Publication List: (* = corresponding/senior author; # = graduate student or post-doc advised by Qi; ## = undergraduate or high school student advised by Qi; † = equal contribution. )
A. Book Chapters
10. Aimee Malzahn#, Yong Zhang, Yiping Qi*. CRISPR-Act2.0: An Improved Multiplexed System for Plant Transcriptional Activation. Methods in Molecular Biology. 2019, 1917: 83-93. https://link.springer.com/protocol/10.1007%2F978-1-4939-8991-1_7
9. Weihang Gu, Dabing Zhang, Yiping Qi, Zheng Yuan. Generating Photoperiod-Sensitive Genic Male Sterile Rice Lines with CRISPR-Cas9. Methods in Molecular Biology. 2019, 1917: 97-107. https://link.springer.com/protocol/10.1007%2F978-1-4939-8991-1_8
8. Jianping Zhou, Zhaohui Zhong, Hongqiao Chen, Mengqiao Yang, Qian Li, Xuelian Zheng, Yiping Qi, Yong Zhang. Knocking out microRNA genes in rice with CRISPR-Cas9. Methods in Molecular Biology. 2019, 1917: 109-119. https://link.springer.com/protocol/10.1007%2F978-1-4939-8991-1_9
7. Yingxiao Zhang#, Yong Zhang, Yiping Qi*. Plant Gene Knockout and Knockdown by CRISPR-Cpf1 (Cas12a) systems. Methods in Molecular Biology. 2019, 1917: 245-256. https://link.springer.com/protocol/10.1007%2F978-1-4939-8991-1_18
6. Levi G. Lowder#, Aimee A Malzahn#, Yiping Qi*. Plant Gene Regulation Using Multiplex CRISPR-dCas9 Artificial Transcription Factors. Methods in Molecular Biology. 2018; 1676:197-214. doi: 10.1007/978-1-4939-7315-6_12. https://link.springer.com/protocol/10.1007%2F978-1-4939-7315-6_12
5. Levi G. Lowder#, Joseph W. Paull, III##, Yiping Qi*. Multiplexed Transcriptional Activation or Repression in Plants Using CRISPR-dCas9-Based Systems. Methods in Molecular Biology. 2017, 1629:167-184. doi: 10.1007/978-1-4939-7125-1_12. https://link.springer.com/protocol/10.1007%2F978-1-4939-7125-1_12
4. Levi G. Lowder#, Aimee A. Malzahn#, Yiping Qi*. Rapid Construction of multiplexed CRISPR-Cas9 system for plant genome editing. Methods in Molecular Biology. 2017; 1578:291-307. doi: 10.1007/978-1-4939-6859-6_25. https://link.springer.com/protocol/10.1007%2F978-1-4939-6859-6_25
3. Yiping Qi*. High efficient genome modification by designed Zinc Finger Nuclease. Advances in New Technology for Targeted Modifications of Plant Genomes, 2015, 39-53. https://link.springer.com/chapter/10.1007/978-1-4939-2556-8_3
2. Yiping Qi, Colby Starker, Feng Zhang, Nicholas Baltes and Daniel Voytas. Tailor-made mutations in Arabidopsis using zinc finger nucleases. Methods in Molecular Biology, 2014, 1062: 193-209. https://link.springer.com/protocol/10.1007%2F978-1-62703-580-4_10
1. Yiping Qi, Fumiaki Katagiri. Purification of resistance protein complexes using a biotinylated affinity tag. Methods in Molecular Biology, 2011, 712: 21-30. https://link.springer.com/protocol/10.1007%2F978-1-61737-998-7_3
B. Articles at Refereed Journals
2020
47. Yingxiao Zhang#, Yiping Qi*. Diverse systems for efficient sequence insertion and replacement in precise plant genome editing. BioDesign Research, 2020. https://spj.sciencemag.org/journals/bdr/2020/8659064/
46. 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, 2020. https://www.cell.com/plant-communications/fulltext/S2590-3462(20)30129-2
45. 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
44. 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
43. Zhaohui ZhongƗ, Shishi LiuƗ, Xiaopei Liu, Binglin Liu, Xu Tang, Qiurong Ren, Jianping Zhou, Xuelian Zheng, Yiping Qi*, Yong Zhang*. Intron-based single transcript unit CRISPR systems for plant genome editing. Rice, 2020. https://thericejournal.springeropen.com/articles/10.1186/s12284-020-0369-8
2019
42. Filiz Gürel, Yingxiao Zhang#, Simon Sretenovic#, Yiping Qi*. CRISPR-Cas nucleases and base editors for plant genome editing. aBiotech, 30 November 2019. https://link.springer.com/article/10.1007/s42994-019-00010-0
41. 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
40. Qiurong Ren, Zhaohui Zhong, Yan Wang, Qian Li, Mingzhu Yuan, Yao He, Qi Yu, Caiyan Qi, Xu Tang, Xuelian Zheng, Tao Zhang, Yiping Qi*, Yong Zhang*. Bidirectional promoter based CRISPR-Cas9 systems for plant genome editing. Frontier in Plant Science, 20 September 2019. https://www.frontiersin.org/articles/10.3389/fpls.2019.01173/full
39. Yingxiao Zhang#, Aimee A Malzahn#, Simon Sretenovic# and Yiping Qi*. The emerging and uncultivated potential of CRISPR technology in plant science. Nature Plants, 2019, DOI: 10.1038/s41477-019-0461-5.
