Shaojie Zhang

57 papers A* 2A 1B 5C 5Journal 27Unranked 16
YearRankTypeTitle / Venue / Authors
2026 J jnl
An Efficient Dynamic Data Structure for Haplotype Matching and Compression on Biobank-Scale Data.
J. Comput. Biol.
Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2025 C conf
An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT.
WABI
Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2025 J jnl
An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT.
CoRR
Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2025 B conf
Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data.
RECOMB
Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2025 — conf
Haplotype-Based Parallel PBWT for Biobank Scale Data.
ICCABS
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2025 J jnl
Recomb-Mix: fast and accurate local ancestry inference.
Bioinform.
Yuan Wei, Degui Zhi, Shaojie Zhang
2023 J jnl
Improving FSM State Enumeration Performance for Hardware Security with RECUT and REFSM-SAT.
CoRR
Jim Geist, Travis Meade, Shaojie Zhang, Yier Jin
2023 — conf
NetViz: A Tool for Netlist Security Visualization.
ISQED
James Geist, Travis Meade, Shaojie Zhang, Yier Jin
2023 J jnl
RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families.
Bioinform.
Md. Mahfuzur Rahaman, Nabila Shahnaz Khan, Shaojie Zhang
2023 J jnl
RaPID-Query for fast identity by descent search and genealogical analysis.
Bioinform.
Yuan Wei, Ardalan Naseri, Degui Zhi, Shaojie Zhang
2023 J jnl
Syllable-PBWT for space-efficient haplotype long-match query.
Bioinform.
Victor Wang, Ardalan Naseri, Shaojie Zhang, Degui Zhi
2022 — conf
A Structural and SAT Analysis of SANSCrypt.
AsianHOST
James Geist, Shaojie Zhang, Yier Jin, Travis Meade
2021 C conf
Efficient Haplotype Block Matching in Bi-Directional PBWT.
WABI
Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi
2021 J jnl
d-PBWT: dynamic positional Burrows-Wheeler transform.
Bioinform.
Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2021 — conf
mcPBWT: Space-Efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching.
ICCABS
Pramesh Shakya, Ardalan Naseri, Degui Zhi, Shaojie Zhang
2020 A* conf
RELIC-FUN: Logic Identification through Functional Signal Comparisons.
DAC
James Geist, Travis Meade, Shaojie Zhang, Yier Jin
2020 B conf
d-PBWT: Dynamic Positional Burrows-Wheeler Transform.
RECOMB
Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2019 J jnl
Efficient haplotype matching between a query and a panel for genealogical search.
Bioinform.
Ardalan Naseri, Erwin Holzhauser, Degui Zhi, Shaojie Zhang
2019 J jnl
Multi-allelic positional Burrows-Wheeler transform.
BMC Bioinform.
Ardalan Naseri, Degui Zhi, Shaojie Zhang
2019 — conf
NETA: when IP fails, secrets leak.
ASP-DAC
Travis Meade, Jason Portillo, Shaojie Zhang, Yier Jin
2019 — conf
RERTL: Finite State Transducer Logic Recovery at Register Transfer Level.
AsianHOST
Jason Portillo, Travis Meade, John Hacker, Shaojie Zhang, Yier Jin
2018 — conf
Hardware Trojan Detection and Functionality Determination for Soft IPs.
IVSW
Thao Le, Lucas Weaver, Jia Di, Shaojie Zhang, Yier Jin
2018 J jnl
The Old Frontier of Reverse Engineering: Netlist Partitioning.
J. Hardw. Syst. Secur.
Travis Meade, Kaveh Shamsi, Thao Le, Jia Di, Shaojie Zhang, Yier Jin
2017 J jnl
IP protection through gate-level netlist security enhancement.
Integr.
Travis Meade, Shaojie Zhang, Yier Jin
2017 — conf
Multi-allelic positional burrows-wheeler transform.
ICCABS
Ardalan Naseri, Degui Zhi, Shaojie Zhang
2017 C conf
Revisit sequential logic obfuscation: Attacks and defenses.
ISCAS
Travis Meade, Zheng Zhao, Shaojie Zhang, David Z. Pan, Yier Jin
2017 B conf
Ultra-Fast Identity by Descent Detection in Biobank-Scale Cohorts Using Positional Burrows-Wheeler Transform.
RECOMB
Ardalan Naseri, Xiaoming Liu, Shaojie Zhang, Degui Zhi
2016 C conf
Gate-level netlist reverse engineering for hardware security: Control logic register identification.
