以学校为第一作者单位发表的SCI论文（截止2021年12月）:

187. Zhang, L.#, Ma, X.#, Zhang, X., Xu, Y., Ibrahim, A. K., Yao, J., ... & Zhang, L*. (2021). Reference genomes of the two cultivated jute species. Plant Biotechnology Journal. 19(11), 2235-2248.

186. Fatima, M.#, Ma, X.#, Zhou, P., Zaynab, M., Ming, R.* (2021). Auxin regulated mechanisms underlying sepal retention and development after pollination in spinach. BMC Plant Biology: 21: 166.

185. Jishan Lin#,Wenping Zhang#, Xingtan Zhang, Xiaokai Ma, Shengcheng Zhang, Chen Shuai, Yibin Wang, Haifeng Jia, Zhenyang Liao, Jing Lin; Mengting Zhu, Xiuming Xu, Mingxing Cai, Hui Zeng, Jifeng Wan, Weihai Yang, Tracie Matsumoto, Craig Hardner, Catherine J. Nock*, Ray Ming*. Signatures of selection in recently domesticated macadamia. Nature Communication.

184. Wenping Zhang#, Jishan Lin#, Jianguo Li#, Shaoquan Zheng#, Xingtan Zhang, Shuai Chen, Xiaokai Ma, Fei Dong, Haifeng Jia, Xiuming Xu, Ziqin Yang, Panpan Ma, Fang Deng, Ban Deng, Yongji Huang, Zhanjie Li, Xiaozhou Lv, Yaying Ma, Zhenyang Liao, Zhicong Lin, Jing Lin, Shengcheng Zhang, Tracie Matsumoto, Rui Xia, Jisen Zhang, Ming Ray. Rambutan genome revealed gene networks for spine formation and aril development. The Plant Journal. 2021.108（4）：1037-1052.

183. Tianyou Wang, Jingping Fang and Jisen Zhang*. Advances in Sugarcane Genomics and Genetics. Sugar Tech. 1-15 DOI：10.1007/s12355-021-01065-4.

182. Gang Wang; Yuanyuan Wang; Lianfu Chen; Hongbo Wang; Lin Guo; Xuan Zhou; Meijie Dou; Baiyu Wang; Jingxian Lin; Lei Liu; Zhengchao Wang; Youjin Deng*; Jisen Zhang*. Genetic structure and evolutionary diversity of mating-type (MAT) loci in Hypsizygus marmoreus. IMA Fungus. DOI : 10.1186/s43008-021-00086-8

181. Baiyu Wang, Wenshun Hu, Yaxue Fang, Xiaoxi Feng, Jingping Fang, Tengyue Zou, Shaoquan Zheng, Ray Ming, Jisen Zhang. Comparative analysis of the MADS-box genes revealed their potential functions for flower and fruit development in longan (Dimocarpus longan). Frontiers in Plant Science. 12:813798. doi: 10.3389/fpls.2021.813798

180. Liping Liu, Mengnan Chai, Youmei Huang, Jingang Qi, Wenhui Zhu, Xinpeng Xi, Fangqian Chen,Qin Y, and Hanyang Cai* (2021) SDG2 regulates Arabidopsis inflorescence architecture through SWR1-ERECTA signaling pathway. iScience, 24:103236

179. Yan M., Jin X., Liu Y., Chen H., Ye T., Hou Z., Su Z., Chen Y., Aslam M., Qin Y*., and Niu X.* (2021) Identification and evaluation of the novel genes for transcript normalization during female gametophyte development in sugarcane. Peer J. DOI 10.7717/peerj.12298.

178. Zhao H, Maokai Y, Cheng H, Guo M, Liu Y, Wang L, Chao S, Zhang M, Lai L, Qin Y*. (2021) Characterization of auxin transporter AUX, PIN and PILS gene families in pineapple and evaluation of expression profiles during reproductive development and under abiotic stresses. PeerJ. 9:e11410. doi: 10.7717/peerj.11410.

177.  Jin X, Liu Y, Hou Z, Zhang Y, Fang Y, Huang Y, Cai H, Qin Y*, Cheng Y*. (2021) Genome-Wide Investigation of SBT Family Genes in Pineapple and Functional Analysis of AcoSBT1.12 in Floral Transition. Frontiers in Genetics. 12: 730821.

176. Mohammadi MA, Cheng Y, Aslam M, Jakada BH, Wai MH, Ye K, He X, Luo T, Ye L, Dong C, Hu B, Priyadarshani SVGN, Wang-Pruski G*, Qin Y*. (2021) ROS and Oxidative Response Systems in Plants Under Biotic and Abiotic Stresses: Revisiting the Crucial Role of Phosphite Triggered Plants Defense Response. Frontiers in Microbiology. 12:631318.