38. Yingxiao Zhang #, Yiping Qi*. CRISPR enables directed evolution in plants. Genome Biology. 2019 Apr 30;20(1):83. doi: 10.1186/s13059-019-1693
37. 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
36. 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 https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0629-5
2018
35. 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
34. Qiwei Shan, Nicholas J Baltes, Paul Atkins, Elida R. Kirkland#, Yong Zhang, Joshua A. Baller, Levi G. Lowder#, Aimee A. Malzahn#, John C. Haugner III, Burckhard Seelig, Daniel F. Voytas*, Yiping Qi*. ZFN, TALEN and CRISPR-Cas9 mediated homology directed gene insertion in Arabidopsis: a disconnect between somatic and germinal cells. Journal of Genetics and Genomics. 2018, https://www.sciencedirect.com/science/article/pii/S1673852718301735
33. 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
32. 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
31. 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
30. Magdalena Klimek-Chodacka, Tomasz Oleszkiewicz, Levi G. Lowder#, Yiping Qi, Rafal Baranski. Efficient CRISPR/Cas9 based genome editing in carrot cells. Plant Cell Reports. 2018 Apr;37(4):575-586. doi: 10.1007/s00299-018-2252-2. https://link.springer.com/article/10.1007%2Fs00299-018-2252-2
29. 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
2017
28. Jianping Zhou, Kejun Deng, Yan Cheng, Zhaohui Zhong, Li Tian, Xu Tang, Aiting Tang, Xuelian Zheng, Tao zhang, Yiping Q*, Yong Zhang*. CRISPR-Cas9 based genome editing reveals new insights into microRNA function and regulation in rice. Front Plant Sci. 2017 Sep 13;8:1598. doi: 10.3389/fpls.2017.01598. https://www.frontiersin.org/articles/10.3389/fpls.2017.01598/full
27. Aimee A. Malzahn#, Levi G. Lowder#, Yiping Qi*. Plant genome editing with TALEN and CRISPR. Cell Biosci. 2017 Apr 24;7:21. doi: 10.1186/s13578-017-0148-4. eCollection 2017. https://cellandbioscience.biomedcentral.com/articles/10.1186/s13578-017-0148-4