ISCAS
Travis Meade, Yier Jin, Mark Tehranipoor, Shaojie Zhang
2016 — conf
Netlist reverse engineering for high-level functionality reconstruction.
ASP-DAC
Travis Meade, Shaojie Zhang, Yier Jin
2016 J jnl
The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.
J. Biomed. Semant.
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
2016 J jnl
The development of non-coding RNA ontology.
Int. J. Data Min. Bioinform.
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
2016 J jnl
WebSTAR3D: a web server for RNA 3D structural alignment.
Bioinform.
Erwin Holzhauser, Ping Ge, Shaojie Zhang
2015 — conf
A domain ontology for the Non-Coding RNA field.
BIBM
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
2014 J jnl
Discovering non-coding RNA elements in Drosophila 3' untranslated regions.
Int. J. Bioinform. Res. Appl.
Cuncong Zhong, Justen Andrews, Shaojie Zhang
2014 A* conf
FIGHT-Metric: Functional Identification of Gate-Level Hardware Trustworthiness.
DAC
Dean Sullivan, Jeff Biggers, Guidong Zhu, Shaojie Zhang, Yier Jin
2014 J jnl
Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.
Int. J. Bioinform. Res. Appl.
Yuan Li, Cuncong Zhong, Shaojie Zhang
2014 J jnl
ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search.
BMC Bioinform.
Ping Ge, Cuncong Zhong, Shaojie Zhang
2014 J jnl
Simultaneous Folding of Alternative RNA Structures with Mutual Constraints: An Application to Next-Generation Sequencing-based RNA Structure Probing.
J. Comput. Biol.
Cuncong Zhong, Shaojie Zhang
2013 J jnl
Efficient alignment of RNA secondary structures using sparse dynamic programming.
BMC Bioinform.
Cuncong Zhong, Shaojie Zhang
2013 J jnl
Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction.
BMC Bioinform.
Ping Ge, Shaojie Zhang
2012 J jnl
A Memory Efficient Method for Structure-Based RNA Multiple Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform.
Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang
2012 — conf
Discovering non-coding RNA elements in drosophila 3′ untranslated regions.
ICCABS
Cuncong Zhong, Justen Andrews, Shaojie Zhang
2012 — conf
Finding consensus stable local optimal structures for aligned RNA sequences.
ICCABS
Yuan Li, Shaojie Zhang
2012 J jnl
Predicting folding pathways between RNA conformational structures guided by RNA stacks.
BMC Bioinform.
Yuan Li, Shaojie Zhang
2011 J jnl
Finding stable local optimal RNA secondary structures.
Bioinform.
Yuan Li, Shaojie Zhang
2011 — conf
Predicting folding pathways between RNA conformational structures guided by RNA stacks.
BCB
Yuan Li, Shaojie Zhang
2011 — conf
TreeLign: simultaneous stepwise alignment and phylogenetic positioning, with its application to automatic phylogenetic assignment of 16S rRNAs.
BCB
Yuan Li, Aaron L. Halpern, Shaojie Zhang
2009 C conf
PMFastR: A New Approach to Multiple RNA Structure Alignment.
WABI
Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang
2008 J jnl
Structural Alignment of Pseudoknotted RNA.
J. Comput. Biol.
Buhm Han, Banu Dost, Vineet Bafna, Shaojie Zhang
2007 — —
Computational methods for genome-wide non-coding RNA discovery and analysis.
Shaojie Zhang
2006 — conf
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements.
ISMB (Supplement of Bioinformatics)
Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, Vineet Bafna
2006 J jnl
Consensus Folding of Unaligned RNA Sequences Revisited.
J. Comput. Biol.
Vineet Bafna, Haixu Tang, Shaojie Zhang
2006 B conf
Structural Alignment of Pseudoknotted RNA.
RECOMB
Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna
2005 B conf
Consensus Folding of Unaligned RNA Sequences Revisited.
RECOMB
Vineet Bafna, Haixu Tang, Shaojie Zhang
2005 J jnl
Searching Genomes for Noncoding RNA Using FastR.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna
2004 — conf
FastR: Fast Database Search Tool for Non-Coding RNA.
CSB
Vineet Bafna, Shaojie Zhang
2000 A conf
A Novel Shape Matching Method using Biological-Sequence Dynamic Alignment.
IEEE International Conference on Multimedia and Expo (I)
Shaojie Zhang, Kai-Kuang Ma