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Dr Qiongyi Zhao
Dr

Qiongyi Zhao

Email: 
Phone: 
+61 7 344 33573

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

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

51 works between 2011 and 2025

1 - 20 of 51 works

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

Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure

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

TRIAGE: an R package for regulatory gene analysis

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

Transcriptome-Wide Profiling of Nascent RNA in Neurons with Enriched H3K27ac Signal Elevates eRNA Identification Efficiency

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

starTracer is an accelerated approach for precise marker gene identification in single-cell RNA-Seq analysis

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

DNA G-quadruplex is a transcriptional control device that regulates memory

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

Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm

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

Chronically high stress hormone levels dysregulate sperm long noncoding RNAs and their embryonic microinjection alters development and affective behaviours

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

Fear extinction is regulated by the activity of long noncoding RNAs at the synapse

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

Experimentally induced active and quiet sleep engage non-overlapping transcriptional programs in Drosophila

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

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

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

Localised Cdr1as activity is required for fear extinction memory

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

Experimentally induced active and quiet sleep engage non-overlapping transcriptomes in Drosophila

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

ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3

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

The people behind the papers - Peter Kozulin, Rodrigo Suárez, Qiong-Yi Zhao, Linda Richards and Laura Fenlon

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

Divergent evolution of developmental timing in the neocortex revealed by marsupial and eutherian transcriptomes

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

Splicing factor proline and glutamine rich intron retention, reduced expression and aggregate formation are pathological features of amyotrophic lateral sclerosis

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

Genome-wide microRNA profiling in brain and blood samples in a mouse model of epileptogenesis

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

Adolescent chronic intermittent toluene inhalation dynamically regulates the transcriptome and neuronal methylome within the rat medial prefrontal cortex

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

Publisher Correction: Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction

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

Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction

Funding

Past funding

  • 2022
    Genotype Imputation Resources for Productive Genetic Disease Studies of Indigenous Oceanic Sub-Populations
    NHMRC IDEAS Grants
    Open grant
  • 2017 - 2018
    Cell-free DNA and ALS; insight into disease mechanisms and progression
    Motor Neurone Disease Research Institute of Australia Inc
    Open grant
  • 2016 - 2017
    Identification of phenotypic modifiers in sporadic ALS through systems genomics (Motor Neuron Disease Research Institute of Australia Inc project administered by Macquarie University)
    Macquarie University
    Open grant
  • 2015 - 2019
    Sporadic ALS Australian Systems Genomics Consortium (SALSA-SGC)
    Motor Neurone Disease Research Institute of Australia Inc
    Open grant
  • 2015
    Ian Potter Foundation Travel Grant to attend Keystone Symposia meeting on Neuroepigenetics, Santa Fe, Mexico, USA, 22-26 February 2015
    Ian Potter Foundation
    Open grant
  • 2014 - 2017
    Discovering deep sleep genes and determining their roles for preserving cognitive functions
    NHMRC Project Grant
    Open grant
  • 2014 - 2015
    Whole exome sequencing of sporadic MND
    Motor Neurone Disease Research Institute of Australia Inc
    Open grant

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

Media

Enquiries

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communications@uq.edu.au