26. Yiping Qi*. Genome editing is revolutionizing biology. Cell Biosci. 2017 Jul. Editorial.
25. Richard Michelmore*, Gitta Coaker*, Rebecca Bart, Gwyn Beattie, Andrew Bent, Toby Bruce, Duncan Cameron, Jeff Dangl, Sophien Kamoun, Savithramma Dinesh-Kumar, Rob Edwards, Sebastian Eves-van den Akker, Walter Gassmann, Jean Greenberg, Richard Harrison, Ping He, Jagger Harvey, Alisa Huffaker, Scot Hulbert, Roger Innes, Jonathan Jones, Isgouhi Kaloshian, Sophien Kamoun, Fumiaki Katagiri, Jan Leach, Wenbo Ma, John McDowell, June Medford, Blake Meyers, Rebecca Nelson, Richard Oliver, Yiping Qi, Diane Saunders, Michael Shaw, Prasanta Subudhi, Lesley Torrance, Bret Tyler, John Walsh. Foundational and translational research opportunities to improve plant health. Mol Plant Microbe Interact. 2017 Apr 11. doi: 10.1094/MPMI-01-17-0010-CR. https://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-01-17-0010-CR
24. 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, doi:10.1038/nplants.2017.18. https://www.nature.com/articles/nplants201718
2016
23. Levi Lowder, Aimee Malzahn, Yiping Qi*. Rapid Evolution of Manifold CRISPR Systems for Plant Genome Editing. Front Plant Sci. 2016 Nov 14; 7:1683. https://www.frontiersin.org/articles/10.3389/fpls.2016.01683/full
22. 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
21. Quanlin Li, Mingjiao Chen, Dabing Zhang, Wanqi Liang, Jiaojun Wei, Yiping Qi, Zheng Yuan. Development of japonica photo-sensitive genic male sterile rice lines by editing Carbon Starved Anther using CRISPR-Cas9. Journal of Genetics & Genomics, 2016, 43(6):415-9. https://www.sciencedirect.com/science/article/pii/S1673852716300479?via%3Dihub
20. Joseph W. Paul, III, Yiping Qi*. CRISPR/Cas9 for plant genome editing: accomplishments, problems and prospects. Plant Cell Reports, 2016, 35 (7): 1417-27. https://link.springer.com/article/10.1007/s00299-016-1985-z
19. Xuelian Zheng, Shixin Yang, Dengwei Zhang, Zhaohui Zhong, Xu Tang, Kejun Deng, Jianping Zhou, Yiping Qi*, Yong Zhang*. Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism. Plant Cell Reports, 2016, 35 (7): 1545-54. https://link.springer.com/article/10.1007%2Fs00299-016-1967-1
18. Wei Fan, Jie Zong, Zhijing Luo, Mingjiao Chen, Xiangxiang Zhao, Dabing Zhang, Yiping Qi, Zheng Yuan. Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding. PLOS One, 2016,11(1): e0147187. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147187
17. Yiping Qi*, Yong Zhang, Joshua A. Baller, Daniel F. Voytas. Histone H2AX and the small RNA pathway modulate both non-homologous end-joining and homologous recombination in plants. Mutation Research, 2016, 783: 9-14. https://www.sciencedirect.com/science/article/pii/S0027510715300531?via%3Dihub
2015
16. 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, 169 (2): 1-15. http://www.plantphysiol.org/content/early/2015/08/21/pp.15.00636
15. Xuelian Zheng, Qian Li, Dongqing Liu, Lili Zang, Kaiyue Zhang, Kejun Deng, Shixin Yang, Zhengyang Xie, Xu Tang, Yiping Qi*, Yong Zhang*. Promoter analysis of the sweet potato ADP-glucose pyrophosphorylase gene in Nicotiana tabacum. Plant Cell Reports, 2015, 34 (11): 1873-1884. https://link.springer.com/article/10.1007/s00299-015-1834-5
2014 and before
14. Yadong Huang, Chun Yao Li, Yiping Qi, Sungjin Park and Susan I. Gibson. SIS8, a putative mitogen-activated protein kinase kinase kinase, regulates suger resistant seedling development in Arabidopsis. The Plant Journal, 2014, 77 (4): 577-588. https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.12404
