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Selected Publications from UCF-CBB Research Group

2024

  1. Zhi, Degui, Shaojie Zhang, Ardalan Naseri, Ahsan Sanaullah, and Erwin Holzhauser. "Methods and system for efficient indexing for genetic genealogical discovery in large genotype databases." U.S. Patent 11,848,073, issued December 19, 2023. DOI: Patent

2023

  1. Wei, Yuan, Degui Zhi, and Shaojie Zhang. "Fast and accurate local ancestry inference with Recomb-Mix." bioRxiv (2023): 2023-11. DOI: 10.1101/2023.11.17.567650
  2. Geist, Jim, Travis Meade, Shaojie Zhang, and Yier Jin. "Improving FSM State Enumeration Performance for Hardware Security with RECUT and REFSM-SAT." arXiv preprint arXiv:2311.10273 (2023). DOI: 10.48550/arXiv.2311.10273 Focus to learn more
  3. Jin, Yier, Shaojie Zhang, James Geist, Travis Meade, and Jason Liam Portillo. "System and method for fast and accurate netlist to RTL reverse engineering." U.S. Patent 11,704,460, issued July 18, 2023. DOI: Patent
  4. Naseri, Ardalan, William Yue, Shaojie Zhang, and Degui Zhi. "Fast inference of genetic recombination rates in biobank scale data." Genome Research (2023): gr-277676. Full Text: Full Text
  5. Sanaullah, Ahsan, Degui Zhi, and Shaojie Zhang. "Minimal positional substring cover is a haplotype threading alternative to Li and Stephens Model." Genome Research (2023): gr-277673. Full Text: Full Text
  6. Rahaman, Md Mahfuzur, Nabila Shahnaz Khan, and Shaojie Zhang. "RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families." Bioinformatics 39, no. Supplement_1 (2023): i337-i346. DOI: 10.1093/bioinformatics/btad223
  7. Khan, Nabila Shahnaz, Md Mahfuzur Rahaman, Shahidul Islam, and Shaojie Zhang. "RNA-NRD: a non-redundant RNA structural dataset for benchmarking and functional analysis." NAR Genomics and Bioinformatics 5, no. 2 (2023): lqad040. DOI: 10.1093/nargab/lqad040
  8. Wei, Yuan, Ardalan Naseri, Degui Zhi, and Shaojie Zhang. "RaPID-Query for fast identity by descent search and genealogical analysis." Bioinformatics 39, no. 6 (2023): btad312. DOI: 10.1093/bioinformatics/btad312
  9. Chen, Xiaoli, and Shaojie Zhang. "CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching." Nucleic Acids Research 51, no. 9 (2023): e53-e53. DOI: 10.1093/nar/gkad222
  10. Pederson, Thoru, Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Maximilaan Huisman, and Shaojie Zhang. "Detection of gene loci with polychromatic crispr-associated protein 9." U.S. Patent Application 17/858,717, filed May 4, 2023. DOI: Patent
  11. Geist, James, Travis Meade, Shaojie Zhang, and Yier Jin. "NetViz: A Tool for Netlist Security Visualization." In 2023 24th International Symposium on Quality Electronic Design (ISQED), pp. 1-8. IEEE, 2023. DOI: 10.1109/ISQED57927.2023.10129374
  12. Liu, Qiuying, Mariah K. Novak, Rachel M. Pepin, Katharine R. Maschhoff, Kailey Worner, Xiaoli Chen, Shaojie Zhang, and Wenqian Hu. "A congenital hydrocephalus‐causing mutation in Trim71 induces stem cell defects via inhibiting Lsd1 mRNA translation." EMBO reports 24, no. 2 (2023): e55843. DOI: 10.15252/embr.202255843
  13. Naseri, Ardalan, William Yue, Shaojie Zhang, and Degui Zhi. "FastRecomb: Fast inference of genetic recombination rates in biobank scale data." In Research in Computational Molecular Biology: 27th Annual International Conference, RECOMB 2023, Istanbul, Turkey, April 16–19, 2023, Proceedings, vol. 13976, p. 212. Springer Nature, 2023. DOI: 10.1101/2023.01.09.523304
  14. Wang, Victor, Ardalan Naseri, Shaojie Zhang, and Degui Zhi. "Syllable-PBWT for space-efficient haplotype long-match query." Bioinformatics 39, no. 1 (2023): btac734. DOI: 10.1093/bioinformatics/btac734

