Selected publications at refereed Journals: (* = corresponding/senior author; # = graduate student or post-doc advised by Qi; ## = undergraduate or high school student advised by Qi; † = equal contribution. )
For publications after 2021 and a more complete list, please check out at : https://scholar.google.com/citations?user=ZYfzV8UAAAAJ&hl=en
36. Jianping Zhou, Rui Zhang, Xinyu Jia, Xu Tang, Yachong Guo, Han Yang, Xuelian Zheng, Qian Qian*, Yiping Qi*, Yong Zhang*. CRISPR-Cas9 mediated OsMIR168a knockout reveals its pleiotropy in rice. Plant Biotechnology Journal, 2021. https://onlinelibrary.wiley.com/doi/10.1111/pbi.13713
35. Kutubuddin Molla*, Simon Sretenovic#, Yiping Qi*. Precise plant genome editing with base editors and prime editors. Nature Plants, 2021, 7: 1166-1187. https://www.nature.com/articles/s41477-021-00991-1
34. Md. Mahmudul Hassan Ɨ, Yingxiao Zhang#, Ɨ, Guoliang Yuan, Kuntal De, Jin-Gui Chen, Wellington Muchero, Gerald A. Tuskan, Yiping Qi*, Xiaohan Yang*. Construct design for CRISPR/Cas-based genome editing in plants. Trends in Plant Science, 2021, https://www.cell.com/trends/plant-science/fulltext/S1360-1385(21)00157-6
33. Changtian Pan#, Xincheng Wu##, Kasey Markel, Aimee A. Malzahn#, Neil Kundagrami##, Simon Sretenovic#, Yingxiao Zhang#, Yanhao Cheng#, Patrick M Shih, Yiping Qi*. CRISPR-Act3.0 for highly efficient multiplexed gene activation in plants. Nature Plants, 2021. https://www.nature.com/articles/s41477-021-00953-7
32. Shujuan Zhang†, Rongzhi Zhang†, Jie Gao, Guoqi Song, Jihu Li, Wei Li, Yiping Qi, Yulian Li*, Genying Li*. CRISPR/Cas9-mediated genome editing for wheat grain quality improvement. Plant Biotechnology Journal, 2021. https://doi.org/10.1111/pbi.13647
31. Qiurong RenƗ, Simon Sretenovic#, Ɨ, Guanqing Liu Ɨ, Zhaohui Zhong, Jiaheng Wang, Lan Huang, Xu Tang, Yachong Guo, Li Liu, Yuechao Wu, Jie Zhou, Yuxin Zhao, Han Yang, Yao He, Shishi Liu, Desuo Yin#, Rocio Mayorga##, Xuelian Zheng, Tao Zhang*, Yiping Qi*, Yong Zhang*. Improved plant cytosine base editors with high editing activity, purity, and specificity. Plant Biotechnology Journal, 2021. https://doi.org/10.1111/pbi.13635
30. Linnell Bentley Randall Ɨ, Simon Sretenovic#, Ɨ, Yuechao WuƗ, Desuo Yin#, Tao Zhang*, Joyce Van Eck*, Yiping Qi*. Genome and transcriptome-wide off-target analyses of an improved cytidine base editor in tomato. Plant Physiology, 2021. https://doi.org/10.1093/plphys/kiab264
29. Yingxiao Zhang#, Ɨ, Qiurong RenƗ, Xu Tang,Ɨ, Shishi Liu, Aimee A. Malzahn#,Jiaheng Wang, Desuo Yin#, Changtian Pan#, Mingzhu Yuan, Lan Huang, Han Yang, Yuxin Zhao, Qing Fang, Xuelian Zheng, Li Tian, Yanhao Cheng, Ysa Le##, Bailey McCoy##, Lidiya Franklin##, Jeremy D. Selengut#, Stephen M. Mount, Qiudeng Que, Yong Zhang*, Yiping Qi*. Expanding the scope of plant genome engineering with novel Cas12a orthologs and highly multiplexable editing systems. Nature Communications, 2021, https://www.nature.com/articles/s41467-021-22330-w