13. Michelle L. Christian†, Yiping Qi†, Yong Zhang and Daniel F. Voytas. Targeted mutagenesis in Arabidopsis thaliana using Engineered TAL effector nucleases (TALENs). G3, 2013, 3 (10) 1697-1705. http://www.g3journal.org/content/3/10/1697.long
12. Yiping Qi, Xiaohong Li, Yong Zhang, Feng Zhang, Colby Starker, Nicholas J. Baltes, Jeffry D. Sander, Deepak Reyon, Drena Dobbs, J Keith Joung, Daniel F. Voytas. Targeted deletion and inversion of tandemly arrayed genes in Arabidopsis thaliana using zinc finger nucleases. G3, 2013, 3 (10) 1707-1715. http://www.g3journal.org/content/3/10/1707
11. 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. http://www.plantcell.org/content/early/2013/03/26/tpc.112.107904
10. 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. https://genome.cshlp.org/content/23/3/547.long
9. Yong Zhang, Feng Zhang, Xiaohong Li, Joshua Baller, Yiping Qi, Colby G. Starker, and Daniel F. Voytas. TALENs enable efficient plant genome engineering. Plant Physiology, 2013, 161(1):20-7
8. Yiping Qi and Fumiaki Katagiri. A membrane microdomain may be a platform for immune signaling. Plant Signaling & Behavior, 2012, 7 (4): 454-456. http://www.plantphysiol.org/content/early/2012/11/02/pp.112.205179
7. 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. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2011.04819.x
6. Yiping Qi, Kenichi Tsuda, Jane Glazebrook and Fumiaki Katagiri. Physical association of PTI and ETI immune receptors in Arabidopsis. Molecular Plant Pathology，2011, 12 (7): 702-708. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1364-3703.2010.00704.x
5. 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
4. Yiping Qi, Kenichi Tsuda, Le V. Nguyen, Xia Wang, Jinshan Lin, Angus S. Murphy, Jane Glazebrook, Hans Thordal-Christensen and Fumiaki Katagiri. Physical association of Arabidopsis hypersensitive induced reaction proteins (HIRs) with the immune receptor RPS2. The Journal of Biological Chemistry, 2011, 286 (36): 31297-31307. http://www.jbc.org/content/286/36/31297.long
3. Yiping Qi, Kenichi Tsuda, Anna Joe, Masanao Sato, Le V. Nguyen, Jane Glazebrook , James R. Alfano, Jerry D. Cohen and Fumiaki Katagiri. A putative RNA-binding protein positively regulates salicylic acid-mediated immunity in Arabidopsis. Molecular Plant Microbe Interaction, 2010, 23(12): 1573-1583. https://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-05-10-0106
2. 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. https://www.ncbi.nlm.nih.gov/pubmed/19000159
1. Yiping Qi, Yue Sun, Lin Xu, Yuquan Xu, Hai Huang. ERECTA is required for protection against heat-stress in the AS1/AS2 pathway to regulate adaxial-abaxial leaf polarity in Arabidopsis. Planta. 2004, 219: 270-276. https://link.springer.com/article/10.1007%2Fs00425-004-1248-z
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Publication and citations are available at Google scholar: https://scholar.google.com/citations?user=ZYfzV8UAAAAJ&hl=en
A. Book Chapters
10. Aimee Malzahn#, Yong Zhang, Yiping Qi*. CRISPR-Act2.0: An Improved Multiplexed System for Plant Transcriptional Activation. Methods in Molecular Biology. 2019, 1917: 83-93. https://link.springer.com/protocol/10.1007%2F978-1-4939-8991-1_7
9. Weihang Gu, Dabing Zhang, Yiping Qi, Zheng Yuan. Generating Photoperiod-Sensitive Genic Male Sterile Rice Lines with CRISPR-Cas9. Methods in Molecular Biology. 2019, 1917: 97-107. https://link.springer.com/protocol/10.1007%2F978-1-4939-8991-1_8
8. Jianping Zhou, Zhaohui Zhong, Hongqiao Chen, Mengqiao Yang, Qian Li, Xuelian Zheng, Yiping Qi, Yong Zhang. Knocking out microRNA genes in rice with CRISPR-Cas9. Methods in Molecular Biology. 2019, 1917: 109-119. https://link.springer.com/protocol/10.1007%2F978-1-4939-8991-1_9