175. Cheng Y, Zhou Q, Li W, Cheng H, Mohammadi M, Liu Y, Deng F, S.V.G.N. Priyadarshani, Sun J, Ye L, He X, Cao L, Cao S, Zheng P, Aslam M, Zhao H, Qin Y*. (2021) De novo transcriptome assembly and gene expression profiling of Ipomoea pes-caprae L. under heat and cold stresses. Scientia Horticulturae, 289,110379

174. Aslam M, Fakher B, Greaves J, Jakada B, Qin R, Qin Y*. (2021) A CBL-interacting protein kinase, AcCIPK18, from Ananas comosus regulates tolerance to salt, drought, heat stress and Sclerotinia sclerotiorum infection in Arabidopsis.Environmental and Experimental Botany. https://doi.org/10.1016/j.envexpbot.2021.104728

173. Hou Z, Liu Y, Zhang M, Zhao L, Jin X, Liu L, Su Z, Cai H, Qin Y*. (2021) High-throughput single-cell transcriptomics reveals the female germline differentiation trajectory in Arabidopsis thaliana. Communications Biology. 4(1):1149.

172. Zhao L, Liu L, Liu Y, Dou X, Cai H, Aslam M, Hou Z, Jin X, Li Y, Wang L, Zhao H, Wang X, Sicard A, Qin Y*. (2021) Characterization of germline development and identification of genes associated with germline specification in pineapple. Horticulture Research. 8(1):239.

      171. Chang-Jiao Ke#, Xian-Ju Lin#, Bao-Yu Zhang, and Li-Yu Chen*. (2021) Turgor regulation defect 1 proteins play a conserved role in pollen tube reproductive innovation of the angiosperms. The Plant Journal. 106, 1356-1365.

       170. Hongying Yu, Yaying Ma, Yijing Lu, Jingjing Yue, Ray Ming*. (2021). Expression profiling of the Dof gene family under abiotic stresses in spinach. Scientific reports. 11(1):14429.

      169. Juan Liu, Li-Yu Chen, Ping Zhou, Zhenyang Liao, Hai Lin, Qingyi Yu, Ray Ming*. (2021). Sex biased expression of hormone related genes at early stage of sex differentiation in papaya flowers. Horticulture Research. 8(1):147.

       168. Yongji Huang, Wenjie Ding, Muqing Zhang, Jinlei Han, Yanfen Jing, Wei Yao, Robert Hasterok, Zonghua Wang, Kai Wang*. (2021). The formation and evolution of centromeric satellite repeats in Saccharum species. Plant Journal. 106(3):616-629.

      167. Zhen Li, Gang Wang, Xihui Liu, Zhengchao Wang, Muqing Zhang*, Jisen Zhang*. (2021). Genome-wide identification and expression profiling of DREB genes in Saccharum spontaneum. BMC Genomics. 22(1), 456.

     166. Qiao Zhou, Liping Liu, Han Cheng, Zeyun Li, MyatHnin Wai, Tiantian Luo, Xingyue Jin, Heming Zhao, S.V.G.N.Priyadarshani, Yuan Qin*. (2021). Genome-wide Identification and Expression Pattern Analysis of the HD-Zip Transcription Factor Family in Pineapple (Ananas Comosus). Tropical Plant Biology. 14(2):120-131.

   165. Lulu Wang, Yanhui Liu, Mengnan Chai, Huihuang Chen, Mohammad Aslam, Xiaoping Niu, Yuan Qin*, Hanyang Cai*. (2021). Genome-wide identification, classification, and expression analysis of the HSF gene family in pineapple (Ananas comosus). PeerJ, 9, e11329.

     164. Yan Shi#, Xingtan Zhang#, Xiaojun Chang#, Maokai Yan#, Heming Zhao, Yuan Qin*, Haifeng Wang*. (2021). Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple. BMC Plant Biology. 21(1), 19.

     163. Yan Cheng#, Xiaoxue He#, S. V. G. N. Priyadarshani, Yu Wang, Li Ye, Chao Shi, Kangzhuo Ye, Qiao Zhou, Ziqiang Luo, Fang Deng, Ling Cao, Ping Zheng, Mohammad Aslam, Yuan Qin*. Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca. BMC Genomics. 22(1), 167.

     162. Hanyang Cai, Liping Liu, Man Zhang, Mengnan Chai, Youmei Huang, Fangqian Chen, Maokai Yan, Zhenxia Su,Ian Henderson, Ravishankar Palanivelu, Xuemei Chen, Yuan Qin*. Spatiotemporal control of miR398 biogenesis, via chromatin remodeling and kinase signaling, ensures proper ovule development. Plant Cell. 33(5): 1530-1553.

     161. Hanyang Cai#, Youmei Huang#, Fangqian Chen#, Liping Liu#, Mengnan Chai, Man Zhang, Maokai Yan, Mohammad Aslam, Qing He, Yuan Qin.* (2021). ERECTA signaling regulates plant immune responses via chromatin-mediated promotion of WRKY33 binding to target genes. New Phytologist. 230(2):737-756.

     160. Chang-Jiao Ke#, Xian-Ju Lin#, Bao-Yu Zhang, Li-Yu Chen*. (2021). Turgor regulation defect proteins play a conserved role in pollen tube reproductive innovation of the angiosperms. The Plant Journal. doi: 10.1111/tpj.15241.