2022

  1. Tang, Kecong, Ardalan Naseri, Yuan Wei, Shaojie Zhang, and Degui Zhi. "Open-source benchmarking of IBD segment detection methods for biobank-scale cohorts." GigaScience 11 (2022): giac111. DOI: 10.1093/gigascience/giac111
  2. Geist, James, Shaojie Zhang, Yier Jin, and Travis Meade. "A Structural and SAT Analysis of SANSCrypt." In 2022 Asian Hardware Oriented Security and Trust Symposium (AsianHOST), pp. 1-6. IEEE, 2022. DOI: 10.1109/AsianHOST56390.2022.10022024
  3. Liu, Qiuying, Mariah K. Novak, Rachel M. Pepin, Katharine R. Maschhoff, Xiaoli Chen, Shaojie Zhang, and Wenqian Hu. "A congenital hydrocephalus causing mutation in Trim71 results in stem cell differentiation defects through inhibiting Lsd1 mRNA translation." bioRxiv (2022): 2022-04. DOI: 10.1101/2022.04.14.488304
  4. Tang, Kecong, Ardalan Naseri, Yuan Wei, Shaojie Zhang, and Degui Zhi. "Open-source benchmarking of IBD segment detection methods for biobank-scale cohorts." GigaScience 11 (2022): giac111. DOI: 10.1093/gigascience/giac111
  5. Sanaullah, Ahsan, Degui Zhi, and Shaoije Zhang. "Haplotype threading using the positional Burrows-Wheeler transform." In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Schloss Dagstuhl-Leibniz-Zentrum für Informatik, 2022. DOI: 10.4230/LIPIcs.WABI.2022.4
  6. Yue, William, Ardalan Naseri, Victor Wang, Pramesh Shakya, Shaojie Zhang, and Degui Zhi. "P-smoother: efficient PBWT smoothing of large haplotype panels." Bioinformatics Advances 2, no. 1 (2022): vbac045. DOI: 10.1093/bioadv/vbac045
  7. Shakya, Pramesh, Ardalan Naseri, Degui Zhi, and Shaojie Zhang. "mcPBWT: Space-efficient multi-column PBWT scanning algorithm for composite haplotype matching." In International Conference on Computational Advances in Bio and Medical Sciences, pp. 115-130. Cham: Springer International Publishing, 2021. DOI: 10.1007/978-3-031-17531-2_10