7. Yingxiao Zhang#, Yong Zhang, Yiping Qi*. Plant Gene Knockout and Knockdown by CRISPR-Cpf1 (Cas12a) systems. Methods in Molecular Biology. 2019, 1917: 245-256. https://link.springer.com/protocol/10.1007%2F978-1-4939-8991-1_18
6. Levi G. Lowder#, Aimee A Malzahn#, Yiping Qi*. Plant Gene Regulation Using Multiplex CRISPR-dCas9 Artificial Transcription Factors. Methods in Molecular Biology. 2018; 1676:197-214. doi: 10.1007/978-1-4939-7315-6_12. https://link.springer.com/protocol/10.1007%2F978-1-4939-7315-6_12
5. Levi G. Lowder#, Joseph W. Paull, III##, Yiping Qi*. Multiplexed Transcriptional Activation or Repression in Plants Using CRISPR-dCas9-Based Systems. Methods in Molecular Biology. 2017, 1629:167-184. doi: 10.1007/978-1-4939-7125-1_12. https://link.springer.com/protocol/10.1007%2F978-1-4939-7125-1_12
4. Levi G. Lowder#, Aimee A. Malzahn#, Yiping Qi*. Rapid Construction of multiplexed CRISPR-Cas9 system for plant genome editing. Methods in Molecular Biology. 2017; 1578:291-307. doi: 10.1007/978-1-4939-6859-6_25. https://link.springer.com/protocol/10.1007%2F978-1-4939-6859-6_25
3. Yiping Qi*. High efficient genome modification by designed Zinc Finger Nuclease. Advances in New Technology for Targeted Modifications of Plant Genomes, 2015, 39-53. https://link.springer.com/chapter/10.1007/978-1-4939-2556-8_3
2. Yiping Qi, Colby Starker, Feng Zhang, Nicholas Baltes and Daniel Voytas. Tailor-made mutations in Arabidopsis using zinc finger nucleases. Methods in Molecular Biology, 2014, 1062: 193-209. https://link.springer.com/protocol/10.1007%2F978-1-62703-580-4_10
1. Yiping Qi, Fumiaki Katagiri. Purification of resistance protein complexes using a biotinylated affinity tag. Methods in Molecular Biology, 2011, 712: 21-30. https://link.springer.com/protocol/10.1007%2F978-1-61737-998-7_3
B. Articles at Refereed Journals
2020
47. Yingxiao Zhang#, Yiping Qi*. Diverse systems for efficient sequence insertion and replacement in precise plant genome editing. BioDesign Research, 2020. https://spj.sciencemag.org/journals/bdr/2020/8659064/
46. 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, 2020. https://www.cell.com/plant-communications/fulltext/S2590-3462(20)30129-2
45. 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
44. 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
43. Zhaohui ZhongƗ, Shishi LiuƗ, Xiaopei Liu, Binglin Liu, Xu Tang, Qiurong Ren, Jianping Zhou, Xuelian Zheng, Yiping Qi*, Yong Zhang*. Intron-based single transcript unit CRISPR systems for plant genome editing. Rice, 2020. https://thericejournal.springeropen.com/articles/10.1186/s12284-020-0369-8
2019
42. Filiz Gürel, Yingxiao Zhang#, Simon Sretenovic#, Yiping Qi*. CRISPR-Cas nucleases and base editors for plant genome editing. aBiotech, 30 November 2019. https://link.springer.com/article/10.1007/s42994-019-00010-0
41. 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
40. Qiurong Ren, Zhaohui Zhong, Yan Wang, Qian Li, Mingzhu Yuan, Yao He, Qi Yu, Caiyan Qi, Xu Tang, Xuelian Zheng, Tao Zhang, Yiping Qi*, Yong Zhang*. Bidirectional promoter based CRISPR-Cas9 systems for plant genome editing. Frontier in Plant Science, 20 September 2019. https://www.frontiersin.org/articles/10.3389/fpls.2019.01173/full
39. Yingxiao Zhang#, Aimee A Malzahn#, Simon Sretenovic# and Yiping Qi*. The emerging and uncultivated potential of CRISPR technology in plant science. Nature Plants, 2019, DOI: 10.1038/s41477-019-0461-5.