28. Gen Li#, †, Simon Sretenovic#, †, Edward Eisenstein, Gary Coleman*, Yiping Qi*. Highly efficient C-to-T and A-to-G base editing in a Populus hybrid. Plant Biotechnology Journal, 2021 Mar 20. onlinelibrary.wiley.com/doi/full/10.1111/pbi.13581
27. Jianping Zhou, Mingzhu Yuan, Yuxin Zhao, Quan Quan, Dong Yu, Han Yang, Xu Tang, Xuhui Xin, Guangze Cai, Qian Qian, Yiping Qi*, Yong Zhang*. Efficient deletion of multiple circle RNA loci by CRISPR‐Cas9 reveals Os06circ02797 as a putative sponge for OsMIR408 in rice. Plant Biotechnology Journal, 2021, https://doi.org/10.1111/pbi.13544
26. Changtian Pan#, Simon Sretenovic#, Yiping Qi*. CRISPR/dCas-mediated transcriptional and epigenetic regulation in plants. Current Opinion in Plant Biology, 2021, 60, 101980. https://doi.org/10.1016/j.pbi.2020.101980
25. Simon Sretenovic#, Ɨ, Desuo Yin#, Ɨ, Adam Levav#, Jeremy D. Selengut#, Stephen M. Mount, Yiping Qi*. Expanding Plant Genome Editing Scope by An Engineered iSpyMacCas9 Targeting the A-rich PAM Sequences. Plant Communications, 2021. https://doi.org/10.1016/j.xplc.2020.100101
24. Yingxiao Zhang#, Brian Iaffaldano, Yiping Qi*. CRISPR ribonucleoprotein-mediated genetic engineering in plants. Plant Communications, 2021..https://doi.org/10.1016/j.xplc.2021.100168
23. Qiurong Ren Ɨ, Simon Sretenovic#, Ɨ, Shishi LiuƗ, Xu Tang, Lan Huang, Yao He, Li Liu, Yachong Guo, Zhaohui Zhong, Guanqing Liu, Yanhao Cheng#, Xuelian Zheng, Changtian Pan#, Desuo Yin#, Yingxiao Zhang#, Wanfeng Li, Liwang Qi, Chenghao Li, Yiping Qi*, Yong Zhang*. PAM-less plant genome editing using a CRISPR–SpRY toolbox. Nature Plants, 2021, 7: 25-33. https://www.nature.com/articles/s41477-020-00827-4
22. Jihu Li, Shujuan Zhang, Rongzhi Zhang, Jie Gao, Yiping Qi, Guoqi Song, Wei Li, Yulian Li, Genying Li. Efficient multiplex genome editing by CRISPR/Cas9 in common wheat. Plant Biotechnology Journal, 2020. https://doi.org/10.1111/pbi.13508
21. Kutubuddin A. Molla, Yiping Qi, Subhasis Karmakar, Mirza J. Baig. Base Editing Landscape Extends to Perform Transversion Mutation. Trends in Genetics, 2020, 36 (12): 899-901. https://doi.org/10.1016/j.tig.2020.09.001
20. Xu Tang Ɨ, Simon Sretenovic#, Ɨ, Qiurong Ren Ɨ, Xinyu Jia, Mengke Li, Tingting Fan Desuo Yin#, Shuyue Xiang, Yachong Guo, Li Liu, Xuelian Zheng, Yiping Qi*, Yong Zhang*. Plant Prime Editors Enable Precise Gene Editing in Rice Cells, Molecular Plant, 2020. https://doi.org/10.1016/j.molp.2020.03.010
19. Meiling Ming#,Ɨ, Qiurong RenƗ, Changtian Pan#,Ɨ, Yao He Ɨ, Yingxiao Zhang#, Ɨ, Shishi Liu, Zhaohui Zhong, Jiaheng Wang, Aimee A. Malzahn#, Jun Wu, Xuelian Zheng, Yong Zhang*, Yiping Qi*. CRISPR-Cas12b enables efficient plant genome engineering. Nature Plants, 2020 Mar;6(3):202-208. https://www.nature.com/articles/s41477-020-0614-6