     159. Pengjie Wang, Jiaxin Yu, Shan Jin, Shuai Chen, Chuan Yue, Wenling Wang, Shuilian Gao, Hongli Cao,Yucheng Zheng, Mengya Gu, Xuejin Chen, Yun Sun, Yuqiong Guo, Jiangfan Yang, Xingtan Zhang*, Naixing Ye*. (2021). Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome. Horticulture Research. 8(1), 107.

       158. Xiaobing Zhao, Jinjin Song, Qiuxia Zeng, Yaying Ma, Hanmei Fang, Liyuan Yang, Ban Deng, Juan Liu, Jingping Fang, Liping Zuo, Jingjing Yue* .(2021) Auxin and cytokinin mediated regulation involved in vitro organogenesis of papaya. Journal of Plant Physiology. 260,153405.

     157. Zhenyang Liao, Xunxiao Zhang, Shengcheng Zhang, Zhicong Lin, Xingtan Zhang*, Ray Ming*. (2021). Structural variations in papaya genomes. BMC Genomics. 22(1), 335.

     156. Mahpara Fatima#, Xiaokai Ma#, Ping Zhou, Madiha Zaynab, Ray Ming*. (2021). Auxin regulated metabolic changes underlying sepal retention and development after pollination in spinach. BMC Plant Biology. 21(1), 166.

     155. Gang Wang, Lianfu Chen, Weiqi Tang, Yuanyuan Wang, Qing Zhang, Hongbo Wang, Xuan Zhou, Haofeng Wu, Lin Guo, Meijie Dou, Lei Liu, Baiyu Wang, Jingxian Lin, Baogui Xie, Zhengchao Wang, Zhong-Jian Liu, Ray Ming, Jisen Zhang*. (2021). A Melanogenesis-related Candidate Gene Identified by a high Quality Genome Assembly and Population Diversity Analysis in Hypsizygus Marmoreus. Journal of Genetics and Genomics. 48(1):75-87.

     154. Fei Dong, Zhicong Lin, Jing Lin, Ray Ming*, Wenping Zhang*. (2021). Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae. Plants. 10(2). DOI10.3390/plants10020283.

     153. Youjin Deng, Xunxiao Zhang, Baogui Xie, Longji Lin, Tom Hsiang, Xiangzhi Lin, Yiying Lin, Xingtan Zhang,Yanhong Ma, Wenjing Miao and Ray Ming. (2020). Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis. BMC Genomics https://doi.org/10.1186/s12864-020-06846-x

     152. Liwu Zhang#*, Yi Xu#, Xingtan Zhang#, Xiaokai Ma#, Lilan Zhang#, Zhenyang Liao, Qing Zhang, Xuebei Wan, Yan Cheng, Jisen Zhang, Dongxu Li, Liemei Zhang, Jiantang Xu, Aifen Tao, Lihui Lin, Pingping Fang, Shuai Chen, Rui Qi, Xiuming Xu, Jianmin Qi, Ray Ming*. (2020). The genome of kenaf (Hibiscus cannabinus L.) provides insights into bast fiber and leaf shape biogenesis. Plant Biotechnology Journal. 10:10. https://doi.org/10.1111/pbi.13341.

      151. Han Lin#, Yangna Sun#, Siren Lan, Xiaokai Ma*. (2020). The complete plastome of Cymbidium tortisepalum (Orchidaceae) hermaphrodite, Mitochondrial DNA Part B. 4(2), 4089 4090.

       150. Wei Lin#, Yuhan Wu#, Jingjing Wang#, Han Lin#, Xiuming Xu, Guanrong He, Bizhu He*, Xiaokai Ma*.(2020). Exploring bio active ingredients and mechanisms of Anoectochilus roxburghii against liver injury through integrating network pharmacology and experimental validation. MedicalScience Monitor. 26: e923533.

       149. Wei Lin#, Jingjing Wang#, Xiuming Xu#, Yuhan Wu, Dongliang Qiu, Bizhu He, Surendra Sarsaiya, Xiaokai Ma*, Jishuang Chen*. (2020). Rapid propagation in vitro andaccumulation of active substances of endangered Dendrobium cariniferum Rchb. f. Bioengineered, 11(1), 386 396.

       148. Mohammad Aslam#, Bello Hassan Jakada#, Beenish Fakher, Joseph G. Greaves, Xiaoping Niu, Zhenxia Su, Yan Cheng, Shijiang Cao, Xiaomei Wang*,Yuan Qin* (2020). Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response. BMC Genomics. 21:735.

      147. Xingyue Jin#, Zhimin Hou#, Lihua Zhao, Liping Liu, S. V. G. N. Priyadarshani, Lulu Wang, Youmei Huang, Fangqian Chen, Yuan Qin*. (2020). Genome-Wide Identification and Evaluation of New Reference Genes in Pineapple (Ananas comosus L.) during Stamen and Ovule Development. Tropical Plant Biology. https://doi.org/10.1007/s12042-020-09269-w.