38. Yingxiao Zhang #, Yiping Qi*. CRISPR enables directed evolution in plants. Genome Biology. 2019 Apr 30;20(1):83. doi: 10.1186/s13059-019-1693
37. 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
36. 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 https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0629-5
2018
35. 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
34. Qiwei Shan, Nicholas J Baltes, Paul Atkins, Elida R. Kirkland#, Yong Zhang, Joshua A. Baller, Levi G. Lowder#, Aimee A. Malzahn#, John C. Haugner III, Burckhard Seelig, Daniel F. Voytas*, Yiping Qi*. ZFN, TALEN and CRISPR-Cas9 mediated homology directed gene insertion in Arabidopsis: a disconnect between somatic and germinal cells. Journal of Genetics and Genomics. 2018, https://www.sciencedirect.com/science/article/pii/S1673852718301735
33. 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
32. 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
31. 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
30. Magdalena Klimek-Chodacka, Tomasz Oleszkiewicz, Levi G. Lowder#, Yiping Qi, Rafal Baranski. Efficient CRISPR/Cas9 based genome editing in carrot cells. Plant Cell Reports. 2018 Apr;37(4):575-586. doi: 10.1007/s00299-018-2252-2. https://link.springer.com/article/10.1007%2Fs00299-018-2252-2
29. 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
2017
28. Jianping Zhou, Kejun Deng, Yan Cheng, Zhaohui Zhong, Li Tian, Xu Tang, Aiting Tang, Xuelian Zheng, Tao zhang, Yiping Q*, Yong Zhang*. CRISPR-Cas9 based genome editing reveals new insights into microRNA function and regulation in rice. Front Plant Sci. 2017 Sep 13;8:1598. doi: 10.3389/fpls.2017.01598. https://www.frontiersin.org/articles/10.3389/fpls.2017.01598/full
27. Aimee A. Malzahn#, Levi G. Lowder#, Yiping Qi*. Plant genome editing with TALEN and CRISPR. Cell Biosci. 2017 Apr 24;7:21. doi: 10.1186/s13578-017-0148-4. eCollection 2017. https://cellandbioscience.biomedcentral.com/articles/10.1186/s13578-017-0148-4
26. Yiping Qi*. Genome editing is revolutionizing biology. Cell Biosci. 2017 Jul. Editorial.
25. Richard Michelmore*, Gitta Coaker*, Rebecca Bart, Gwyn Beattie, Andrew Bent, Toby Bruce, Duncan Cameron, Jeff Dangl, Sophien Kamoun, Savithramma Dinesh-Kumar, Rob Edwards, Sebastian Eves-van den Akker, Walter Gassmann, Jean Greenberg, Richard Harrison, Ping He, Jagger Harvey, Alisa Huffaker, Scot Hulbert, Roger Innes, Jonathan Jones, Isgouhi Kaloshian, Sophien Kamoun, Fumiaki Katagiri, Jan Leach, Wenbo Ma, John McDowell, June Medford, Blake Meyers, Rebecca Nelson, Richard Oliver, Yiping Qi, Diane Saunders, Michael Shaw, Prasanta Subudhi, Lesley Torrance, Bret Tyler, John Walsh. Foundational and translational research opportunities to improve plant health. Mol Plant Microbe Interact. 2017 Apr 11. doi: 10.1094/MPMI-01-17-0010-CR. https://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-01-17-0010-CR
24. 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, doi:10.1038/nplants.2017.18. https://www.nature.com/articles/nplants201718
2016
23. Levi Lowder, Aimee Malzahn, Yiping Qi*. Rapid Evolution of Manifold CRISPR Systems for Plant Genome Editing. Front Plant Sci. 2016 Nov 14; 7:1683. https://www.frontiersin.org/articles/10.3389/fpls.2016.01683/full
22. 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
21. Quanlin Li, Mingjiao Chen, Dabing Zhang, Wanqi Liang, Jiaojun Wei, Yiping Qi, Zheng Yuan. Development of japonica photo-sensitive genic male sterile rice lines by editing Carbon Starved Anther using CRISPR-Cas9. Journal of Genetics & Genomics, 2016, 43(6):415-9. https://www.sciencedirect.com/science/article/pii/S1673852716300479?via%3Dihub
20. Joseph W. Paul, III, Yiping Qi*. CRISPR/Cas9 for plant genome editing: accomplishments, problems and prospects. Plant Cell Reports, 2016, 35 (7): 1417-27. https://link.springer.com/article/10.1007/s00299-016-1985-z
19. Xuelian Zheng, Shixin Yang, Dengwei Zhang, Zhaohui Zhong, Xu Tang, Kejun Deng, Jianping Zhou, Yiping Qi*, Yong Zhang*. Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism. Plant Cell Reports, 2016, 35 (7): 1545-54. https://link.springer.com/article/10.1007%2Fs00299-016-1967-1