18. Shaoya Li, Yingxiao Zhang#, Lanqin Xia*, Yiping Qi*. CRISPR-Cas12a enables efficient biallelic gene targeting in rice. Plant Biotechnology Journal. 2019 Nov 15. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13295
17. Yingxiao Zhang#, Aimee A Malzahn#, Simon Sretenovic# and Yiping Qi*. The emerging and uncultivated potential of CRISPR technology in plant science. Nature Plants, 2019, https://www.nature.com/articles/s41477-019-0461-5
16. Zhaohui Zhong Ɨ, Simon Sretenovic Ɨ,#, Qiurong RenƗ, Lijia Yang, Yu Bao, Caiyan Qi, Mingzhu Yuan, Yao He, Shishi Liu, Xiaopei Liu, Jiaheng Wang, Lan Huang,Yan Wang, Dibin Baby##, David Wang##, Tao Zhang, Yiping Qi*, Yong Zhang*. Improving plant genome editing with high-fidelity xCas9 and non-canonical PAM-targeting Cas9-NG. Molecular Plant. 2019 Mar. https://doi.org/10.1016/j.molp.2019.03.011
15. Aimee A. Malzahn†,#, Xu Tang†, Keunsub Lee, Qiurong Ren, Simon Sretenovic#, Yingxiao Zhang#, Hongqiao Chen, Minjeong Kang, Yu Bao, Xuelian Zheng, Kejun Deng, Tao Zhang, Valeria Salcedo##, Kan Wang, Yong Zhang*, Yiping Qi*. Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis. BMC Biology. 2019 Jan 31;17(1):9. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0629-5
14. Xu Tang†, Qiurong Ren† Lijia Yang, Yu Bao, Zhaohui Zhong, Yao He, Shishi Liu, Caiyan Qi, Binglin Liu, Yan Wang, Simon Sretenovic#, Yingxiao Zhang#, Xuelian Zheng, Tao Zhang*, Yiping Qi*, Yong Zhang*. Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas12a mediated plant genome editing. Plant Biotechnology Journal. 2018, https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.13068
13. Keunsub Lee, Yingxiao Zhang#, Benjamin P. Kleinstiver, Jimmy A. Guo, Martin J. Aryee, Jonah Miller, Aimee Malzahn#, Scott Zarecor, Carolyn J. Lawrence-Dill, J. Keith Joung, Yiping Qi*, and Kan Wang*. Activities and specificities of CRISPR-Cas9 and Cas12a nucleases for targeted mutagenesis in maize. Plant Biotechnology Journal. 2018, https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.12982
12. Xu TangƗ, Guanqing LiuƗ, Jianping ZhouƗ, Qiurong Ren, Qi You, Li Tian, Xuhui Xin, Zhaohui Zhong, Binglin Liu, Xuelian Zheng, Dengwei Zhang, Aimee Malzahn#, Zhiyun Gong, Yiping Qi*, Tao Zhang*, Yong Zhang*. A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biology. 2018, 19:84 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1458-5
11. Zhaohui Zhong†, Yingxiao Zhang†,#, Qi You†, Xu Tang, Qiurong Ren, Shishi Liu, Lijia Yang, Yan Wang, Xiaopei Liu, Binglin Liu, Tao Zhang, Xuelian Zheng, Ysa Le##, Yong Zhang*, Yiping Qi*. Plant genome editing using FnCpf1 and LbCpf1 nucleases at redefined and altered PAM sites. Molecular Plant. 2018. DOI: https://doi.org/10.1016/j.molp.2018.03.008
10. Levi G. Lowder#, Jianping Zhou, Yingxiao Zhang#, Aimee Malzahn#, Zhaohui Zhong, Tzung-Fu Hsieh, Daniel F. Voytas, Yong Zhang, Yiping Qi*. Robust transcriptional activation in plants using multiplexed CRISPR-Act2.0 and mTALE-Act systems. Molecular Plant. 2018 Feb 5;11(2):245-256. doi: 10.1016/j.molp.2017.11.010. http://www.cell.com/molecular-plant/fulltext/S1674-2052(17)30344-1
