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2025 Journal Article Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressureShen, 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 |
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2025 Journal Article TRIAGE: an R package for regulatory gene analysisZhao, 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 |
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2024 Journal Article Transcriptome-Wide Profiling of Nascent RNA in Neurons with Enriched H3K27ac Signal Elevates eRNA Identification EfficiencyJiang, 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 |
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2024 Journal Article starTracer is an accelerated approach for precise marker gene identification in single-cell RNA-Seq analysisZhang, 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 |
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2024 Journal Article DNA G-quadruplex is a transcriptional control device that regulates memoryMarshall, 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 |
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2024 Journal Article Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesodermWu, 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 |
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2023 Journal Article Chronically high stress hormone levels dysregulate sperm long noncoding RNAs and their embryonic microinjection alters development and affective behavioursHoffmann, 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 |
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2023 Journal Article Fear extinction is regulated by the activity of long noncoding RNAs at the synapseLiau, 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 |
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2023 Journal Article Experimentally induced active and quiet sleep engage non-overlapping transcriptional programs in DrosophilaAnthoney, 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 |
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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 memoryMadugalle, 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 |
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2023 Journal Article Localised Cdr1as activity is required for fear extinction memoryLau 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 |
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2023 Journal Article Experimentally induced active and quiet sleep engage non-overlapping transcriptomes in DrosophilaAnthoney, 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 |
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2022 Journal Article ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3Wei, 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 |
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2022 Journal Article The people behind the papers - Peter Kozulin, Rodrigo Suárez, Qiong-Yi Zhao, Linda Richards and Laura FenlonKozulin, 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 |
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2022 Journal Article Divergent evolution of developmental timing in the neocortex revealed by marsupial and eutherian transcriptomesKozulin, 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 |
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2021 Journal Article Splicing factor proline and glutamine rich intron retention, reduced expression and aggregate formation are pathological features of amyotrophic lateral sclerosisHogan, 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 |
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2020 Journal Article Genome-wide microRNA profiling in brain and blood samples in a mouse model of epileptogenesisChen, 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 |
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2020 Journal Article Adolescent chronic intermittent toluene inhalation dynamically regulates the transcriptome and neuronal methylome within the rat medial prefrontal cortexDick, 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 |
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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 extinctionMarshall, 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 |
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2020 Journal Article Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinctionMarshall, 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 |
