Shaojie Zhang

Proceedings of the 25th International Conference on Algorithms for Bioinformatics, 2025

Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2025

2023

Syllable-PBWT for space-efficient haplotype long-match query.

[BibT_eX]

[DOI]

Bioinform., January, 2023

Improving FSM State Enumeration Performance for Hardware Security with RECUT and REFSM-SAT.

[BibT_eX]

[DOI]

CoRR, 2023

RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families.

[BibT_eX]

[DOI]

Md. Mahfuzur Rahaman

Nabila Shahnaz Khan

Bioinform., 2023

NetViz: A Tool for Netlist Security Visualization.

[BibT_eX]

[DOI]

Proceedings of the 24th International Symposium on Quality Electronic Design, 2023

2022

A Structural and SAT Analysis of SANSCrypt.

[BibT_eX]

[DOI]

Proceedings of the Asian Hardware Oriented Security and Trust Symposium, 2022

2021

d-PBWT: dynamic positional Burrows-Wheeler transform.

[BibT_eX]

[DOI]

Ahsan Sanaullah

Degui Zhi

Bioinform., 2021

Efficient Haplotype Block Matching in Bi-Directional PBWT.

[BibT_eX]

[DOI]

Proceedings of the 21st International Workshop on Algorithms in Bioinformatics, 2021

mcPBWT: Space-Efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching.

[BibT_eX]

[DOI]

Proceedings of the Computational Advances in Bio and Medical Sciences: 11th International Conference, 2021

2020

RELIC-FUN: Logic Identification through Functional Signal Comparisons.

[BibT_eX]

[DOI]

Proceedings of the 57th ACM/IEEE Design Automation Conference, 2020

2019

Multi-allelic positional Burrows-Wheeler transform.

[BibT_eX]

[DOI]

Ardalan Naseri

Degui Zhi

BMC Bioinform., 2019

Efficient haplotype matching between a query and a panel for genealogical search.

[BibT_eX]

[DOI]

Bioinform., 2019

NETA: when IP fails, secrets leak.

[BibT_eX]

[DOI]

Proceedings of the 24th Asia and South Pacific Design Automation Conference, 2019

RERTL: Finite State Transducer Logic Recovery at Register Transfer Level.

[BibT_eX]

[DOI]

Proceedings of the Asian Hardware Oriented Security and Trust Symposium, 2019

2018

The Old Frontier of Reverse Engineering: Netlist Partitioning.

[BibT_eX]

[DOI]

J. Hardw. Syst. Secur., 2018

Hardware Trojan Detection and Functionality Determination for Soft IPs.

[BibT_eX]

[DOI]

Proceedings of the 3rd IEEE International Verification and Security Workshop, 2018

2017

IP protection through gate-level netlist security enhancement.

[BibT_eX]

[DOI]

Travis Meade

Yier Jin

Integr., 2017

Ultra-Fast Identity by Descent Detection in Biobank-Scale Cohorts Using Positional Burrows-Wheeler Transform.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2017

Revisit sequential logic obfuscation: Attacks and defenses.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Symposium on Circuits and Systems, 2017

2016

The development of non-coding RNA ontology.

[BibT_eX]

[DOI]

Int. J. Data Min. Bioinform., 2016

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.

[BibT_eX]

[DOI]

J. Biomed. Semant., 2016

WebSTAR3D: a web server for RNA 3D structural alignment.

[BibT_eX]

[DOI]

Erwin Holzhauser

Ping Ge

Bioinform., 2016

Gate-level netlist reverse engineering for hardware security: Control logic register identification.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Symposium on Circuits and Systems, 2016

Netlist reverse engineering for high-level functionality reconstruction.

[BibT_eX]

[DOI]

Travis Meade

Yier Jin

Proceedings of the 21st Asia and South Pacific Design Automation Conference, 2016

2015

A domain ontology for the Non-Coding RNA field.

[BibT_eX]

[DOI]

Michael T. Zimmermann

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014

Simultaneous Folding of Alternative RNA Structures with Mutual Constraints: An Application to Next-Generation Sequencing-based RNA Structure Probing.

[BibT_eX]

[DOI]

J. Comput. Biol., 2014

Discovering non-coding RNA elements in Drosophila 3' untranslated regions.

[BibT_eX]

[DOI]

Justen Andrews

Int. J. Bioinform. Res. Appl., 2014

Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.

[BibT_eX]

[DOI]

Int. J. Bioinform. Res. Appl., 2014

ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search.

[BibT_eX]

[DOI]

Ping Ge

BMC Bioinform., 2014

FIGHT-Metric: Functional Identification of Gate-Level Hardware Trustworthiness.

[BibT_eX]

[DOI]

Proceedings of the 51st Annual Design Automation Conference 2014, 2014

2013

Efficient alignment of RNA secondary structures using sparse dynamic programming.

[BibT_eX]

[DOI]

BMC Bioinform., 2013

Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction.

[BibT_eX]

[DOI]

Ping Ge

BMC Bioinform., 2013

2012

A Memory Efficient Method for Structure-Based RNA Multiple Alignment.

[BibT_eX]

[DOI]

Daniel DeBlasio

Jocelyne Bruand

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Predicting folding pathways between RNA conformational structures guided by RNA stacks.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

Finding consensus stable local optimal structures for aligned RNA sequences.

[BibT_eX]

[DOI]

Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

2011

Finding stable local optimal RNA secondary structures.

[BibT_eX]

[DOI]

Bioinform., 2011

TreeLign: simultaneous stepwise alignment and phylogenetic positioning, with its application to automatic phylogenetic assignment of 16S rRNAs.

[BibT_eX]

[DOI]

Aaron L. Halpern

Proceedings of the ACM International Conference on Bioinformatics, 2011

2009

PMFastR: A New Approach to Multiple RNA Structure Alignment.

[BibT_eX]

[DOI]

Daniel DeBlasio

Jocelyne Bruand

Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

2008

Structural Alignment of Pseudoknotted RNA.

[BibT_eX]

[DOI]

J. Comput. Biol., 2008

2007

Computational methods for genome-wide non-coding RNA discovery and analysis.

[BibT_eX]

[DOI]

PhD thesis, 2007

2006

Consensus Folding of Unaligned RNA Sequences Revisited.

[BibT_eX]

[DOI]

Vineet Bafna

Haixu Tang

J. Comput. Biol., 2006

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements.

[BibT_eX]

[DOI]

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

Searching Genomes for Noncoding RNA Using FastR.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2005

2004

FastR: Fast Database Search Tool for Non-Coding RNA.

[BibT_eX]

[DOI]

Vineet Bafna

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2000

A Novel Shape Matching Method using Biological-Sequence Dynamic Alignment.

[BibT_eX]

[DOI]