9. Xu Tang†, Levi G. Lowder†, Tao Zhang, Aimee A. Malzahn, Xuelian Zheng, Daniel F. Voytas, Zhaohui Zhong, Yiyi Chen, Qiurong Ren, Qian Li, Elida R. Kirkland, Yong Zhang*, Yiping Qi*. A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nature Plants, 2017, https://www.nature.com/articles/nplants201718
8. Xu Tang, Xuelian Zheng, Yiping Qi, Dengwei Zhang, Yan Cheng, Aiting Tang, Daniel F Voytas, Yong Zhang. A single transcript CRISPR-Cas9 system for efficient genome editing in plants. Molecular Plant, 2016, 9 (7): 1088-1091. http://www.cell.com/molecular-plant/abstract/S1674-2052%2816%2930057-0
7. Levi G. Lowder†#, Dengwei Zhang†, Nicholas J. Baltes, Joseph W. Paul, III##, Tang Xu, Xuelian Zheng, Daniel F. Voytas , Tzung-Fu Hsieh, Yong Zhang*, Yiping Qi*. A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation. Plant Physiology, 2015 Oct;169(2):971-85. https://academic.oup.com/plphys/article/169/2/971/6114041
6. Hua Shi, Qiujing Shen, Yiping Qi, Haozhen Nie, Yongfang Chen, Ting Zhao,Fumiaki Katagiri, Dingzhong Tang. Arabidopsis BR-SIGNALING KINASE1 physically associates with the PAMP receptor FLAGELLIN SENSING2 and regulates plant innate immunity. Plant Cell, 2013, 25 (3):1143-57. academic.oup.com/plcell/article/25/3/1143/6097647
5. Yiping Qi†, Yong Zhang†, Feng Zhang, Joshua A. Baller, Spencer C. Cleland#, Yungil Ryu#, Colby G. Starker and Daniel F. Voytas. Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways. Genome Research, 2013, 23 (3):547-54.genome.cshlp.org/content/23/3/547.short
4. Yong Zhang, Feng Zhang, Xiaohong Li, Joshua Baller, Yiping Qi, Colby G. Starker, and Daniel F. Voytas. Transcription Activator-Like Effector Nucleases enable efficient plant genome engineering. Plant Physiology, 2013, 161(1):20-7.https://academic.oup.com/plphys/article/161/1/20/6110556
3. Kenichi Tsuda, Yiping Qi, Le V. Nguyen, Gerit Bethke, Yayoi Tsuda, Jane Glazebrook, and Fumiaki Katagiri. An efficient Agrobacterium-mediated transient transformation of Arabidopsis. The Plant Journal, 2012, 69 (4): 713-719. onlinelibrary.wiley.com/doi/full/10.1111/j.1365-313X.2011.04819.x
2. Jeffry D Sander,Elizabeth J Dahlborg,Mathew J Goodwin,Lindsay Cade,Feng Zhang,Daniel Cifuentes,Shaun J Curtin,Jessica S Blackburn,Stacey Thibodeau-Beganny,Yiping Qi,Christopher J Pierick,Ellen Hoffman,Morgan L Maeder,Cyd Khayter,Deepak Reyon,Drena Dobbs,David M Langenau,Robert M Stupar,Antonio J Giraldez,Daniel F Voytas,Randall T Peterson,Jing-Ruey J Yeh& J Keith Joung. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nature Methods, 2011,8: 67-69. https://www.nature.com/articles/nmeth.1542