      146. Hanyang Cai, Mengnan Chai, Fangqian Chen, Youmei Huang, Man Zhang, Qing He, Liping Liu, Maokai Yan, Yuan Qin*. (2020) HBI1 acts downstream of ERECTA and SWR1 in regulating inflorescence architecture through the activation of the brassinosteroid and auxin signaling pathways. New Phytologist. DOI: 10.1111/nph.16840.

      145. Qingfang Lin#, Song Wang#, Yihang Dao, Jianyong Wang, Kai Wang*. (2020). The Arabidopsis thaliana trehalose-6-phosphate phosphatase gene AtTPPI enhances drought tolerance by regulating stomatal apertures. Journal of Experimental Botany. 71:4285-4297.

144. Qing Zhang#, Xiuting Hua#, Hong Liu#, Yuan Yuan, Yan Shi, Zhengchao Wang, Muqing Zhang, Ray Ming, Jisen Zhang*.(2020). Evolutionary Expansion and Functional Divergence of Sugar Transporters in Saccharum (S. spontaneum and S. officinarum). The Plant Journal. doi.org/10.1111/tpj.15076.

143. Xuequn Chen#, Chaobo Tong#, Xingtan Zhang, Wei Dong, Ming Hu, Aixia Song, Fei Chen, Youping Wang, Jinxing Tu, Shengyi Liu*, Haibao Tang*, Liangsheng Zhang*. (2020). C A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13493.

142. Xingtan Zhang#, Gang Wang#, Shengcheng Zhang, Shuai Chen, Yibin Wang, Ping Wen, Xiaokai Ma, Yan Shi, Rui Qi, Yang Yang, Zhenyang Liao, Jing Lin, Jishan Lin, Xiuming Xu, Xuequn Chen, Xindan Xu, Fang Deng, Lihua Zhao, Yi-lun Lee, Rong Wang, Xiao-Yong Chen, Yann-Rong Lin, Jisen Zhang, Haibao Tang, Jin Chen*, Ray Ming*. (2020). Genomes of banyan fig and pollinator wasp provide insights into fig-wasp coevolution. Cell.183(4), 875-889.

141. Man Zhang#, Yanhui Liu#, Qing He, Mengnan Chai, Youmei Huang, Fangqian Chen, Xiaomei Wang,Yeqiang Liu, Hanyang Cai*,Yuan Qin*. (2020). Genome-wide investigation of calcium-dependent protein kinase gene family inpineapple: evolution and expressionprofiles during development and stress.BMC Genomics. 21:72.

140.Man Zhang, Yanhui Liu, Hanyang Cai, Mingliang Guo, Mengnan Chai, Zeyuan She,Li Ye, Yan Cheng, Bingrui Wang*,Yuan Qin*. (2020). The bZIP Transcription Factor GmbZIP15 NegativelyRegulates Salt- and Drought-Stress Responsesin Soybean. International Journal ofMolecular Sciences,21, 7778.

139. Youmei Huang#, Yanhui Liu#, Man Zhang, Mengnan Chai, Qing He,Bello Hassan Jakada, Fangqian Chen, Huihuang Chen, Xingyue Jin,Hanyang Cai, Yuan Qin*. (2020). Genome-wide identification andexpression analysis of the ERFtranscription factor family in pineapple(Ananas comosus (L.) Merr.). PeerJ, 8:e10014.

138. Huihuang Chen, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang,Qing He, Mengnan Chai, Xiaoping Niu*, Yuan Qin*. (2020). AcoMYB4, an Ananas comosus L. MYB TranscriptionFactor, Functions in Osmotic Stress through NegativeRegulation of ABA Signaling. International Journal ofMolecular Sciences. 21, 5727.

137. Naiyan Xiao, Hengbo Wang, Wei Yao, Muqing Zhang, Ray Ming, Jisen Zhang*. (2020). Development and Evaluation of SSR Markers Based on LargeScale Full-Length Transcriptome Sequencing in Sugarcane.Tropical Plant Biology.https://doi.org/10.1007/s12042-020-09260-5.

136.Heming Zhao, Mingliang Guo, Maokai Yan, Han Cheng, Yanhui Liu, Zeyuan She, Linyi Lai, Chao Shi, Minqian Zhang, Yi Li, Deshu Lin, Yuan Qin*. (2020).Comparative Expression Profiling Reveals GenesInvolved in Megasporogenesis.Plant Physiology. 182, 2006-2024.

135. Yanhui Liu, Mengnan Chai, Man Zhang, Qing He, Zhenxia Su, S. V. G. N. Priyadarshani,Liping Liu, Guanxi Dong, and Yuan Qin*. (2020).Genome-Wide Analysis, Characterization, and ExpressionProfile of the Basic Leucine Zipper Transcription FactorFamily in Pineapple.International Journal of Genomics.https://doi.org/10.1155/2020/3165958.

