Shaojie Zhang

Shaojie Zhang, Cuncong Zhong, Justen Andrews, 2012, 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS).

Predicting folding pathways between RNA conformational structures guided by RNA stacks

Yuan Li, Shaojie Zhang, Shaojie Zhang, 2012, BMC Bioinformatics.

Finding consensus stable local optimal structures for aligned RNA sequences

Shaojie Zhang, Yuan Li, 2012, 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS).

Finding stable local optimal RNA secondary structures

Yuan Li, Shaojie Zhang, Shaojie Zhang, 2011, Bioinform..

Searching genomes for noncoding RNA using FastR

Eleazar Eskin, Vineet Bafna, Shaojie Zhang, 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

RNAMotifScanX: a graph alignment approach for RNA structural motif identification

Shaojie Zhang, Cuncong Zhong, Shaojie Zhang, 2015, RNA.

RaPID-Query for Fast Identity by Descent Search and Genealogical Analysis

D. Zhi, Shaojie Zhang, A. Naseri, 2022, bioRxiv.

Ieee/acm Transactions on Computational Biology and Bioinformatics 1 a Memory Efficient Method for Structure-based Rna Multiple Alignment

Shaojie Zhang, Dan F. DeBlasio, Jocelyne Bruand, 2022 .

PMFastR: A New Approach to Multiple RNA Structure Alignment

Shaojie Zhang, Dan F. DeBlasio, Jocelyne Bruand, 2009, WABI.

Consensus Folding of Unaligned RNA Sequences Revisited

Vineet Bafna, Haixu Tang, Shaojie Zhang, 2005, RECOMB.

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

Xiaowei Wang, Karen Eilbeck, Yu Lin, 2016, J. Biomed. Semant..

The development of non-coding RNA ontology

Xiaowei Wang, Karen Eilbeck, Yu Lin, 2016, Int. J. Data Min. Bioinform..

A domain ontology for the Non-Coding RNA field

Xiaowei Wang, Karen Eilbeck, Yu Lin, 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Ultra-fast Identity by Descent Detection in Biobank-Scale Cohorts using Positional Burrows–Wheeler Transform

Xiaoming Liu, D. Zhi, Shaojie Zhang, 2017, bioRxiv.

FastRecomb: Fast inference of genetic recombination rates in biobank scale data

Shaojie Zhang, A. Naseri, D. Zhi, 2023, bioRxiv.

Translation repression via modulation of the cytoplasmic poly(A)-binding protein in the inflammatory response

Wenqian Hu, Shaojie Zhang, Xu Zhang, 2017, eLife.

Structural Alignment of Pseudoknotted RNA

Vineet Bafna, Buhm Han, Shaojie Zhang, 2006, RECOMB.

Structural Alignment of Pseudoknotted RNA

Vineet Bafna, Buhm Han, Shaojie Zhang, 2006, RECOMB.

Open-source benchmarking of IBD segment detection methods for biobank-scale cohorts

D. Zhi, Shaojie Zhang, A. Naseri, 2022, GigaScience.

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

Shaojie Zhang, Cuncong Zhong, Shaojie Zhang, 2014, J. Comput. Biol..

RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment

Haixu Tang, Shaojie Zhang, Cuncong Zhong, 2010, Nucleic acids research.

CRISPR-Sirius: RNA Scaffolds for Signal Amplification in Genome Imaging

D. Grunwald, Hanhui Ma, Shaojie Zhang, 2018, Nature Methods.

Personalized genealogical history of UK individuals inferred from biobank-scale IBD segments

Shaojie Zhang, A. Naseri, Xiaoming Liu, 2021, BMC Biology.

Efficient Haplotype Block Matching in Bi-Directional PBWT

Shaojie Zhang, Ardalan Naseri, William Yue, 2021, WABI.

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

Yuan Li, Aaron L. Halpern, Shaojie Zhang, 2011, BCB '11.

Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions.

Wenqian Hu, Shaojie Zhang, Xiaoli Chen, 2019, Methods.

RERTL: Finite State Transducer Logic Recovery at Register Transfer Level

Yier Jin, Shaojie Zhang, Travis Meade, 2019, 2019 Asian Hardware Oriented Security and Trust Symposium (AsianHOST).

