
Overview
Background
I am a Research Fellow in Bioinformatics, holding a joint position with QBI the Bredy group (50%) and IMB the Palpant group (50%). With over 15 years of experience in the bioinformatics/NGS field, my journey began with the greenfield development of three NGS platforms: 454, Illumina, and SOLiD. This experience has equipped me with extensive expertise in bioinformatic analysis, particularly in analyzing a variety of NGS data types. As the leader of the bioinformatics core facility at QBI from 2012 to 2022, my role was primarily focused on providing bioinformatics services. However, I have also been actively engaged in custom programming and analysis for numerous projects, allowing me to make significant intellectual contributions and deepen my involvement in research studies. Despite the typical service-oriented position of bioinformaticians, my publication record is notable, featuring over 40 peer-reviewed publications, with me serving as the first, co-first, or last author on 16 of them. Since 2019, my work has garnered 1,525 citations (as per Google Scholar, as of 12 Jan 2024), with 41.2% of my publications ranking in the top 10% of journals based on the CiteScore Percentile Source from SciVal. My contributions to bioinformatics are showcased in prestigious journals, with notable examples including lncRNA capture sequencing and ATAC-seq data analysis (Nature Communications, 2023) and (Cell Reports, 2022), de novo transcriptome assembly (Development, 2022), noncanonical structure Z-DNA analysis (Nature Neuroscience, 2020), DNA modification m6dA data analysis (Nature Neuroscience, 2019), whole-exome sequencing data analysis (Genome Medicine, 2017), and cross-ethnic meta-analysis (Nature Communications, 2017).
Availability
- Dr Qiongyi Zhao is:
- Available for supervision
Fields of research
Qualifications
- Bachelor of Engineering, Shanghai Jiao Tong University
- Doctoral Diploma of Science (Advanced), University of the Chinese Academy of Science
Works
Search Professor Qiongyi Zhao’s works on UQ eSpace
2025
Journal Article
Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure
Shen, Sophie, Werner, Tessa, Lukowski, Samuel W., Andersen, Stacey, Sun, Yuliangzi, Shim, Woo Jun, Mizikovsky, Dalia, Kobayashi, Sakurako, Outhwaite, Jennifer, Chiu, Han Sheng, Chen, Xiaoli, Chapman, Gavin, Martin, Ella M. M. A., Xia, Di, Pham, Duy, Su, Zezhuo, Kim, Daniel, Yang, Pengyi, Tan, Men Chee, Sinniah, Enakshi, Zhao, Qiongyi, Negi, Sumedha, Redd, Meredith A., Powell, Joseph E., Dunwoodie, Sally L., Tam, Patrick P. L., Bodén, Mikael, Ho, Joshua W. K., Nguyen, Quan and Palpant, Nathan J. (2025). Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure. Nature Communications, 16 (1) 1356, 1356-1. doi: 10.1038/s41467-025-56533-2
2025
Journal Article
TRIAGE: an R package for regulatory gene analysis
Zhao, Qiongyi, Shim, Woo Jun, Sun, Yuliangzi, Sinniah, Enakshi, Shen, Sophie, Boden, Mikael and Palpant, Nathan J. (2025). TRIAGE: an R package for regulatory gene analysis. Briefings in Bioinformatics, 26 (1) bbaf004, 1-13. doi: 10.1093/bib/bbaf004
2024
Journal Article
Transcriptome-Wide Profiling of Nascent RNA in Neurons with Enriched H3K27ac Signal Elevates eRNA Identification Efficiency
