The University of Queensland

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, e0093232024. doi: 10.1523/jneurosci.0093-23.2024

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. doi: 10.1016/j.devcel.2024.01.019

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, 1-12. doi: 10.1038/s41380-023-02350-2

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

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

Synapse-enriched m⁶A-modified Malat1 interacts with the novel m⁶A 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

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

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

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

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

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

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

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

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

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

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

Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression

Tarr, Ingrid S., McCann, Emily P., Benyamin, Beben, Peters, Timothy J., Twine, Natalie A., Zhang, Katharine Y., Zhao, Qiongyi, Zhang, Zong-Hong, Rowe, Dominic B., Nicholson, Garth A., Bauer, Denis, Clark, Susan J., Blair, Ian P. and Williams, Kelly L. (2019). Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression. Scientific Reports, 9 (1) 8254, 8254. doi: 10.1038/s41598-019-44765-4

The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction

Li, Xiang, Zhao, Qiongyi, Wei, Wei, Lin, Quan, Magnan, Christophe, Emami, Michael R., Wearick-Silva, Luis E., Viola, Thiago W., Marshall, Paul R., Yin, Jiayu, Madugalle, Sachithrani U., Wang, Ziqi, Nainar, Sarah, Vågbø, Cathrine Broberg, Leighton, Laura J., Zajaczkowski, Esmi L., Ke, Ke, Grassi-Oliveira, Rodrigo, Bjørås, Magnar, Baldi, Pierre F., Spitale, Robert C. and Bredy, Timothy W. (2019). The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction. Nature Neuroscience, 22 (4), 534-544. doi: 10.1038/s41593-019-0339-x

Bioorthogonal metabolic labeling of nascent RNA in neurons improves the sensitivity of transcriptome-wide profiling

Zajaczkowski, Esmi L., Zhao, Qiong-Yi, Zhang, Zong Hong, Li, Xiang, Wei, Wei, Marshall, Paul R., Leighton, Laura J., Nainar, Sarah, Feng, Chao, Spitale, Robert C. and Bredy, Timothy W. (2018). Bioorthogonal metabolic labeling of nascent RNA in neurons improves the sensitivity of transcriptome-wide profiling. ACS Chemical Neuroscience, 9 (7), 1858-1865. doi: 10.1021/acschemneuro.8b00197

A Functional Role for the Epigenetic Regulator ING1 in Activity-induced Gene Expression in Primary Cortical Neurons

Leighton, Laura J., Zhao, Qiongyi, Li, Xiang, Dai, Chuanyang, Marshall, Paul R., Liu, Sha, Wang, Yi, Zajaczkowski, Esmi L., Khandelwal, Nitin, Kumar, Arvind, Bredy, Timothy W. and Wei, Wei (2017). A Functional Role for the Epigenetic Regulator ING1 in Activity-induced Gene Expression in Primary Cortical Neurons. Neuroscience, 369, 248-260. doi: 10.1016/j.neuroscience.2017.11.018

Whole-exome sequencing in amyotrophic lateral sclerosis suggests NEK1 is a risk gene in Chinese

Gratten, Jacob, Zhao, Qiongyi, Benyamin, Beben, Garton, Fleur, He, Ji, Leo, Paul J., Mangelsdorf, Marie, Anderson, Lisa, Zhang, Zong-Hong, Chen, Lu, Chen, Xiang-Ding, Cremin, Katie, Deng, Hong-Weng, Edson, Janette, Han, Ying-Ying, Harris, Jessica, Henders, Anjali K., Jin, Zi-Bing, Li, Zhongshan, Lin, Yong, Liu, Xiaolu, Marshall, Mhairi, Mowry, Bryan J., Ran, Shu, Reutens, David C., Song, Sharon, Tan, Li-Jun, Tang, Lu, Wallace, Robyn H. ... Fan, Dongsheng (2017). Whole-exome sequencing in amyotrophic lateral sclerosis suggests NEK1 is a risk gene in Chinese. Genome Medicine, 9 (97) 97, 97. doi: 10.1186/s13073-017-0487-0

Cross-ethnic meta-analysis identifies association of the GPX3-TNIP1 locus with amyotrophic lateral sclerosis