2021

  1. Naseri, Ardalan, Kecong Tang, Xin Geng, Junjie Shi, Jing Zhang, Pramesh Shakya, Xiaoming Liu, Shaojie Zhang, and Degui Zhi. "Personalized genealogical history of UK individuals inferred from biobank-scale IBD segments." BMC biology 19 (2021): 1-12. DOI: 10.1186/s12915-021-00964-y
  2. Pederson, Thoru, Scot Andrew Wolfe, Hanhui Ma, Metewo Selase Kosi Enuameh, Nicola Anne Kearns, Ryan Michael Jude Genga, Rene Maehr, Shaojie Zhang, Ardalan Naseri, and Manuel Garber. "Compositions and methods for differential cas9 gene labeling and/or editing." U.S. Patent Application 17/200,398, filed November 4, 2021. DOI: Patent
  3. Sanaullah, Ahsan, Degui Zhi, and Shaojie Zhang. "d-PBWT: dynamic positional Burrows–Wheeler transform." Bioinformatics 37, no. 16 (2021): 2390-2397. DOI: 10.1093/bioinformatics/btab117
  4. Islam, Shahidul, Md Mahfuzur Rahaman, and Shaojie Zhang. "RNAMotifContrast: a method to discover and visualize RNA structural motif subfamilies." Nucleic acids research 49, no. 11 (2021): e61-e61. DOI: 10.1093/nar/gkab131
  5. Liu, Qiuying, Xiaoli Chen, Mariah K. Novak, Shaojie Zhang, and Wenqian Hu. "Repressing Ago2 mRNA translation by Trim71 maintains pluripotency through inhibiting let-7 microRNAs." elife 10 (2021): e66288. DOI: 10.7554/eLife.66288
  6. Naseri, Ardalan, Junjie Shi, Xihong Lin, Shaojie Zhang, and Degui Zhi. "RAFFI: accurate and fast familial relationship inference in large scale biobank studies using RaPID." PLoS Genetics 17, no. 1 (2021): e1009315. DOI: 10.1371/journal.pgen.1009315
  7. Naseri, A., W. Yue, S. Zhang, and D. Zhi. "Leibniz International Proceedings in Informatics (LIPIcs)." (2021): 1-19.
  8. Naseri, Ardalan, William Yue, Shaojie Zhang, and Degui Zhi. "Efficient haplotype block matching in bi-directional pbwt." In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Schloss Dagstuhl-Leibniz-Zentrum für Informatik, 2021. DOI: 10.4230/LIPIcs.WABI.2021.19

2020

  1. Feng, Ying, Yao Wang, Xiangnan Wang, Xiaohui He, Chen Yang, Ardalan Naseri, Thoru Pederson et al. "Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription." Genome biology 21, no. 1 (2020): 1-24. DOI: 10.1186/s13059-020-02201-1
  2. Naseri, Ardalan, Degui Zhi, and Shaojie Zhang. "Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in uk biobank." medRxiv (2020). DOI: 10.1101/2020.10.26.20220004
  3. Chen, Xiaoli, Nabila Shahnaz Khan, and Shaojie Zhang. "LocalSTAR3D: a local stack-based RNA 3D structural alignment tool." Nucleic acids research 48, no. 13 (2020): e77-e77. DOI: 10.1093/nar/gkaa453
  4. Geist, James, Travis Meade, Shaojie Zhang, and Yier Jin. "RELIC-FUN: Logic identification through functional signal comparisons." In 2020 57th ACM/IEEE Design Automation Conference (DAC), pp. 1-6. IEEE, 2020. DOI: 10.1109/DAC18072.2020.9218616
  5. Kuo, Tsung-Ting, Xiaoqian Jiang, Haixu Tang, XiaoFeng Wang, Tyler Bath, Diyue Bu, Lei Wang et al. "iDASH secure genome analysis competition 2018: blockchain genomic data access logging, homomorphic encryption on GWAS, and DNA segment searching." BMC medical genomics 13, no. 7 (2020): 1-12. DOI: 10.1186/s12920-020-0715-0
  6. Feng, Ying, Yao Wang, Chen Yang, Ardalan Naseri, Thoru Pederson, Jing Zheng, Xiao Xiao, Shaojie Zhang, Wei Xie, and Hanhui Ma. "CRISPR-based Live Imaging of Epigenetic Modification-Mediated Genome Reorganization." bioRxiv (2020): 2020-02. DOI: 10.1101/2020.02.18.954610
  7. Wei, Yuan, Ryan Lewis, Ardalan Naseri, Shaojie Zhang, and Degui Zhi. "Genealogical Search using whole-genome genotype profiles." In Responsible Genomic Data Sharing, pp. 51-94. Academic Press, 2020. DOI: 10.1016/B978-0-12-816197-5.00004-8