Jiang, Jiazhi, Liu, Sha, Xu, Ziyue, Yu, Shuangqi, Wang, Lesheng, Long, Shengrong, Ye, Shengda, Yan, Yu, Xu, Hongyu, Zhang, Jianjian, Wei, Wei, Zhao, Qiongyi and Li, Xiang (2024). Transcriptome-Wide Profiling of Nascent RNA in Neurons with Enriched H3K27ac Signal Elevates eRNA Identification Efficiency. Acs Chemical Neuroscience. doi: 10.1021/acschemneuro.4c00047
2024
Journal Article
starTracer is an accelerated approach for precise marker gene identification in single-cell RNA-Seq analysis
Zhang, Feiyang, Huang, Kaixin, Chen, Ruixi, Liu, Zechen, Zhao, Qiongyi, Hou, Shengqun, Ma, Wenhao, Li, Yanze, Peng, Yan, Chen, Jincao, Wang, Dan Ohtan, Wei, Wei and Li, Xiang (2024). starTracer is an accelerated approach for precise marker gene identification in single-cell RNA-Seq analysis. Communications Biology, 7 (1) 1128. doi: 10.1038/s42003-024-06790-6
2024
Journal Article
DNA G-quadruplex is a transcriptional control device that regulates memory
Marshall, Paul R., Davies, Joshua, Zhao, Qiongyi, Liau, Wei-Siang, Lee, Yujin, Basic, Dean, Periyakaruppiah, Ambika, Zajaczkowski, Esmi L., Leighton, Laura J., Madugalle, Sachithrani U., Musgrove, Mason, Kielar, Marcin, Brueckner, Arie Maeve, Gong, Hao, Ren, Haobin, Walsh, Alexander, Kaczmarczyk, Lech, Jackson, Walker S., Chen, Alon, Spitale, Robert C. and Bredy, Timothy W. (2024). DNA G-quadruplex is a transcriptional control device that regulates memory. The Journal of Neuroscience, 44 (15) e0093232024, 1-20. doi: 10.1523/jneurosci.0093-23.2024
2024
Journal Article
Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm
Wu, Zhixuan, Shen, Sophie, Mizikovsky, Dalia, Cao, Yuanzhao, Naval-Sanchez, Marina, Tan, Siew Zhuan, Alvarez, Yanina D., Sun, Yuliangzi, Chen, Xiaoli, Zhao, Qiongyi, Kim, Daniel, Yang, Pengyi, Hill, Timothy A., Jones, Alun, Fairlie, David P., Pébay, Alice, Hewitt, Alex W., Tam, Patrick P.L., White, Melanie D., Nefzger, Christian M. and Palpant, Nathan J. (2024). Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm. Developmental Cell, 59 (6), 705-722.e8. doi: 10.1016/j.devcel.2024.01.019
2023
Journal Article
Chronically high stress hormone levels dysregulate sperm long noncoding RNAs and their embryonic microinjection alters development and affective behaviours
Hoffmann, L. B., Li, B., Wei, W., Zhao, Q., Leighton, L. J., Bredy, T. W., Pang, T. Y. and Hannan, A. J. (2023). Chronically high stress hormone levels dysregulate sperm long noncoding RNAs and their embryonic microinjection alters development and affective behaviours. Molecular Psychiatry, 29 (3), 590-601. doi: 10.1038/s41380-023-02350-2
2023
Journal Article
Fear extinction is regulated by the activity of long noncoding RNAs at the synapse
Liau, Wei-Siang, Zhao, Qiongyi, Bademosi, Adekunle, Gormal, Rachel S., Gong, Hao, Marshall, Paul R., Periyakaruppiah, Ambika, Madugalle, Sachithrani U., Zajaczkowski, Esmi L., Leighton, Laura J., Ren, Haobin, Musgrove, Mason, Davies, Joshua, Rauch, Simone, He, Chuan, Dickinson, Bryan C., Li, Xiang, Wei, Wei, Meunier, Frédéric A., Fernández-Moya, Sandra M., Kiebler, Michael A., Srinivasan, Balakumar, Banerjee, Sourav, Clark, Michael, Spitale, Robert C. and Bredy, Timothy W. (2023). Fear extinction is regulated by the activity of long noncoding RNAs at the synapse. Nature Communications, 14 (1) 7616, 1-16. doi: 10.1038/s41467-023-43535-1
2023
Journal Article
Experimentally induced active and quiet sleep engage non-overlapping transcriptional programs in Drosophila
