaojie Zhang:
d-PBWT: Dynamic Positional Burrows-Wheeler Transform. RECOMB 2020: 269-270
2010 – 2019
- 2019
- [j19]Ardalan Naseri, Erwin Holzhauser, Degui Zhi, Shaojie Zhang:
Efficient haplotype matching between a query and a panel for genealogical search. Bioinform. 35(14): i233-i241 (2019) - [j18]Ardalan Naseri, Degui Zhi, Shaojie Zhang:
Multi-allelic positional Burrows-Wheeler transform. BMC Bioinform. 20-S(11): 279:1-279:8 (2019) - [c20]Jason Portillo, Travis Meade, John Hacker, Shaojie Zhang, Yier Jin:
RERTL: Finite State Transducer Logic Recovery at Register Transfer Level. AsianHOST 2019: 1-6 - [c19]Travis Meade, Jason Portillo, Shaojie Zhang, Yier Jin:
NETA: when IP fails, secrets leak. ASP-DAC 2019: 90-95 - 2018
- [j17]Travis Meade, Kaveh Shamsi, Thao Le, Jia Di, Shaojie Zhang, Yier Jin:
The Old Frontier of Reverse Engineering: Netlist Partitioning. J. Hardw. Syst. Secur. 2(3): 201-213 (2018) - [c18]Thao Le, Lucas Weaver, Jia Di, Shaojie Zhang, Yier Jin:
Hardware Trojan Detection and Functionality Determination for Soft IPs. IVSW 2018: 56-61 - 2017
- [j16]Travis Meade, Shaojie Zhang, Yier Jin:
IP protection through gate-level netlist security enhancement. Integr. 58: 563-570 (2017) - [c17]Ardalan Naseri, Degui Zhi, Shaojie Zhang:
Multi-allelic positional burrows-wheeler transform. ICCABS 2017: 1 - [c16]Travis Meade, Zheng Zhao, Shaojie Zhang, David Z. Pan, Yier Jin:
Revisit sequential logic obfuscation: Attacks and defenses. ISCAS 2017: 1-4 - [c15]Ardalan Naseri, Xiaoming Liu, Shaojie Zhang, Degui Zhi:
Ultra-Fast Identity by Descent Detection in Biobank-Scale Cohorts Using Positional Burrows-Wheeler Transform. RECOMB 2017: 387-388 - 2016
- [j15]Erwin Holzhauser, Ping Ge, Shaojie Zhang:
WebSTAR3D: a web server for RNA 3D structural alignment. Bioinform. 32(23): 3673-3675 (2016) - [j14]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, Ming Tan:
The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. J. Biomed. Semant. 7: 24 (2016) - [j13]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, Nisansa de Silva, Mohan Vamsi Kasukurthi, Vikash Kumar Jha, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan:
The development of non-coding RNA ontology. Int. J. Data Min. Bioinform. 15(3): 214-232 (2016) - [c14]Travis Meade, Shaojie Zhang, Yier Jin:
Netlist reverse engineering for high-level functionality reconstruction. ASP-DAC 2016: 655-660 - [c13]Travis Meade, Yier Jin, Mark Tehranipoor, Shaojie Zhang:
Gate-level netlist reverse engineering for hardware security: Control logic register identification. ISCAS 2016: 1334-1337 - 2015
- [c12]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. BIBM 2015: 621-624 - 2014
- [j12]Ping Ge, Cuncong Zhong, Shaojie Zhang:
ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search. BMC Bioinform. 15(S-9): S15 (2014) - [j11]Cuncong Zhong, Justen Andrews, Shaojie Zhang:
Discovering non-coding RNA elements in Drosophila 3' untranslated regions. Int. J. Bioinform. Res. Appl. 10(4/5): 479-497 (2014) - [j10]Yuan Li, Cuncong Zhong, Shaojie Zhang:
Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements. Int. J. Bioinform. Res. Appl. 10(4/5): 498-518 (2014) - [j9]Cuncong Zhong, Shaojie Zhang:
Simultaneous Folding of Alternative RNA Structures with Mutual Constraints: An Application to Next-Generation Sequencing-based RNA Structure Probing. J. Comput. Biol. 21(8): 609-621 (2014) - [c11]Dean Sullivan, Jeff Biggers, Guidong Zhu, Shaojie Zhang, Yier Jin:
FIGHT-Metric: Functional Identification of Gate-Level Hardware Trustworthiness. DAC 2014: 173:1-173:4 - 2013
- [j8]Ping Ge, Shaojie Zhang:
Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction. BMC Bioinform. 14: 142 (2013) - [j7]Cuncong Zhong, Shaojie Zhang:
Efficient alignment of RNA secondary structures using sparse dynamic programming. BMC Bioinform. 14: 269 (2013) - 2012
- [j6]Yuan Li, Shaojie Zhang:
Predicting folding pathways between RNA conformational structures guided by RNA stacks. BMC Bioinform. 13(S-3): S5 (2012) - [j5]Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang:
A Memory Efficient Method for Structure-Based RNA Multiple Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 9(1): 1-11 (2012) - [c10]Yuan Li, Shaojie Zhang:
Finding consensus stable local optimal structures for aligned RNA sequences. ICCABS 2012: 1-6 - [c9]Cuncong Zhong, Justen Andrews, Shaojie Zhang:
Discovering non-coding RNA elements in drosophila 3′ untranslated regions. ICCABS 2012: 1-6 - 2011
- [j4]Yuan Li, Shaojie Zhang:
Finding stable local optimal RNA secondary structures. Bioinform. 27(21): 2994-3001 (2011) - [c8]Yuan Li, Shaojie Zhang:
Predicting folding pathways between RNA conformational structures guided by RNA stacks. BCB 2011: 245-253 - [c7]Yuan Li, Aaron L. Halpern, Shaojie Zhang:
TreeLign: simultaneous stepwise alignment and phylogenetic positioning, with its application to automatic phylogenetic assignment of 16S rRNAs. BCB 2011: 451-456
2000 – 2009
- 2009
- [c6]Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang:
PMFastR: A New Approach to Multiple RNA Structure Alignment. WABI 2009: 49-61 - 2008
- [j3]Buhm Han, Banu Dost, Vineet Bafna, Shaojie Zhang:
Structural Alignment of Pseudoknotted RNA. J. Comput. Biol. 15(5): 489-504 (2008) - 2007
- [b1]Shaojie Zhang:
Computational methods for genome-wide non-coding RNA discovery and analysis. University of California, San Diego, USA, 2007 - 2006
- [j2]Vineet Bafna, Haixu Tang, Shaojie Zhang:
Consensus Folding of Unaligned RNA Sequences Revisited. J. Comput. Biol. 13(2): 283-295 (2006) - [c5]Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, Vineet Bafna:
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. ISMB (Supplement of Bioinformatics) 2006: 557-565 - [c4]Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna:
Structural Alignment of Pseudoknotted RNA. RECOMB 2006: 143-158 - 2005
- [j1]Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna:
Searching Genomes for Noncoding RNA Using FastR. IEEE ACM Trans. Comput. Biol. Bioinform. 2(4): 366-379 (2005) - [c3]Vineet Bafna, Haixu Tang, Shaojie Zhang:
Consensus Folding of Unaligned RNA Sequences Revisited. RECOMB 2005: 172-187 - 2004
- [c2]Vineet Bafna, Shaojie Zhang:
FastR: Fast Database Search Tool for Non-Coding RNA. CSB 2004: 52-61 - 2000
- [c1]Shaojie Zhang, Kai-Kuang Ma:
A Novel Shape Matching Method using Biological-Sequence Dynamic Alignment. IEEE International Conference on Multimedia and Expo (I) 2000: 343-346
Coauthor Index
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