134.Qing He, Hanyang Cai, Mengyan Bai, Man Zhang, Fangqian Chen, Youmei Huang,S. V. G. N. Priyadarshani, Mengnan Chai, Liping Liu, Yanhui Liu , Huihuang Chen,Yuan Qin*. (2020). A Soybean bZIP Transcription Factor GmbZIP19Confers Multiple Biotic and Abiotic Stress Responsesin Plant. International Journal ofMolecular Sciences. 21, 4701.

133. Mengnan Chai#, Han Cheng#, Maokai Yan, SVGN Priyadarshani,Man Zhang, Qing He, Youmei Huang, Fangqian Chen, Liping Liu,Xiaoyi Huang, Linyi Lai, Huihuang Chen , Hanyang Cai,Yuan Qin*. (2020). Identification and expression analysis ofthe DREB transcription factor family inpineapple (Ananas comosus (L.) Merr.). PeerJ. 8:e9006.

132. Shijiang Cao, Sijia He, Hongwei Lv, Jiashuo Zhang, Mohammad Aslam, Han Cheng, Anqi Hu, Guangqiu Cao, Xingtan Zhang, Yuan Yu, Yuan Qin*. (2020). Genome-Wide Analysis of the Cryptochrome Gene Family in Plants.Tropical Plant Biology.https://doi.org/10.1007/s12042-019-09249-9.

131. Liping Liu, Lihua Zhao, Piaojuan Chen, Hanyang Cai, Zhimin Hou, Xingyue Jin, Mohammad Aslam, Mengnan Chai,Linyi Lai, Qing He, Yanhui Liu, Xiaoyi Huang, Huihuang Chen, Yingzhi Chen, Yuan Qin*. (2020). ATP binding cassette transporters ABCG1 and ABCG16 affectreproductive development via auxin signalling in Arabidopsis. The Plant Journal.102, 1172-1186.

130. Zhicong Lin, Ping Zhou, Xinyi Ma, Youjin Deng, Zhenyang Liao, Ruoyu Li, Ray Ming*. (2020). Comparative analysis of chloroplastgenomes in Vasconcellea pubescensA.Dc. and Carica papaya L.Scientific Reports.10:15799.

129. Lulu Wang, Yi Li, Xingyue Jin, Liping Liu , Xiaozhuan Dai , Yanhui Liu, Lihua Zhao , Ping Zheng,Xiaomei Wang, Yeqiang Liu, Deshu Lin, Yuan Qin*. (2020). Floral transcriptomes reveal gene networks inpineapple floral growth and fruit development.Comunications Biology. 3:500.

128. Panpan Ma#, Xingtan Zhang#, Lanping Chen, Qian Zhao, Qing Zhang, Xiuting Hua, Zhengchao Wang, Haibao Tang, Qingyi Yu, Muqing Zhang, Ray Ming, Jisen Zhang*. (2020). Comparative analysis of sucrose phosphatesynthase (SPS) gene family betweenSaccharum officinarum and Saccharumspontaneum.BMC Plant Biology. 20:422.

127. Haibao Tang*, Liangsheng Zhang, Fei Chen, Xingtan Zhang, Feng Chen, Hong Ma, Yves Van de Peer. (2020). Nymphaea colorata (Blue-Petal Water Lily).Trends in Genetics.

126. Qiongli Wang#, Guangrun Yu#, Zhiyong Chen, Jinlei Han, Yufang Hu, Kai Wang*. (2020). Optimization of protoplast isolation, transformation and its application in sugarcane(Saccharum spontaneum L). The Crop Journal.

125. Ping Zhou, Xiaodan Zhang, Mahpara Fatima, Xinyi Ma, Hongkun Fang, Hansong Yan，Ray Ming*. (2020). DNA methylome and transcriptome landscapesrevealed differential characteristics of dioeciousflowers in papaya.Horticulture Research.7:81.

124. Jinlei Han, Pengxi Wang, Qiongli Wang, Qingfang Lin, Zhiyong Chen, Guangrun Yu,Chenyong Miao, Yihang Dao, Ruoxi Wu, James C. Schnable, Haibao Tang*, Kai Wang*. (2020). Genome-wide Characterization of DNase I-hypersensitive Sites and ColdResponse Regulatory Landscapes in Grasses.The Plant Cell. 32: 2457-2473.

123. Mingxing Cai#, Jishan Lin#, Zeyun Li, Zhicong Lin, Yaying Ma, Yibin Wang ,Ray Ming*. (2020). Allele specific expression of Dof genesresponding to hormones and abiotic stressesin sugarcane. PLoSONE. 15(1):e0227716.

122. Xiaodan Zhang, Mahpara Fatima, Ping Zhou, Qing Ma and Ray Ming*. (2020). Analysis of MADS-box genes revealedmodified flowering gene network and

diurnal expression in pineapple. BMC Genomics. 21:8.