Anthoney, Niki, Tainton-Heap, Lucy, Luong, Hang, Notaras, Eleni, Kewin, Amber B., Zhao, Qiongyi, Perry, Trent, Batterham, Philip, Shaw, Paul J. and van Swinderen, Bruno (2023). Experimentally induced active and quiet sleep engage non-overlapping transcriptional programs in Drosophila. eLife, 12 RP88198. doi: 10.7554/elife.88198
2023
Journal Article
Synapse-enriched m<sup>6</sup>A-modified Malat1 interacts with the novel m<sup>6</sup>A reader, DPYSL2, and is required for fear-extinction memory
Madugalle, Sachithrani U., Liau, Wei-Siang, Zhao, Qiongyi, Li, Xiang, Gong, Hao, Marshall, Paul R., Periyakaruppiah, Ambika, Zajaczkowski, Esmi L., Leighton, Laura J., Ren, Haobin, Musgrove, Mason R. B., Davies, Joshua W. A., Kim, Gwangmin, Rauch, Simone, He, Chuan, Dickinson, Bryan C., Fulopova, Barbora, Fletcher, Lee N., Williams, Stephen R., Spitale, Robert C. and Bredy, Timothy W. (2023). Synapse-enriched m6A-modified Malat1 interacts with the novel m6A reader, DPYSL2, and is required for fear-extinction memory. The Journal of Neuroscience, 43 (43), 7084-7100. doi: 10.1523/jneurosci.0943-23.2023
2023
Journal Article
Localised Cdr1as activity is required for fear extinction memory
Lau Zajaczkowski, Esmi, Zhao, Qiongyi, Liau, Wei-Siang, Gong, Hao, Madugalle, Sachithrani Umanda, Periyakaruppiah, Ambika, Leighton, Laura Jane, Musgrove, Mason, Ren, Haobin, Davies, Joshua, Marshall, Paul Robert and Bredy, Timothy William (2023). Localised Cdr1as activity is required for fear extinction memory. Neurobiology of Learning and Memory, 203 107777, 107777. doi: 10.1016/j.nlm.2023.107777
2023
Journal Article
Experimentally induced active and quiet sleep engage non-overlapping transcriptomes in Drosophila
Anthoney, Niki, Tainton-Heap, Lucy A. L., Luong, Hang, Notaras, Eleni, Zhao, Qiongyi, Perry, Trent, Batterham, Philip, Shaw, Paul J. and van Swinderen, Bruno (2023). Experimentally induced active and quiet sleep engage non-overlapping transcriptomes in Drosophila. eLife, 12. doi: 10.7554/eLife.88198.1
2022
Journal Article
ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3
Wei, Wei, Zhao, Qiongyi, Wang, Ziqi, Liau, Wei-Siang, Basic, Dean, Ren, Haobin, Marshall, Paul R., Zajaczkowski, Esmi L., Leighton, Laura J., Madugalle, Sachithrani U., Musgrove, Mason, Periyakaruppiah, Ambika, Shi, Jichun, Zhang, Jianjian, Mattick, John S., Mercer, Timothy R., Spitale, Robert C., Li, Xiang and Bredy, Timothy W. (2022). ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3. Cell Reports, 38 (12) 110546, 110546. doi: 10.1016/j.celrep.2022.110546
2022
Journal Article
The people behind the papers - Peter Kozulin, Rodrigo Suárez, Qiong-Yi Zhao, Linda Richards and Laura Fenlon
Kozulin, Peter, Zhao, Qiong-Yi, Richards, Linda, Fenlon, Laura and Suárez, Rodrigo (2022). The people behind the papers - Peter Kozulin, Rodrigo Suárez, Qiong-Yi Zhao, Linda Richards and Laura Fenlon. Development, 149 (3) dev200543. doi: 10.1242/dev.200543
2022
Journal Article
Divergent evolution of developmental timing in the neocortex revealed by marsupial and eutherian transcriptomes
Kozulin, Peter, Suárez, Rodrigo, Zhao, Qiong-Yi, Paolino, Annalisa, Richards, Linda J. and Fenlon, Laura R. (2022). Divergent evolution of developmental timing in the neocortex revealed by marsupial and eutherian transcriptomes. Development, 149 (3) dev200212. doi: 10.1242/dev.200212
2021
Journal Article