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

Mark Mohammad Tehranipoor, Shaojie Zhang, Yier Jin, 2016, 2016 IEEE International Symposium on Circuits and Systems (ISCAS).

Netlist reverse engineering for high-level functionality reconstruction

Shaojie Zhang, Yier Jin, Travis Meade, 2016, 2016 21st Asia and South Pacific Design Automation Conference (ASP-DAC).

CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching

Shaojie Zhang, Xiaoli Chen, 2023, Nucleic Acids Research.

Predicting folding pathways between RNA conformational structures guided by RNA stacks

Shaojie Zhang, Yuan Li, 2011, BCB '11.

De novo discovery of structural motifs in RNA 3D structures through clustering

Shaojie Zhang, Cuncong Zhong, Shahidul Islam, 2017, bioRxiv.

Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment

Shaojie Zhang, Cuncong Zhong, Shaojie Zhang, 2011, Nucleic acids research.

DRREP: deep ridge regressed epitope predictor

Gene I. Sher, Shaojie Zhang, D. Zhi, 2017, BMC Genomics.

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

Roded Sharan, Vineet Bafna, Shaojie Zhang, 2006, ISMB.

Multicolor CRISPR labeling of chromosomal loci in human cells

Hanhui Ma, S. Wolfe, Shaojie Zhang, 2015 .

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

Shaojie Zhang, Ping Ge, Cuncong Zhong, 2014, BMC Bioinformatics.

Accurate and Efficient Mapping of the Cross-Linked microRNA-mRNA Duplex Reads

Shaojie Zhang, Cuncong Zhong, Shaojie Zhang, 2019, iScience.

CLAN: the CrossLinked reads ANalyais tool

Shaojie Zhang, Cuncong Zhong, Shaojie Zhang, 2017, bioRxiv.

RNA-NRD: a non-redundant RNA structural dataset for benchmarking and functional analysis

Shaojie Zhang, M. Rahaman, Shahidul Islam, 2023, NAR genomics and bioinformatics.

RNAMotifContrast: a method to discover and visualize RNA structural motif subfamilies

Shaojie Zhang, S. Islam, M. Rahaman, 2021, Nucleic acids research.

Revisit sequential logic obfuscation: Attacks and defenses

David Z. Pan, Shaojie Zhang, Yier Jin, 2017, 2017 IEEE International Symposium on Circuits and Systems (ISCAS).

Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data

Peter D. Tonner, Shaojie Zhang, V. Srinivasasainagendra, 2012, BMC Genomics.

Interrogation of CRISPR Dynamics with Fluorescent Single Guide RNAs in Live Cells

D. Grunwald, Hanhui Ma, Shaojie Zhang, 2016 .

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

Shaojie Zhang, Ping Ge, 2013, BMC Bioinformatics.

Fast and accurate local ancestry inference with Recomb-Mix

Shaojie Zhang, Yuan Wei, Degui Zhi, 2023, bioRxiv.

Cis‐suppression to arrest protein aggregation in mammalian cells

Shaojie Zhang, Inchan Kwon, J. Costanzo, 2014, Biotechnology and bioengineering.

Finding stable local optimal RNA secondary structures

Shaojie Zhang, Yuan Li, 2011, Bioinform..

The Old Frontier of Reverse Engineering: Netlist Partitioning

Jia Di, Shaojie Zhang, Yier Jin, 2018, Journal of Hardware and Systems Security.

RELIC-FUN: Logic Identification through Functional Signal Comparisons

Yier Jin, Shaojie Zhang, James Geist, 2020, 2020 57th ACM/IEEE Design Automation Conference (DAC).

Fast inference of genetic recombination rates in biobank scale data

Shaojie Zhang, A. Naseri, William Yue, 2023, Genome research.

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

Degui Zhi, Ardalan Naseri, Erwin Holzhauser, 2019, Bioinform..

Genealogical search using whole-genome genotype profiles

Shaojie Zhang, A. Naseri, R. Lewis, 2020 .

Multi-allelic positional Burrows-Wheeler transform

Shaojie Zhang, Degui Zhi, Ardalan Naseri, 2017, BMC Bioinformatics.