1. Yiping Qi, Fumiaki Katagiri. Purification of low-abundance Arabidopsis plasma- membrane protein complexes and identification of candidate components. The Plant Journal, 2009, 57(5): 932-944. onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2008.03736.x
--------
Complete publication list and citations are available at Google scholar: https://scholar.google.com/citations?user=ZYfzV8UAAAAJ&hl=en
For publications after 2021 and a more complete list, please check out at : https://scholar.google.com/citations?user=ZYfzV8UAAAAJ&hl=en
36. Jianping Zhou, Rui Zhang, Xinyu Jia, Xu Tang, Yachong Guo, Han Yang, Xuelian Zheng, Qian Qian*, Yiping Qi*, Yong Zhang*. CRISPR-Cas9 mediated OsMIR168a knockout reveals its pleiotropy in rice. Plant Biotechnology Journal, 2021. https://onlinelibrary.wiley.com/doi/10.1111/pbi.13713
35. Kutubuddin Molla*, Simon Sretenovic#, Yiping Qi*. Precise plant genome editing with base editors and prime editors. Nature Plants, 2021, 7: 1166-1187. https://www.nature.com/articles/s41477-021-00991-1
34. Md. Mahmudul Hassan Ɨ, Yingxiao Zhang#, Ɨ, Guoliang Yuan, Kuntal De, Jin-Gui Chen, Wellington Muchero, Gerald A. Tuskan, Yiping Qi*, Xiaohan Yang*. Construct design for CRISPR/Cas-based genome editing in plants. Trends in Plant Science, 2021, https://www.cell.com/trends/plant-science/fulltext/S1360-1385(21)00157-6
33. Changtian Pan#, Xincheng Wu##, Kasey Markel, Aimee A. Malzahn#, Neil Kundagrami##, Simon Sretenovic#, Yingxiao Zhang#, Yanhao Cheng#, Patrick M Shih, Yiping Qi*. CRISPR-Act3.0 for highly efficient multiplexed gene activation in plants. Nature Plants, 2021. https://www.nature.com/articles/s41477-021-00953-7
32. Shujuan Zhang†, Rongzhi Zhang†, Jie Gao, Guoqi Song, Jihu Li, Wei Li, Yiping Qi, Yulian Li*, Genying Li*. CRISPR/Cas9-mediated genome editing for wheat grain quality improvement. Plant Biotechnology Journal, 2021. https://doi.org/10.1111/pbi.13647
31. Qiurong RenƗ, Simon Sretenovic#, Ɨ, Guanqing Liu Ɨ, Zhaohui Zhong, Jiaheng Wang, Lan Huang, Xu Tang, Yachong Guo, Li Liu, Yuechao Wu, Jie Zhou, Yuxin Zhao, Han Yang, Yao He, Shishi Liu, Desuo Yin#, Rocio Mayorga##, Xuelian Zheng, Tao Zhang*, Yiping Qi*, Yong Zhang*. Improved plant cytosine base editors with high editing activity, purity, and specificity. Plant Biotechnology Journal, 2021. https://doi.org/10.1111/pbi.13635
30. Linnell Bentley Randall Ɨ, Simon Sretenovic#, Ɨ, Yuechao WuƗ, Desuo Yin#, Tao Zhang*, Joyce Van Eck*, Yiping Qi*. Genome and transcriptome-wide off-target analyses of an improved cytidine base editor in tomato. Plant Physiology, 2021. https://doi.org/10.1093/plphys/kiab264
29. Yingxiao Zhang#, Ɨ, Qiurong RenƗ, Xu Tang,Ɨ, Shishi Liu, Aimee A. Malzahn#,Jiaheng Wang, Desuo Yin#, Changtian Pan#, Mingzhu Yuan, Lan Huang, Han Yang, Yuxin Zhao, Qing Fang, Xuelian Zheng, Li Tian, Yanhao Cheng, Ysa Le##, Bailey McCoy##, Lidiya Franklin##, Jeremy D. Selengut#, Stephen M. Mount, Qiudeng Que, Yong Zhang*, Yiping Qi*. Expanding the scope of plant genome engineering with novel Cas12a orthologs and highly multiplexable editing systems. Nature Communications, 2021, https://www.nature.com/articles/s41467-021-22330-w