Splicing factor proline and glutamine rich intron retention, reduced expression and aggregate formation are pathological features of amyotrophic lateral sclerosis
Hogan, Alison L., Grima, Natalie, Fifita, Jennifer A., McCann, Emily P., Heng, Benjamin, Fat, Sandrine Chan Moi, Wu, Sharlynn, Maharjan, Ram, Cain, Amy K., Henden, Lyndal, Rayner, Stephanie, Tarr, Ingrid, Zhang, Katharine Y., Zhao, Qiongyi, Zhang, Zong-Hong, Wright, Amanda, Lee, Albert, Morsch, Marco, Yang, Shu, Williams, Kelly L. and Blair, Ian P. (2021). Splicing factor proline and glutamine rich intron retention, reduced expression and aggregate formation are pathological features of amyotrophic lateral sclerosis. Neuropathology and Applied Neurobiology, 47 (7) nan.12749, 990-1003. doi: 10.1111/nan.12749
2020
Journal Article
Genome-wide microRNA profiling in brain and blood samples in a mouse model of epileptogenesis
Chen, Min, Zhao, Qiong-Yi, Edson, Janette, Zhang, Zong Hong, Li, Xiang, Wei, Wei, Bredy, Timothy and Reutens, David C. (2020). Genome-wide microRNA profiling in brain and blood samples in a mouse model of epileptogenesis. Epilepsy Research, 166 106400, 106400. doi: 10.1016/j.eplepsyres.2020.106400
2020
Journal Article
Adolescent chronic intermittent toluene inhalation dynamically regulates the transcriptome and neuronal methylome within the rat medial prefrontal cortex
Dick, Alec L. W., Zhao, Qiongyi, Crossin, Rose, Baker-Andresen, Danay, Li, Xiang, Edson, Janette, Roeh, Simone, Marshall, Victoria, Bredy, Timothy W., Lawrence, Andrew J. and Duncan, Jhodie R. (2020). Adolescent chronic intermittent toluene inhalation dynamically regulates the transcriptome and neuronal methylome within the rat medial prefrontal cortex. Addiction Biology, 26 (3) e12937, e12937. doi: 10.1111/adb.12937
2020
Journal Article
Publisher Correction: Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction
Marshall, Paul R., Zhao, Qiongyi, Li, Xiang, Wei, Wei, Periyakaruppiah, Ambika, Zajaczkowski, Esmi L., Leighton, Laura J., Madugalle, Sachithrani U., Basic, Dean, Wang, Ziqi, Yin, Jiayu, Liau, Wei-Siang, Gupte, Ankita, Walkley, Carl R. and Bredy, Timothy W. (2020). Publisher Correction: Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction. Nature Neuroscience, 23 (8), 1034-1034. doi: 10.1038/s41593-020-0669-8
2020
Journal Article
Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction
Marshall, Paul R., Zhao, Qiongyi, Li, Xiang, Wei, Wei, Periyakaruppiah, Ambika, Zajaczkowski, Esmi L., Leighton, Laura J., Madugalle, Sachithrani U., Basic, Dean, Wang, Ziqi, Yin, Jiayu, Liau, Wei-Siang, Gupte, Ankita, Walkley, Carl R. and Bredy, Timothy W. (2020). Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction. Nature Neuroscience, 23 (6), 718-729. doi: 10.1038/s41593-020-0627-5
Funding
Past funding
Supervision
Availability
- Dr Qiongyi Zhao is:
- Available for supervision
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Supervision history
Current supervision
-
Doctor Philosophy
Exploring the role of chromatin associated RNAs and trans splicing in learning and memory
Associate Advisor
Other advisors: Professor Timothy Bredy
Completed supervision
-
2023
Master Philosophy
Long Noncoding RNAs: Needles or Straw in the Haystack?
Associate Advisor
Other advisors: Professor Timothy Bredy
Media
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