2019

  1. Portillo, Jason, Travis Meade, John Hacker, Shaojie Zhang, and Yier Jin. "RERTL: finite state transducer logic recovery at register transfer level." In 2019 Asian Hardware Oriented Security and Trust Symposium (AsianHOST), pp. 1-6. IEEE, 2019. DOI: 10.1109/AsianHOST47458.2019.9006699
  2. Ardalan Naseri, Xiaoming Liu, Kecong Tang, Shaojie Zhang*, and Degui Zhi*. "RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts". Genome biology, 20(1), 143, 2019. DOI: 10.1186/s13059-019-1754-8
  3. Ardalan Naseri, Erwin Holzhauser, Degui Zhi*, and Shaojie Zhang*. "Efficient haplotype matching between a query and a panel for genealogical search". Bioinformatics, 35(14), i233-i241, 2019. (ISMB 2019) DOI: 10.1093/bioinformatics/btz347
  4. Ardalan Naseri, Degui Zhi, and Shaojie Zhang*. "Multi-allelic positional Burrows-Wheeler transform". BMC bioinformatics, 20(11), 279, 2019. DOI: 10.1186/s12859-019-2821-6
  5. Cuncong Zhong and Shaojie Zhang. "Accurate and Efficient Mapping of the Cross-Linked microRNA-mRNA Duplex Reads." iScience, 18, 11-19, 2019. (RECOMB-Seq 2019) DOI: 10.1016/j.isci.2019.05.038
  6. Hanhui Ma, Li-Chun Tu, Yu-Chieh Chung, Ardalan Naseri, David Grunwald, Shaojie Zhang, and Thoru Pederson. "Cell cycle - and genomic distance - dependent dynamics of a discrete chromosomal region." Journal of Cell Biology, jcb-201807162, 2019. DOI: 10.1083/jcb.201807162
  7. Xiaoli Chen, Sarah A. Castro, Qiuying Liu, Wenqian Hu, Shaojie Zhang*. "Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-Protein interactions." Methods, 155, 49-57, 2019. DOI: 10.1016/j.ymeth.2018.12.002

2018

  1. Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Yu-Chieh Chung, David Grunwald, Shaojie Zhang, and Thoru Pederson. "CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging". Nature Methods, 15, 928--931, 2018. DOI: 10.1038/s41592-018-0174-0
  2. Travis Meade, Kaveh Shamsi, Thao Le, Jia Di, Shaojie Zhang, and Yier Jin. "The Old Frontier of Reverse Engineering: Netlist Partitioning." Journal of hardware and Systems Security (HASS), 2(3), 201-213, 2018. DOI: 10.1007/s41635-018-0043-4
  3. Ping Ge, Shahidul Islam, Cuncong Zhong, Shaojie Zhang*; "De novo discovery of structural motifs in RNA 3D structures through clustering", Nucleic Acids Research, 09 March 2018, gky139. DOI: 10.1093/nar/gky139

2017

  1. Ardalan Naseri, Degui Zhi and Shaojie Zhang*, "Multi-allelic positional burrows-wheeler transform", IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2017. DOI: 10.1109/ICCABS.2017.8114291
  2. Shahidul Islam, Ping Ge, and Shaojie Zhang*. "CompAnnotate: A comparative approach for RNA base-pair annotation". Nucleic Acids Research. 2017, 45(14):e136. DOI: 10.1093/nar/gkx538
  3. Xu Zhang, Xiaoli Chen, Qiuying Liu, Shaojie Zhang, Wenqian Hu. "Translation repression via modulation of the cytoplasmic poly(A)-binding protein in the inflammatory response". eLife. 2017, 6:e27786. DOI: 10.7554/eLife.27786
  4. Gene Sher, Degui Zhi, and Shaojie Zhang. "DRREP: deep ridge regressed epitope predictor". BMC Genomics. 2017, 18(Suppl 6):676. DOI: 10.1186/s12864-017-4024-8
  5. Bongyong Lee, Anupama Sahoo, John Marchica, Erwin Holzhauser, Xiaoli Chen, Jian-Liang Li,Tatsuya Seki, Subramaniam Shyamala Govindarajan, Fatu Badiane Markey, Mona Batish, Sonali J. Lokhande, Shaojie Zhang, Animesh Ray, and Ranjan J. Perera, "The long noncoding RNA SPRIGHTLY acts as an intranuclear organizing hub for pre-mRNA molecules", Science Advances, 03 May 2017, Vol. 3, no. 5, e1602505. DOI: 10.1126/sciadv.1602505
  6. Ardalan Naseri, Xiaoming Liu, Shaojie Zhang* and Degui Zhi*, "Ultra-fast Identity by Descent Detection in Biobank-Scale Cohorts using Positional Burrows-Wheeler Transform", Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2017. DOI: 10.1101/103325
  7. Travis Meade, Zheng Zhao, Shaojie Zhang, David Pan, and Yier Jin, "Revisit Sequential Logic Obfuscation: Attacks and Defenses," IEEE International Symposium on Circuits and Systems (ISCAS), 2017. DOI: 10.1109/ISCAS.2017.8050606
  8. Travis Meade, Shaojie Zhang, and Yier Jin, "IP protection through gate-level netlist security enhancement", Integration, the VLSI Journal, Available online 5 November 2016. DOI: 10.1016/j.vlsi.2016.10.014