28. Gen Li#, †, Simon Sretenovic#, †, Edward Eisenstein, Gary Coleman*, Yiping Qi*. Highly efficient C-to-T and A-to-G base editing in a Populus hybrid. Plant Biotechnology Journal, 2021 Mar 20. onlinelibrary.wiley.com/doi/full/10.1111/pbi.13581
27. Jianping Zhou, Mingzhu Yuan, Yuxin Zhao, Quan Quan, Dong Yu, Han Yang, Xu Tang, Xuhui Xin, Guangze Cai, Qian Qian, Yiping Qi*, Yong Zhang*. Efficient deletion of multiple circle RNA loci by CRISPR‐Cas9 reveals Os06circ02797 as a putative sponge for OsMIR408 in rice. Plant Biotechnology Journal, 2021, https://doi.org/10.1111/pbi.13544
26. Changtian Pan#, Simon Sretenovic#, Yiping Qi*. CRISPR/dCas-mediated transcriptional and epigenetic regulation in plants. Current Opinion in Plant Biology, 2021, 60, 101980. https://doi.org/10.1016/j.pbi.2020.101980
25. Simon Sretenovic#, Ɨ, Desuo Yin#, Ɨ, Adam Levav#, Jeremy D. Selengut#, Stephen M. Mount, Yiping Qi*. Expanding Plant Genome Editing Scope by An Engineered iSpyMacCas9 Targeting the A-rich PAM Sequences. Plant Communications, 2021. https://doi.org/10.1016/j.xplc.2020.100101
24. Yingxiao Zhang#, Brian Iaffaldano, Yiping Qi*. CRISPR ribonucleoprotein-mediated genetic engineering in plants. Plant Communications, 2021..https://doi.org/10.1016/j.xplc.2021.100168
23. Qiurong Ren Ɨ, Simon Sretenovic#, Ɨ, Shishi LiuƗ, Xu Tang, Lan Huang, Yao He, Li Liu, Yachong Guo, Zhaohui Zhong, Guanqing Liu, Yanhao Cheng#, Xuelian Zheng, Changtian Pan#, Desuo Yin#, Yingxiao Zhang#, Wanfeng Li, Liwang Qi, Chenghao Li, Yiping Qi*, Yong Zhang*. PAM-less plant genome editing using a CRISPR–SpRY toolbox. Nature Plants, 2021, 7: 25-33. https://www.nature.com/articles/s41477-020-00827-4
22. Jihu Li, Shujuan Zhang, Rongzhi Zhang, Jie Gao, Yiping Qi, Guoqi Song, Wei Li, Yulian Li, Genying Li. Efficient multiplex genome editing by CRISPR/Cas9 in common wheat. Plant Biotechnology Journal, 2020. https://doi.org/10.1111/pbi.13508
21. Kutubuddin A. Molla, Yiping Qi, Subhasis Karmakar, Mirza J. Baig. Base Editing Landscape Extends to Perform Transversion Mutation. Trends in Genetics, 2020, 36 (12): 899-901. https://doi.org/10.1016/j.tig.2020.09.001
20. Xu Tang Ɨ, Simon Sretenovic#, Ɨ, Qiurong Ren Ɨ, Xinyu Jia, Mengke Li, Tingting Fan Desuo Yin#, Shuyue Xiang, Yachong Guo, Li Liu, Xuelian Zheng, Yiping Qi*, Yong Zhang*. Plant Prime Editors Enable Precise Gene Editing in Rice Cells, Molecular Plant, 2020. https://doi.org/10.1016/j.molp.2020.03.010
19. Meiling Ming#,Ɨ, Qiurong RenƗ, Changtian Pan#,Ɨ, Yao He Ɨ, Yingxiao Zhang#, Ɨ, Shishi Liu, Zhaohui Zhong, Jiaheng Wang, Aimee A. Malzahn#, Jun Wu, Xuelian Zheng, Yong Zhang*, Yiping Qi*. CRISPR-Cas12b enables efficient plant genome engineering. Nature Plants, 2020 Mar;6(3):202-208. https://www.nature.com/articles/s41477-020-0614-6