Benyamin, Beben, He, Ji, Zhao, Qiongyi, Gratten, Jacob, Garton, Fleur, Leo, Paul J., Liu, Zhijun, Mangelsdorf, Marie, Al-Chalabi, Ammar, Anderson, Lisa, Butler, Timothy J., Chen, Lu, Chen, Xiang-Ding, Cremin, Katie, Deng, Hong-Weng, Devine, Matthew, Edson, Janette, Fifita, Jennifer A., Furlong, Sarah, Han, Ying-Ying, Harris, Jessica, Henders, Anjali K., Jeffree, Rosalind L., Jin, Zi-Bing, Li, Zhongshan, Li, Ting, Li, Mengmeng, Lin, Yong, Liu, Xiaolu ... Fan, Dongsheng (2017). Cross-ethnic meta-analysis identifies association of the GPX3-TNIP1 locus with amyotrophic lateral sclerosis. Nature Communications, 8 (1) 611, 611. doi: 10.1038/s41467-017-00471-1

Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort

Garton, Fleur C., Benyamin, Beben, Zhao, Qiongyi, Liu, Zhijun, Gratten, Jacob, Henders, Anjali K., Zhang, Zong-Hong, Edson, Janette, Furlong, Sarah, Morgan, Sarah, Heggie, Susan, Thorpe, Kathryn, Pfluger, Casey, Mather, Karen A., Sachdev, Perminder S., McRae, Allan F., Robinson, Matthew R., Shah, Sonia, Visscher, Peter M., Mangelsdorf, Marie, Henderson, Robert D., Wray, Naomi R. and McCombe, Pamela A. (2017). Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics and Genomic Medicine, 5 (4), 418-428. doi: 10.1002/mgg3.302

Experience-dependent accumulation of N6-methyladenosine in the prefrontal cortex is associated with memory processes in mice

Widagdo, Jocelyn, Zhao, Qiong-Yi, Kempen, Marie-Jeanne, Tan, Men Chee, Ratnu, Vikram S., Wei, Wei, Leighton, Laura, Spadaro, Paola A., Edson, Janette, Anggono, Victor and Bredy, Timothy W. (2016). Experience-dependent accumulation of N6-methyladenosine in the prefrontal cortex is associated with memory processes in mice. Journal of Neuroscience, 36 (25), 6771-6777. doi: 10.1523/JNEUROSCI.4053-15.2016

De novo assembly of transcriptome from next-generation sequencing data

Li, Xuan, Kong, Yimeng, Zhao, Qiong-Yi, Li, Yuan-Yuan and Hao, Pei (2016). De novo assembly of transcriptome from next-generation sequencing data. Quantitative Biology, 4 (2), 94-105. doi: 10.1007/s40484-016-0069-y

Mapping and differential expression analysis from short-read RNA-Seq data in model organisms

Zhao, Qiong-Yi, Gratten, Jacob, Restaudi, Restuadi and Li, Xuan (2016). Mapping and differential expression analysis from short-read RNA-Seq data in model organisms. Quantitative Biology, 4 (1), 22-35. doi: 10.1007/s40484-016-0060-7

Rare DNA variants in the brain-derived neurotrophic factor gene increase risk for attention-deficit hyperactivity disorder: a next-generation sequencing study

Hawi, Z., Cummins, T.D.R., Tong, J., Arcos-Burgos, M., Zhao, Q., Matthews, N., Newman, D. P., Johnson, B., Vance, A., Heussler, H. S., Levy, F., Easteal, S., Wray, N. R., Kenny, E., Morris, D., Kent, L., Gill, M. and Bellgrove, M. A. (2016). Rare DNA variants in the brain-derived neurotrophic factor gene increase risk for attention-deficit hyperactivity disorder: a next-generation sequencing study. Molecular Psychiatry, 22 (4), 580-584. doi: 10.1038/mp.2016.117

Persistent variations in neuronal DNA methylation following cocaine self-administration and protracted abstinence in mice

Baker-Andresen, Danay, Zhao, Qiongyi, Li, Xiang, Jupp, Bianca, Chesworth, Rose, Lawrence, Andrew J. and Bredy, Timothy (2015). Persistent variations in neuronal DNA methylation following cocaine self-administration and protracted abstinence in mice. Neuroepigenetics, 4, 1-11. doi: 10.1016/j.nepig.2015.10.001

Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis)

Li, Chun-Fang, Zhu, Yan, Yu, Yao, Zhao, Qiong-Yi, Wang, Sheng-Jun, Wang, Xin-Chao, Yao, Ming-Zhe, Luo, Da, Li, Xuan, Chen, Liang and Yang, Ya-Jun (2015). Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis). BMC Genomics, 16 (560) 560. doi: 10.1186/s12864-015-1773-0