121. Li-Yu Chen, Yinghui Xin, Ching Man Wai, Juan Liu, Ray Ming*. (2020) The role of cis-elements in the evolution of crassulacean acid metabolism photosynthesis. Horticulture Research. 7, 5.

120. Yangna Sun, Yanqiong Chen, Han Lin, Xiaokai Ma*. (2019). The complete chloroplast genome of a Cymbidium tortisepalum (Orchidaceae) male mutant. Mitochondrial DNA Part B, 4(2), 4087-4088.

119. Zhen Li, Xiuting Hua, Weiming Zhong, Yuan Yuan, Yongjun Wang, Zhengchao Wang, Ray Ming, Jisen Zhang*. (2019). Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in the Autopolyploid Saccharum spontaneum. Plant Cell Physiology. 10.1093/pcp/pcz227.

118. Song Wang, Kai Ouyang, Kai Wang *. (2019). Genome-wide identification, evolution, and expression analysis of TPS and TPP gene families in Brachypodium distachyon. Plants. 8:362.

117. Qing He, Yanhui Liu, Man Zhang, Mengyan Bai, S. V. G. N. Priyadarshani, Mengnan Chai, Fangqian Chen, Youmei Huang, Liping Liu, Hanyang Cai, Yuan Qin*. (2019). Genome-Wide Identification and Expression Analysis of the NAC Transcription Factor Family in Pineapple. Tropical Plant Biology. https://doi.org/10.1007/s12042-019-09233-3.

116.Guangrun Yu# , Jianyong Wang#, Li Miao, Mengli Xi*, Qiongli Wang*, Kai Wang*. (2019). Optimization of Mature Embryo-Based TissueCulture and Agrobacterium-Mediated Transformationin Model Grass Brachypodium distachyon. International Journal ofMolecular Sciences, 20, 5448.

115.Liangsheng Zhang*#, Fei Chen#, Xingtan Zhang#, Zhen Li#, Yiyong Zhao#,Rolf Lohaus#, Xiaojun Chang#, Wei Dong, Simon Y. W. Ho, Xing Liu, Aixia Song,Junhao Chen, Wenlei Guo, Zhengjia Wang, Yingyu Zhuang, Haifeng Wang, Xuequn Chen,Juan Hu, Yanhui Liu, Yuan Qin, Kai Wang, Shanshan Dong, Yang Liu, Shouzhou Zhang,Xianxian Yu, Qian Wu, Liangsheng Wang, Xueqing Yan, Yuannian Jiao,Hongzhi Kong, Xiaofan Zhou, Cuiwei Yu, Yuchu Chen, Fan Li, Jihua Wang,Wei Chen, Xinlu Chen, Qidong Jia, Chi Zhang, Yifan Jiang, Wanbo Zhang, Guanhua Liu,Jianyu Fu, Feng Chen, Hong Ma, Yves Van de Peer, Haibao Tang. (2019). The water lily genome and the earlyevolution of flowering plants. Nature.https://doi.org/10.1038/s41586-019-1852-5.

114. Yongji Huang#, Hong Chen#, Jinlei Han, Ya Zhang, Shulin Ma, Guangrun Yu, Zonghua Wang*, Kai Wang*. (2019).Species-specific abundant retrotransposons elucidate the genomiccomposition of modern sugarcane cultivars. Chromosoma. doi.org/10.1007/s00412-019-00729-1.

113. Hengbo Wang, Naiyan Xiao, Yongjun Wang, Jinlong Guo, Jisen Zhang*. (2019).Establishment of a qualitative PCR assay for the detection of Xanthomonas albilineans (Ashby) Dowson in sugarcane. Crop protection. doi: https://doi.org/10.1016/j.cropro.2019.105053.

112. Ying Zhang, Wei Dong, Xinghua Zhao, Aixia Song, Kangwei Guo, Zhongjian Liu, Liangsheng Zhang*. (2019). Transcriptomic Analysis of Differentially Expressed Genes andAlternative Splicing Events Associated with Crassulacean AcidMetabolism in Orchids. Horticultural Plant Journal. 5(6):268-280.

111. Mohammad Aslam, Beenish Fakher, Bello Hassan Jakada, Shijiang Cao ,Yuan Qin*. (2019). SWR1 Chromatin Remodeling Complex:A Key Transcriptional Regulator in Plants. Cells. 8, 1621.

110. Qingfang Lin#, Jiao Yang#, Qiongli Wang, Hong Zhu, Zhiyong Chen, Yihang Dao, Kai Wang*. (2019). Overexpression of the trehalose-6-phosphate phosphatase family gene AtTPPFimproves the drought tolerance ofArabidopsis thaliana.BMC Plant Biology.19:381.

109. Xiaokai Ma, Han Lin, Yanqiong Chen, Siren Lan, Ray Ming. (2019). Thecomplete chloroplast genome of a gynodioecious deciduous orchid Satyriumciliatum (Orchidaceae)female, Mitochondrial DNA Part B-Resources, 4:2, 3876-3877.