18. Shaoya Li, Yingxiao Zhang#, Lanqin Xia*, Yiping Qi*. CRISPR-Cas12a enables efficient biallelic gene targeting in rice. Plant Biotechnology Journal. 2019 Nov 15. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13295
17. Yingxiao Zhang#, Aimee A Malzahn#, Simon Sretenovic# and Yiping Qi*. The emerging and uncultivated potential of CRISPR technology in plant science. Nature Plants, 2019, https://www.nature.com/articles/s41477-019-0461-5
16. Zhaohui Zhong Ɨ, Simon Sretenovic Ɨ,#, Qiurong RenƗ, Lijia Yang, Yu Bao, Caiyan Qi, Mingzhu Yuan, Yao He, Shishi Liu, Xiaopei Liu, Jiaheng Wang, Lan Huang,Yan Wang, Dibin Baby##, David Wang##, Tao Zhang, Yiping Qi*, Yong Zhang*. Improving plant genome editing with high-fidelity xCas9 and non-canonical PAM-targeting Cas9-NG. Molecular Plant. 2019 Mar. https://doi.org/10.1016/j.molp.2019.03.011
15. Aimee A. Malzahn†,#, Xu Tang†, Keunsub Lee, Qiurong Ren, Simon Sretenovic#, Yingxiao Zhang#, Hongqiao Chen, Minjeong Kang, Yu Bao, Xuelian Zheng, Kejun Deng, Tao Zhang, Valeria Salcedo##, Kan Wang, Yong Zhang*, Yiping Qi*. Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis. BMC Biology. 2019 Jan 31;17(1):9. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0629-5
14. Xu Tang†, Qiurong Ren† Lijia Yang, Yu Bao, Zhaohui Zhong, Yao He, Shishi Liu, Caiyan Qi, Binglin Liu, Yan Wang, Simon Sretenovic#, Yingxiao Zhang#, Xuelian Zheng, Tao Zhang*, Yiping Qi*, Yong Zhang*. Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas12a mediated plant genome editing. Plant Biotechnology Journal. 2018, https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.13068
13. Keunsub Lee, Yingxiao Zhang#, Benjamin P. Kleinstiver, Jimmy A. Guo, Martin J. Aryee, Jonah Miller, Aimee Malzahn#, Scott Zarecor, Carolyn J. Lawrence-Dill, J. Keith Joung, Yiping Qi*, and Kan Wang*. Activities and specificities of CRISPR-Cas9 and Cas12a nucleases for targeted mutagenesis in maize. Plant Biotechnology Journal. 2018, https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.12982
12. Xu TangƗ, Guanqing LiuƗ, Jianping ZhouƗ, Qiurong Ren, Qi You, Li Tian, Xuhui Xin, Zhaohui Zhong, Binglin Liu, Xuelian Zheng, Dengwei Zhang, Aimee Malzahn#, Zhiyun Gong, Yiping Qi*, Tao Zhang*, Yong Zhang*. A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biology. 2018, 19:84 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1458-5
11. Zhaohui Zhong†, Yingxiao Zhang†,#, Qi You†, Xu Tang, Qiurong Ren, Shishi Liu, Lijia Yang, Yan Wang, Xiaopei Liu, Binglin Liu, Tao Zhang, Xuelian Zheng, Ysa Le##, Yong Zhang*, Yiping Qi*. Plant genome editing using FnCpf1 and LbCpf1 nucleases at redefined and altered PAM sites. Molecular Plant. 2018. DOI: https://doi.org/10.1016/j.molp.2018.03.008