2016

  1. Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Maximiliaan Huisman, Shaojie Zhang, David Grunwald, and Thoru Pederson, "CRISPR-Cas9 nuclear dynamics and target recognition in living cells", Journal of Cell Biology, August 22, 2016. DOI: 10.1083/jcb.201604115
  2. Erwin Holzhauser, Ping Ge, and Shaojie Zhang*, "WebSTAR3D: a web server for RNA 3D structural alignment", Bioinformatics, August 6, 2016. DOI: 10.1093/bioinformatics/btw502
  3. Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Maximiliaan Huisman, Shaojie Zhang, David Grunwald & Thoru Pederson, "Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow", Nature Biotechnology, 34, 528-530, 2016. DOI: 10.1038/nbt.3526
  4. 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 and Ming Tan, "The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology", Journal of Biomedical Semantics, 7:24, 2016. DOI: 10.1186/s13326-016-0066-0
  5. Travis Meade, Yier Jin, Mark Tehranipoor, and Shaojie Zhang, "Gate-Level Netlist Reverse Engineering for Hardware Security: Control Logic Register Identification," in IEEE International Symposium on Circuits and Systems (ISCAS 2016), pp. 1334-1337, 2016. DOI: 10.1109/ISCAS.2016.7527495
  6. Travis Meade, Shaojie Zhang, and Yier Jin, "Netlist Reverse Engineering for High-Level Functionality Reconstruction," in 21st Asia and South Pacific Design Automation Conference (ASP-DAC 2016), 2016. DOI: 10.1109/ASPDAC.2016.7428086

2015

  1. 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", in 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-2015), pp. 621-624, 2015. DOI: 10.1109/BIBM.2015.7359755
  2. Ping Ge and Shaojie Zhang*, "STAR3D: a stack-based RNA 3D structural alignment tool", Nucleic Acids Research, July 15, 2015. DOI: 10.1093/nar/gkv697
  3. Ping Ge and Shaojie Zhang*, "Computational analysis of RNA structures with chemical probing data". Methods, June 2015, Vol 79-80, Pages 60-66. DOI: 10.1016/j.ymeth.2015.02.003
  4. Hanhui Ma, Ardalan Naseri, Pablo Reyes-Gutierrez, Scot A. Wolfe, Shaojie Zhang, and Thoru Pederson, "Multicolor CRISPR labeling of chromosomal loci in human cells". Proc Natl Acad Sci USA, 2015 Feb 23. DOI: 10.1073/pnas.142002411
  5. Cuncong Zhong and Shaojie Zhang*, "RNAMotifScanX: a graph alignment approach for RNA structural motif identification" RNA, 2015 0: rna.044891.114v1-14. DOI: 10.1261/rna.044891.114