108.Jishan Lin#, Mengting Zhu#, Mingxing Cai,Wenping Zhang, Mahpara Fatima,Haifeng Jia,Feifei Li,Ray Ming*. (2019). Identification and Expression Analysis of TCP Genes in Saccharum spontaneum L.Tropical Plant Biology.https://doi.org/10.1007/s12042-019-09238-y.

107.Zeyun Li# , Gang Li#, Mingxing Cai, Samaranayaka V.G.N. Priyadarshani,Mohammad Aslam, Qiao Zhou, Xiaoyi Huang, Xiaomei Wang, Yeqiang Liu, Yuan Qin*. (2019). Genome-Wide Analysis of the YABBY TranscriptionFactor Family in Pineapple and FunctionalIdentification of AcYABBY4 Involvement in Salt Stress. International Journal of Molecular Sciences.20, 586.

106. Yan Cheng#, Pan Yang#, Lihua Zhao, S.V.G.N. Priyadarshani , Qiao Zhou, Zeyun Li, Weimin Li ,Junjie Xiong, Zhibin Lin, Li Li, Xinyu Huang, Jindian Liu, Mohammad Aslam, Heming Zhao , Gang Li ,Jinbiao Ma, Lei Li , Yuan Qin*. (2019). Studies on genome size estimation, chromosome number, gametophyte development and plant morphology of salt-tolerant halophyte Suaeda salsa. BMC Plant Biology. 19: 473-485.

105. S.V.G.N.Priyadarshani, Hanyang Cai, Qiao Zhou, Yanhui Liu, Yan Cheng,Junjie Xiong, Dikoko Lesego Patson, Shijiang Cao, Heming Zhao ,Yuan Qin*. (2019) An Efficient Agrobacterium Mediated Transformation of Pineapple with GFP-Tagged Protein Allows Easy, Non-Destructive Screening of Transgenic Pineapple Plants. Biomolecules. 9, 617.

104. Mohammad Aslam*, Beenish Fakher, Bello Hassan Jakada, Lihua Zhao, Shijiang Cao, Yan Cheng, Yuan Qin*. (2019) Genome-Wide Identification and Expression Profiling of CBL-CIPK Gene Family in Pineapple (Ananas comosus) and the Role of AcCBL1 in Abiotic and Biotic Stress Response. Biomolecules. 9, 293.

103. Bello Hassan Jakada, Mohammad Aslam, Beenish Fakher, Joseph G. Greaves,Zeyun Li, Weimin Li, Linyi Lai, Oyekunle Adenike Ayoade, Yan Cheng, Shijiang Cao, Gang Li, Jer-Ming Hu, Yuan Qin*. (2019). Identification of SWI2/SNF2-Related 1 Chromatin Remodeling Complex (SWR1-C) Subunits in Pineapple and the Role of Pineapple SWR1 COMPLEX 6 (AcSWC6) in Biotic andAbiotic Stress Response. Biomolecules. 9, 364.

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21. Jinlei Han#, Rick E Masonbrink#, Wenbo Shan#, Fengqin Song, Jisen Zhang, Weichang Yu, Kunbo Wang, Yufeng Wu, Haibao Tang, Jonathan F Wendel, Kai Wang*. (2016). Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton. The Plant Journal. 88(6): 992-1005.

20. Jingping Fang, Aiting Lin, Weijing Qiu, Hanyang Cai, Muhammad Umar, Rukai Chen, Ray Ming*. (2016). Transcriptome Profiling Revealed Stress-Induced and Disease Resistance Genes Up-Regulated in PRSV Resistant Transgenic Papaya. Frontiers in Plant Science.7: 855.

19. Jisen Zhang, Anupma Sharma, Qingyi Yu, Jianping Wang, Leiting Li, Lin Zhu , Xingtan Zhang,Youqiang Chen, Ray Ming*. (2016). Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum. BMC Genomics.17: 446.

18. Qing Zhang, Weichang Hu, Fan Zhu, Liming Wang, Qingyi Yu, Ray Ming, Jisen Zhang*. (2016). Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum .BMC Genomics.17: 88.

17. Liangsheng Zhang*#, Fei Chen#, Guo-Qiang Zhang, Yong-Qiang Zhang, Shance Ni, Jin-Song Xiong, Zhenguo Lin, Zong-Ming (Max) Cheng*, Zhong-Jian Liu*. (2016). Origin and mechanism of crassulacean acid metabolism in orchids as implied by comparative transcriptomics and genomics of the carbon fixation pathway. The Plant Journal. DOI: 10.1111/tpj.13159.

16. Haibao Tang, Matthew D. Bomhoff, Evan Briones, Liangsheng Zhang, James C. Schnable, Eric Lyons*. (2015). SynFind: compiling syntenic regions across any set of genomes on demand. Genome Biology and Evolution. DOI: 10.1093/gbe/evv219.

15. Jinlei Han#, Baoliang Zhou#, Wenbo Shan, Liying Yu, Weiren Wu, Kai Wang*. (2015). A and D genomes spatial separation at somatic metaphase in tetraploid cotton: evidence for genomic disposition in a polyploid plant. The Plant Journal. 84(6): 1167-1177.