10. Levi G. Lowder#, Jianping Zhou, Yingxiao Zhang#, Aimee Malzahn#, Zhaohui Zhong, Tzung-Fu Hsieh, Daniel F. Voytas, Yong Zhang, Yiping Qi*. Robust transcriptional activation in plants using multiplexed CRISPR-Act2.0 and mTALE-Act systems. Molecular Plant. 2018 Feb 5;11(2):245-256. doi: 10.1016/j.molp.2017.11.010. http://www.cell.com/molecular-plant/fulltext/S1674-2052(17)30344-1
9. Xu Tang†, Levi G. Lowder†, Tao Zhang, Aimee A. Malzahn, Xuelian Zheng, Daniel F. Voytas, Zhaohui Zhong, Yiyi Chen, Qiurong Ren, Qian Li, Elida R. Kirkland, Yong Zhang*, Yiping Qi*. A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nature Plants, 2017, https://www.nature.com/articles/nplants201718
8. Xu Tang, Xuelian Zheng, Yiping Qi, Dengwei Zhang, Yan Cheng, Aiting Tang, Daniel F Voytas, Yong Zhang. A single transcript CRISPR-Cas9 system for efficient genome editing in plants. Molecular Plant, 2016, 9 (7): 1088-1091. http://www.cell.com/molecular-plant/abstract/S1674-2052%2816%2930057-0
7. Levi G. Lowder†#, Dengwei Zhang†, Nicholas J. Baltes, Joseph W. Paul, III##, Tang Xu, Xuelian Zheng, Daniel F. Voytas , Tzung-Fu Hsieh, Yong Zhang*, Yiping Qi*. A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation. Plant Physiology, 2015 Oct;169(2):971-85. https://academic.oup.com/plphys/article/169/2/971/6114041
6. Hua Shi, Qiujing Shen, Yiping Qi, Haozhen Nie, Yongfang Chen, Ting Zhao,Fumiaki Katagiri, Dingzhong Tang. Arabidopsis BR-SIGNALING KINASE1 physically associates with the PAMP receptor FLAGELLIN SENSING2 and regulates plant innate immunity. Plant Cell, 2013, 25 (3):1143-57. academic.oup.com/plcell/article/25/3/1143/6097647
5. Yiping Qi†, Yong Zhang†, Feng Zhang, Joshua A. Baller, Spencer C. Cleland#, Yungil Ryu#, Colby G. Starker and Daniel F. Voytas. Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways. Genome Research, 2013, 23 (3):547-54.genome.cshlp.org/content/23/3/547.short
4. Yong Zhang, Feng Zhang, Xiaohong Li, Joshua Baller, Yiping Qi, Colby G. Starker, and Daniel F. Voytas. Transcription Activator-Like Effector Nucleases enable efficient plant genome engineering. Plant Physiology, 2013, 161(1):20-7.https://academic.oup.com/plphys/article/161/1/20/6110556
3. Kenichi Tsuda, Yiping Qi, Le V. Nguyen, Gerit Bethke, Yayoi Tsuda, Jane Glazebrook, and Fumiaki Katagiri. An efficient Agrobacterium-mediated transient transformation of Arabidopsis. The Plant Journal, 2012, 69 (4): 713-719. onlinelibrary.wiley.com/doi/full/10.1111/j.1365-313X.2011.04819.x
2. Jeffry D Sander,Elizabeth J Dahlborg,Mathew J Goodwin,Lindsay Cade,Feng Zhang,Daniel Cifuentes,Shaun J Curtin,Jessica S Blackburn,Stacey Thibodeau-Beganny,Yiping Qi,Christopher J Pierick,Ellen Hoffman,Morgan L Maeder,Cyd Khayter,Deepak Reyon,Drena Dobbs,David M Langenau,Robert M Stupar,Antonio J Giraldez,Daniel F Voytas,Randall T Peterson,Jing-Ruey J Yeh& J Keith Joung. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nature Methods, 2011,8: 67-69. https://www.nature.com/articles/nmeth.1542
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