2014

  1. Dean Sullivan, Jeff Biggers, Guidong Zhu, Shaojie Zhang, and Yier Jin. "FIGHT-Metric: Functional Identification of Gate-Level Hardware Trustworthiness". In Proceedings of the The 51st Annual Design Automation Conference on Design Automation Conference (DAC '14), June 2014. DOI: 10.1145/2593069.2596681
  2. Ping Ge, Cuncong Zhong, and Shaojie Zhang*, "ProbeAlign: incorporating high-throughput sequencing based structure probing information into ncRNA homology search". In Proceedings of 4th Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-SEQ), March 31 - April 1, 2014, and BMC Bioinformatics. 2014, 15 Suppl 9:S15. DOI: 10.1186/1471-2105-15-S9-S15
  3. Cuncong Zhong and Shaojie Zhang*, "Simultaneous Folding of Alternative RNA Structures with Mutual Constraints: An Application to Next-Generation Sequencing-based RNA Structure Probing", Journal of Computational Biology, Online Ahead of Print: April 1, 2014. DOI: 10.1089/cmb.2013.0044
  4. Yuan Li, Cuncong Zhong, and Shaojie Zhang*, "Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements", Accepted on January 21, 2013, Int J Bioinform Res Appl. 2014: 10(4):498-518. DOI: 10.1504/IJBRA.2014.062997
  5. Cuncong Zhong, Justen Andrews and Shaojie Zhang*, "Discovering non-coding RNA elements in Drosophila 3' untranslated regions", Accepted on August 6, 2012, Int J Bioinform Res Appl. 2014: 10(4): 479-497. DOI: 10.1504/IJBRA.2014.062996

2013

  1. Jian-Liang Li, Joseph Mazar, Cuncong Zhong, Geoffrey J. Faulkner, Subramaniam S. Govindarajan, Zhan Zhang, Marcel E. Dinger, Gavin Meredith, Christopher Adams, Shaojie Zhang, John S. Mattick, Animesh Ray & Ranjan J. Perera, "Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network", Scientific Reports, 3:2962, 2013. DOI: 10.1038/srep02962
  2. Cuncong Zhong and Shaojie Zhang*, "Efficient alignment of RNA secondary structures using sparse dynamic programming", BMC Bioinformatics, 14:269, 2013. DOI: 10.1186/1471-2105-14-269
  3. Ping Ge and Shaojie Zhang*, "Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction", BMC Bioinformatics, 14:142, 2013. DOI: 10.1186/1471-2105-14-142

2012

  1. Peter Tonner, Vinodh Srinivasasainagendra, Shaojie Zhang* and Degui Zhi*, "Detecting transcription of ribosomal protein pseudogenes in diverse human tissues in RNA-seq data", BMC Genomics, 13:412, 2012. DOI: 10.1186/1471-2164-13-412
  2. Cuncong Zhong, Justen Andrews and Shaojie Zhang*, "Discovering Non-coding RNA Elements in Drosophila 3' Untranslated Regions", IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) 2012, Feb. 23-25, 2012, Las Vegas, Nevada, USA. DOI: 10.1109/ICCABS.2012.6182650
  3. Yuan Li and Shaojie Zhang*, "Finding consensus stable local optimal structures for aligned RNA sequences", IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) 2012, Feb. 23-25, 2012, Las Vegas, Nevada, USA. DOI: 10.1504/IJBRA.2014.062997
  4. Cuncong Zhong and Shaojie Zhang*, "Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment", Nucleic Acids Research, first published online: October 5, 2011. DOI: 10.1093/nar/gkr804
  5. Yuan Li and Shaojie Zhang*, "Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks", In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), 2011. DOI: 10.1186/1471-2105-13-S3-S5