Purification of neural precursor cells reveals the presence of distinct, stimulus-specific subpopulations of quiescent precursors in the adult mouse hippocampus

Jhaveri, Dhanisha J., O'Keeffe, Imogen, Robinson, Gregory J., Zhao, Qiong-Yi, Zhang, Zong Hong, Nink, Virginia, Narayanan, Ramesh K., Osborne, Geoffrey W., Wray, Naomi R. and Bartlett, Perry F. (2015). Purification of neural precursor cells reveals the presence of distinct, stimulus-specific subpopulations of quiescent precursors in the adult mouse hippocampus. Journal of Neuroscience, 35 (21), 8132-8144. doi: 10.1523/JNEUROSCI.0504-15.2015

New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis

Lee, S. Hong, Byrne, Enda M., Hultman, Christina M., Kahler, Anna, Vinkhuyzen, Anna A. E., Ripke, Stephan, Andreassen, Ole A., Frisell, Thomas, Gusev, Alexander, Hu, Xinli, Karlsson, Robert, Mantzioris, Vasilis X., McGrath, John J., Mehta, Divya, Stahl, Eli A., Zhao, Qiongyi, Kendler, Kenneth S., Sullivan, Patrick F., Price, Alkes L., O'Donovan, Michael, Okada, Yukinori, Mowry, Bryan J., Raychaudhuri, Soumya, Wray, Naomi R., Schizophrenia Working Group of the Psychiatric Genomics Consortium, Rheumatoid Arthritis Consortium International and Visscher, Peter M . (2015). New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis. International Journal of Epidemiology, 44 (5) dyv136, 1-16. doi: 10.1093/ije/dyv136

Developing conversed microsatellite markers and their implications in evolutionary analysis of the Bemisia tabaci complex

Wang, Hua-Ling, Yang, Jiao, Boykin, Laura M., Zhao, Qiong-Yi, Wang, Yu-Jun, Liu, Shu-Sheng and Wang, Xiao-Wei (2014). Developing conversed microsatellite markers and their implications in evolutionary analysis of the Bemisia tabaci complex. Scientific Reports, 4 (1) 6351, 6351. doi: 10.1038/srep06351

Methyl CpG Binding Domain Ultra-Sequencing: a novel method for identifying inter-individual and cell-type-specific variation in DNA methylation

Li, X., Baker-Andresen, D., Zhao, Q., Marshall, V. and Bredy, T. W. (2014). Methyl CpG Binding Domain Ultra-Sequencing: a novel method for identifying inter-individual and cell-type-specific variation in DNA methylation. Genes, Brain and Behavior, 13 (7), 721-731. doi: 10.1111/gbb.12150

A comparative study of techniques for differential expression analysis on RNA-seq data

Zhang, Zong Hong, Jhaveri, Dhanisha J., Marshall, Vikki M., Bauer, Denis C., Edson, Janette, Narayanan, Ramesh K., Robinson, Gregory J., Lundberg, Andreas E., Bartlett, Perry F., Wray, Naomi R. and Zhao, Qiong-Yi (2014). A comparative study of techniques for differential expression analysis on RNA-seq data. PLoS One, 9 (8) e103207, 1-11. doi: 10.1371/journal.pone.0103207

Towards a molecular characterization of autism spectrum disorders: an exome sequencing and systems approach

An, J. Y., Cristino, A. S., Zhao, Q., Edson, J., Williams, S. M., Ravine, D., Wray, J., Marshall, V. M., Hunt, A., Whitehouse, A. J. O. and Claudianos, C. (2014). Towards a molecular characterization of autism spectrum disorders: an exome sequencing and systems approach. Translational Psychiatry, 4 (6) e394, e394.1-e394.9. doi: 10.1038/tp.2014.38

Transcriptomic analyses reveal the adaptive features and biological differences of guts from two invasive whitefly species

Ye, Xiao-Dong, Su, Yun-Lin, Zhao, Qiong-Yi, Xia, Wen-Qiang, Liu, Shu-Sheng and Wang, Xiao-We (2014). Transcriptomic analyses reveal the adaptive features and biological differences of guts from two invasive whitefly species. BMC Genomics, 15 (1) 370. doi: 10.1186/1471-2164-15-370

Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation

Li, Xiang, Wei, Wei, Zhao, Qiong-Yi, Widagdo, Jocelyn, Baker-Andresen, Danay, Flavell, Charlotte R., D'Alessio, Ana, Zhang, Yi and Bredy, Timothy W. (2014). Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation. Proceedings of the National Academy of Sciences, 111 (19), 7120-7125. doi: 10.1073/pnas.1318906111

Development of SNP and InDel markers via de novo transcriptome assembly in Sesamum indicum L

Wei, Libin, Miao, Hongmei, Li, Chun, Duan, Yinghui, Niu, Jiaojiao, Zhang, Tide, Zhao, Qiongyi and Zhang, Haiyang (2014). Development of SNP and InDel markers via de novo transcriptome assembly in Sesamum indicum L. Molecular Breeding, 34 (4), 2205-2217. doi: 10.1007/s11032-014-0174-4

Global transcriptome profiles of Camellia sinensis during cold acclimation

Wang, Xin-Chao, Zhao, Qiong-Yi, Ma, Chun-Lei, Zhang, Zong-Hong, Cao, Hong-Li, Kong, Yi-Meng, Yue, Chuan, Hao, Xin-Yuan, Chen, Liang, Ma, Jian-Qiang, Jin, Ji-Qiang, Li, Xuan and Yang, Ya-Jun (2013). Global transcriptome profiles of Camellia sinensis during cold acclimation. BMC Genomics, 14 (1) 415. doi: 10.1186/1471-2164-14-415

The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabaci complex

Wang, Hua-Ling, Yang, Jiao, Boykin, Laura M., Zhao, Qiong-Yi, Li, Qian, Wang, Xiao-Wei and Liu, Shu-Sheng (2013). The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabaci complex. BMC Genomics, 14 (1) 401. doi: 10.1186/1471-2164-14-401

Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species

Wang, Xiao-Wei, Zhao, Qiong-Yi, Luan, Jun-Bo, Wang, Yu-Jun, Yan, Gen-Hong and Liu, Shu-Sheng (2012). Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species. BMC Genomics, 13 (1) 529, 529.1-529.13. doi: 10.1186/1471-2164-13-529

Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome

Shao, Wei, Zhao, Qiong-Yi, Wang, Xiu-Ye, Xu, Xin-Yan, Tang, Qing, Li, Muwang, Li, Xuan and Xu, Yong-Zhen (2012). Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome. RNA, 18 (7), 1395-1407. doi: 10.1261/rna.029751.111

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

Zhao, Qiong-Yi, Wang, Yi, Kong, Yi-Meng, Luo, Da, Li, Xuan and Hao, Pei (2011). Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics, 12 (Suppl. 14) S2, 1-12. doi: 10.1186/1471-2105-12-S14-S2

Activity-dependent RNA methylation in learning and memory

Widagdo, J., Zhao, Q. -Y., Anggono, V. and Bredy, T. (2015). Activity-dependent RNA methylation in learning and memory. 25th Biennial Meeting of the International Society for Neurochemistry Jointly with the 13th Meeting of the Asian Pacific Society for Neurochemistry in Conjunction with the 35th Meeting of the Australasian Neuroscience Society, Cairns, QLD Australia, 23-27 August 2015. Chichester, West Sussex, United Kingdom: Wiley-Blackwell Publishing. doi: 10.1111/jnc.13188

Epitranscriptomic mechanisms of memory stability

Bredy, T., Widagdo, J. and Zhao, Q.-Y. (2015). Epitranscriptomic mechanisms of memory stability. 25th Biennial Meeting of the International Society for Neurochemistry Jointly with the 13th Meeting of the Asian Pacific Society for Neurochemistry in Conjunction with the 35th Meeting of the Australasian Neuroscience Society, Cairns, QLD Australia, 23-27 August 2015. Chichester, West Sussex, United Kingdom: Wiley-Blackwell Publishing. doi: 10.1111/jnc.13185

Exploring the role of histone demethylase, UTX, in mediating sex differences in fear-related learning and memory

Ratnu, V., Li, X., Emami, M., Zhao, Q. -Y. and Bredy, T. (2015). Exploring the role of histone demethylase, UTX, in mediating sex differences in fear-related learning and memory. 25th Biennial Meeting of the International Society for Neurochemistry Jointly with the 13th Meeting of the Asian Pacific Society for Neurochemistry in Conjunction with the 35th Meeting of the Australasian Neuroscience Society, Cairns, QLD Australia, 23-27 August 2015. Chichester, West Sussex, United Kingdom: Wiley-Blackwell Publishing. doi: 10.1111/jnc.13188