18. Wei Fan, Jie Zong, Zhijing Luo, Mingjiao Chen, Xiangxiang Zhao, Dabing Zhang, Yiping Qi, Zheng Yuan. Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding. PLOS One, 2016,11(1): e0147187. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147187
17. Yiping Qi*, Yong Zhang, Joshua A. Baller, Daniel F. Voytas. Histone H2AX and the small RNA pathway modulate both non-homologous end-joining and homologous recombination in plants. Mutation Research, 2016, 783: 9-14. https://www.sciencedirect.com/science/article/pii/S0027510715300531?via%3Dihub
2015
16. 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, 169 (2): 1-15. http://www.plantphysiol.org/content/early/2015/08/21/pp.15.00636
15. Xuelian Zheng, Qian Li, Dongqing Liu, Lili Zang, Kaiyue Zhang, Kejun Deng, Shixin Yang, Zhengyang Xie, Xu Tang, Yiping Qi*, Yong Zhang*. Promoter analysis of the sweet potato ADP-glucose pyrophosphorylase gene in Nicotiana tabacum. Plant Cell Reports, 2015, 34 (11): 1873-1884. https://link.springer.com/article/10.1007/s00299-015-1834-5
2014 and before
14. Yadong Huang, Chun Yao Li, Yiping Qi, Sungjin Park and Susan I. Gibson. SIS8, a putative mitogen-activated protein kinase kinase kinase, regulates suger resistant seedling development in Arabidopsis. The Plant Journal, 2014, 77 (4): 577-588. https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.12404
13. Michelle L. Christian†, Yiping Qi†, Yong Zhang and Daniel F. Voytas. Targeted mutagenesis in Arabidopsis thaliana using Engineered TAL effector nucleases (TALENs). G3, 2013, 3 (10) 1697-1705. http://www.g3journal.org/content/3/10/1697.long
12. Yiping Qi, Xiaohong Li, Yong Zhang, Feng Zhang, Colby Starker, Nicholas J. Baltes, Jeffry D. Sander, Deepak Reyon, Drena Dobbs, J Keith Joung, Daniel F. Voytas. Targeted deletion and inversion of tandemly arrayed genes in Arabidopsis thaliana using zinc finger nucleases. G3, 2013, 3 (10) 1707-1715. http://www.g3journal.org/content/3/10/1707
11. 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. http://www.plantcell.org/content/early/2013/03/26/tpc.112.107904
10. 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. https://genome.cshlp.org/content/23/3/547.long
9. Yong Zhang, Feng Zhang, Xiaohong Li, Joshua Baller, Yiping Qi, Colby G. Starker, and Daniel F. Voytas. TALENs enable efficient plant genome engineering. Plant Physiology, 2013, 161(1):20-7
8. Yiping Qi and Fumiaki Katagiri. A membrane microdomain may be a platform for immune signaling. Plant Signaling & Behavior, 2012, 7 (4): 454-456. http://www.plantphysiol.org/content/early/2012/11/02/pp.112.205179
7. 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. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2011.04819.x
6. Yiping Qi, Kenichi Tsuda, Jane Glazebrook and Fumiaki Katagiri. Physical association of PTI and ETI immune receptors in Arabidopsis. Molecular Plant Pathology，2011, 12 (7): 702-708. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1364-3703.2010.00704.x
5. 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
4. Yiping Qi, Kenichi Tsuda, Le V. Nguyen, Xia Wang, Jinshan Lin, Angus S. Murphy, Jane Glazebrook, Hans Thordal-Christensen and Fumiaki Katagiri. Physical association of Arabidopsis hypersensitive induced reaction proteins (HIRs) with the immune receptor RPS2. The Journal of Biological Chemistry, 2011, 286 (36): 31297-31307. http://www.jbc.org/content/286/36/31297.long
3. Yiping Qi, Kenichi Tsuda, Anna Joe, Masanao Sato, Le V. Nguyen, Jane Glazebrook , James R. Alfano, Jerry D. Cohen and Fumiaki Katagiri. A putative RNA-binding protein positively regulates salicylic acid-mediated immunity in Arabidopsis. Molecular Plant Microbe Interaction, 2010, 23(12): 1573-1583. https://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-05-10-0106
2. 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. https://www.ncbi.nlm.nih.gov/pubmed/19000159
1. Yiping Qi, Yue Sun, Lin Xu, Yuquan Xu, Hai Huang. ERECTA is required for protection against heat-stress in the AS1/AS2 pathway to regulate adaxial-abaxial leaf polarity in Arabidopsis. Planta. 2004, 219: 270-276. https://link.springer.com/article/10.1007%2Fs00425-004-1248-z
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