2011

  1. Yuan Li and Shaojie Zhang*, "Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks", BMC Bioinformatics,Volume 13 (Supplement 3): S5, 2012. DOI: 10.1145/2147805.2147832
  2. Joseph Mazar, Divya Khaitan, Dan DeBlasio, Cuncong Zhong, Subramaniam S. Govindarajan, Sharmila Kopanathi, Shaojie Zhang, Animesh Ray, Ranjan J. Perera*, "Epigenetic Regulation of Micro-RNA Genes and the Role of miR-34b in Cell Invasion and Motility in Human Melanoma", PLoS ONE, 6(9): e24922, 2011. DOI: 10.1371/journal.pone.0024922
  3. Yuan Li and Shaojie Zhang*, "Finding Stable Local Optimal RNA Secondary Structures", Bioinformatics, 27(21) 2994-3001, 2011. (Epub 2011 Sep 8). DOI: 10.1093/bioinformatics/btr510
  4. Yuan Li, Aaron Halpern and Shaojie Zhang*, "TreeLign: simultaneous stepwise alignment and phylogenetic positioning, with its application to automatic phylogenetic assignment of 16S rRNAs", In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), 2011. DOI: 10.1145/2147805.2147868
  5. Joseph Mazar, Dan DeBlasio, Subramaniam Govindarajan, Shaojie Zhang, and Ranjan J. Perera*, "Epigenetic regulation of microRNA-375 and its role in melanoma development in humans", FEBS Letters, 26 Jun 2011. DOI: 10.1016/j.febslet.2011.06.025
  6. Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang*, "A Memory Efficient Method for Structure-Based RNA Multiple Alignment," IEEE/ACM Transactions on Computational Biology and Bioinformatics, Accepted on 29 Apr. 2011. DOI: 10.1109/TCBB.2011.86

2010

  1. Shaojie Zhang* and Cuncong Zhong, "Computational tools for RNA structural motif identification", Biotech International, Vol 22, page 6-9, Nov. 2010. Full Text: Full Text
  2. Cuncong Zhong, Haixu Tang, and Shaojie Zhang*, "RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment", Nucleic Acids Research Aug. 8, 2010. DOI: 10.1093/nar/gkq672

2009

  1. Daniel DeBlasio, Jocelyne Bruand, and Shaojie Zhang*, "PMFastR: A new approach to multiple RNA structure alignment", In: Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI 2009), Berlin: Springer-Verlag: LNBI Vol. 5724, pp. 49-61, 2009. DOI: 10.1007/978-3-642-04241-6_5

2006

  1. Buhm Han, Banu Dost, Vineet Bafna and Shaojie Zhang*, "Structural alignment of pseudoknotted RNA", Journal of Computational Biology, 15(5) page 489-504, 2008. DOI: 10.1007/11732990_13
  2. Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan and Vineet Bafna, "A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements", Bioinformatics (Proceedings of ISMB 2006) Vol. 22, No. 14, page e557-e565, 2006. DOI: 10.1093/bioinformatics/btl232
  3. Banu Dost, Buhm Han, Shaojie Zhang and Vineet Bafna, "Structural alignment of pseudoknotted RNA", In RECOMB 2006: Proceedings of the 10th annual international conference on research in computational molecular biology, 2006. DOI: 10.1007/11732990_13
  4. Vineet Bafna, Haixu Tang and Shaojie Zhang, "Consensus folding of unaligned RNA sequences revisited", Journal of Computational Biology, Vol. 13, No. 2, page 283-295, 2006. DOI: 10.1089/cmb.2006.13.283
  5. Vineet Bafna, Haixu Tang and Shaojie Zhang, "Consensus folding of unaligned RNA sequences revisited", In RECOMB 2005: Proceedings of the 9th annual international conference on research in computational molecular biology, 2005. DOI: 10.1089/cmb.2006.13.283

2005

  1. Shaojie Zhang, Brian Haas, Eleazar Eskin and Vineet Bafna, "Searching Genomes for non-coding RNA using FastR", IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 2(4) 366-379, 2005. DOI: 10.1109/TCBB.2005.57

2004

  1. Vineet Bafna and Shaojie Zhang, "FastR: Fast Database Search Tool for Non-coding RNA", In Proceedings of IEEE Computational Systems Bioinformatics (CSB 2004) Conference, page:52-61, 2004. DOI: 10.1109/csb.2004.1332417

2000

  1. Wen Zhang, Shaojie Zhang, Haixu Tang and Dafu Ding, "Reverse-Translated Alignment of EST Sequence with Protein Sequence", Acta. Biophysica Sinica, 16(2) page 322-333, 2000.