14. Ray Ming#*, Robert VanBuren#, Ching Man Wai#, Haibao Tang#, Michael C Schatz, John E Bowers, Eric Lyons, Ming-Li Wang, Jung Chen, Eric Biggers, Jisen Zhang, Lixian Huang, Lingmao Zhang, Wenjing Miao, Jian Zhang, Zhangyao Ye, Chenyong Miao, Zhicong Lin, Hao Wang, Hongye Zhou, Won C Yim, Henry D Priest, Chunfang Zheng, Margaret Woodhouse, Patrick P Edger, Romain Guyot, Hao-Bo Guo, Hong Guo, Guangyong Zheng, Ratnesh Singh, Anupma Sharma, Xiangjia Min, Yun Zheng, Hayan Lee, James Gurtowski, Fritz J Sedlazeck, Alex Harkess, Michael R McKain, Zhenyang Liao, Jingping Fang, Juan Liu, Xiaodan Zhang, Qing Zhang, Weichang Hu, Yuan Qin, Kai Wang, Li-Yu Chen, Neil Shirley, Yann-Rong Lin, Li-Yu Liu, Alvaro G Hernandez, Chris L Wright, Vincent Bulone, Gerald A Tuskan, Katy Heath, Francis Zee, Paul H Moore, Ramanjulu Sunkar, James H Leebens-Mack, Todd Mockler, Jeffrey L Bennetzen, Michael Freeling, David Sankoff, Andrew H Paterson, Xinguang Zhu, Xiaohan Yang, J Andrew C Smith, John C Cushman, Robert E Paull*, Qingyi Yu*. (2015). The pineapple genome and the evolution of CAM. Nature Genetics. 47: 1435-1442.

13. Yuan Qin, Juan Dong*. (2015). Focusing on the focus: what else beyond the master switches for polar cell growth? Molecular Plant. 8(4): 582-594.

12.Yuan Qin, Ramin Yadegari, Ravishankar Palanivelu*. (2015). ACTIN-RELATED PROTEIN 6 regulates DISRUPTED MEIOTIC cDNA 1 gene expression in ovules. Molecular Reproduction and Development. 82(7-8): 499.

11. Haibao Tang*, Eric Lyons, Christopher D Town. (2015). Optical mapping in plant comparative genomics. Gigascience. DOI: 10.1186/s13742-015-0044-y.

10. Haibao Tang*, Xingtan Zhang, Chenyong Miao, Jisen Zhang, Ray Ming, James C Schnable, Patrick S Schnable, Eric Lyons, Jianguo Lu. (2015). ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biology. 16(9): 3.

9. Ray Ming*, Ching Man Wai. (2015). Assembling allopolyploid genomes: no longer formidable. Genome Biology. 16(8): 27.

8. Robert VanBuren#, Fanchang Zeng#, Cuixia Chen#, Jisen Zhang#, Ching Man Wai, Jennifer Han, Rishi Aryal, Andrea R. Gschwend, Jianping Wang, Jong-Kuk Na, Lixian Huang, Lingmao Zhang, Wenjing Miao, Jiqing Gou, Jie Arro, Romain Guyot, Richard C. Moore, Ming-Li Wang, Francis Zee, Deborah Charlesworth, Paul H. Moore, Qingyi Yu, Ray Ming*. (2015). Origin and domestication of papaya Yh chromosome. Genome Research. 25(7): 524-533.

7. Deshu Lin*, Huibo Ren, Ying Fu. (2015). ROP GTPase-mediated auxin signaling regulates pavement cell interdigitation in Arabidopsis thaliana. Journal of Integrative Plant Biology. 57(6): 31-39.

6. Huibo Ren, Deshu Lin*. (2015). ROP GTPase Regulation of Auxin Transport in Arabidopsis. Molecular Plant. 8(5): 193-195.

5. Lihua Zhao, Jiangman He, Hanyang Cai, Haiyan Lin, Renyi Liu, Zhenbiao Yang, Yuan Qin*. (2014). Comparative expression profiling reveals novel gene functions in female meiosis and gametophyte development in Arabidopsis. The Plant Journal. 80(4): 615-628.

4. Jisen Zhang, Juan Liu, Ray Ming*. (2014). Genomic analyses of the CAM plant pineapple. Journal of Experimental Botany. 65(13): 3395-3404.

3. Jisen Zhang, Adnane Boualem, Abdelhafid Bendahmane*, Ray Ming*. (2014). Genomics of sex determination. Current Opinion in Plant Biology. 18: 110-116.

2. Haibao Tang*, Eric Lyons, James C. Schnable. (2014). Early History of the Angiosperms. Advances in Botanical Research. 69: 195-222.

1. Jianping Wang*, Spurthi Nayak, Karen Koch, Ray Ming. (2013). Carbon partitioning in sugarcane (Saccharum species). Frontiers in Plant Science. 4: 201.