130. Wei Xue, Sarah Anderson, Xufeng Wang, Liyan Yang, Peter Crisp, Qing Li, Jaclyn Noshay, Patrice Albert, James Birchler, Paul Bilinski, Michelle Stitzer, Jeffrey Ross-Ibarra, Xuemei Chen, Nathan Springer, and John Doebley*. (2019). Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize. Genetics, in press.

129. Yu Yu, Yuchan Zhang, Xuemei Chen* and Yueqin Chen*. (2019). Plant noncoding RNAs: hidden players in development and stress responses. Annu. Rev. Cell Dev. Biol., in press.

128. Hailei Zhang, Huan Zhong, Shoudong Zhang, Xiaojian Shao, Min Ni, Zongwei Cai, Xuemei Chen*, and Yiji Xia*. (2019). NAD tagSeq revealed that NAD+-capped RNAs are produced from a large number of protein-coding genes in Arabidopsis, PNAS 116, 12072-12077. PMCID: PMC6575590.

127. Yuan Wang, Shaofang Li, Yonghui Zhao, Chenjiang You, Brandon Le, Zhizhong Gong, Beixin Mo, Yiji Xia and Xuemei Chen*. (2019). NAD+-capped RNAs are widespread in the Arabidopsis transcriptome and can probably be translated. PNAS 116, 12094-12102. PMCID: PMC6575598.

126. Suikang Wang, Li Quan, Shaofang Li, Chenjiang You, Lei Gao, Liping Zeng, Lin Liu, Yanhua Qi, Beixin Mo*, and Xuemei Chen*. (2019). The protein phosphatase 4 complex promotes transcription and processing of primary microRNAs in Arabidopsis. Plant Cell 31, 486-501. PMCID: PMC6447022.

125. Yingnan Hou, Yi Zhai, Li Feng, Hana Z. Karimi, Brian D. Rutter, Liping Zeng, Du Seok Choi, Bailong Zhang, Weifeng Gu, Xuemei Chen, Wenwu Ye, Roger W. Innes, Jixian Zhai, and Wenbo Ma*. (2019). A Phytophthora effector suppresses trans-kingdom RNAi to promote disease susceptibility. Cell Host & Microbe 25, 153-165.

124. Qiang Cai, Chao Liang, Suikang Wang, Yingnan Hou, Lei Gao, Li Liu, Wenrong He, Wenbo Ma, Beixing Mo*, Xuemei Chen*. (2018). The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs. Nature Comms. 9: 5080. PMCID: PMC6265325.

123. Lin Liu and Xuemei Chen*. (2018). Intercellular and systemic trafficking of RNAs in plants. Nature Plants 4, 869-878.

122. Ting Peng, Mengmeng Qiao, Haiping Liu, Sachin Teotia, Yafan Zhao, Dongjie Zhao, Lina Shi, Brandon Le, Kestrel Rogers, Chathura Gunasekara, Haitang Duan, Yiyou Gu, Lei Tian, Zhanhui Zhang, Fanrong Meng, Lan Huang, Qinghui Chen, Zhenlin Wang, Jinshan Tang, Xiaoqing Tang, Hairong Wei, Xuemei Chen, Quanzhi Zhao, and Guiliang Tang*. (2018). A Resource for inactivation of microRNAs using Short Tandem Target Mimic technology in model and crop plants. Mol. Plant 11, 1400–1417.

121. Qili Fei, Yu Yu, Li Liu, Yu Zhang, Patricia Baldrich, Qing Dai, Xuemei Chen and Blake Meyers*. (2018). Biogenesis of a 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation. PNAS 115, 8037-8042. PMCID: PMC6077734.

120. Jiayi Chen, Li Liu, Chenjiang You, Jiaqi Gu, Wenjie Ruan, Lu Zhang, Jianhua Gan, Chunyang Cao, Ying Huang*, Xuemei Chen*, and Jinbiao Ma* (2018). Structural and biochemical insights into small RNA 3' end trimming by Arabidopsis SDN1.
Nature Comms. 9, 3585. PMCID: PMC6123492.

119. Chenlong Li, Chen Chen, Huhui Chen, Suikang Wang, Xuemei Chen, and Yuhai Cui*. (2018). Verification of DNA Motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis. Plant Biotech. J. 16, 1446–1451. PMCID: PMC6041440.

118. Juan Caballero-Pérez, Annie Espinal-Centeno, Francisco Falcon, Luis F. García-Ortega, Everardo Curiel-Quesada, Andrés Cruz-Hernández, Laszlo Bako, Xuemei Chen, Octavio Martínez, Mario Alberto Arteaga-Vázquez, Luis Herrera-Estrella, Alfredo Cruz-Ramírez. (2018). Transcriptional landscapes of Axolotl (Ambystoma mexicanum). Dev. Biol. 433, 227–239.

117. Xuan Ma, Chunyan Liu, Lianfeng Gu, Beixin Mo, Xiaofeng Cao, and Xuemei Chen*. (2018). TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants. Bioinformatics 34, 1574-1576. PMCID: PMC6248703.

116. Lihua Zhao, Hanyang Cai, Zhenxia Su, Lulu Wang, Xinyu Huang, Man Zhang, Piaojuan Chen, Xiaozhuan Dai, Heming Zhao, Ravishankar Palanivelu, Xuemei Chen*, and Yuan Qin*. (2017). KLU suppresses megasporocyte cell fate through SWR1-mediated activation of WRKY28 expression in Arabidopsis. PNAS www.pnas.org/cgi/doi/10.1073/pnas.1716054115; E526–E535. PMCID: PMC5776990.

115. Yu Yu, Tianran Jia, and Xuemei Chen*. (2017). The ‘how’ and ‘where’ of plant microRNAs. New Phytologist 216, 1002-1017. PMCID: PMC6040672.

114. Tianran Jia, Bailong Zhang, Chenjiang You, Yong Zhang, Liping Zeng, Shengjun Li, Kaeli C.M. Johnson, Bin Yu, Xin Li, Xuemei Chen*. (2017). Arabidopsis MOS4-associated complex promotes microRNA biogenesis and pre-mRNA splicing. Plant Cell 29: 2626-2643. doi:10.1105/tpc.17.00370. PMCID: PMC5774577.

113. Chenjiang You, Jie Cui, Hui Wang, Xinping Qi, Li-Yaung Kuo, Hong Ma, Beixin Mo* and Xuemei Chen*. (2017). Conservation and divergence of small RNA pathways and microRNAs in land plants. Genome Biology 18:158. PMCID: PMC5569507.

112. Zhenxia Su, Lihua Zhao, Yuanyuan Zhao, Shaofang Li, So Youn Won, Hanyang Cai, Lulu Wang, Zhenfang Li, Yuan Qin*, and Xuemei Chen*. (2017). The THO complex non-cell autonomously represses female germline specification through the TAS3-ARF3 module. Current Biology 27, 1597–1609. PMCID: PMC5544534.

111. Dongming Li, Ana Marie S Palanca, So Youn Won, Lei Gao, Ying Feng, Ajay A Vashisht, Li Liu, Yuanyuan Zhao, Xigang Liu, Xiuyun Wu, Shaofang Li, Brandon Le, Yun Ju Kim, Guodong Yang, Shengben Li, Jinyuan Liu, James A Wohlschlegel, Hongwei Guo, Beixin Mo, Xuemei Chen*, and Julie A Law*. (2017). The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status. eLife 2017;10.7554/eLife.19893. PMCID: PMC5462541.

110. Yu Yu, Lijuan Ji, Brandon Le, Jixian Zhai, Jiayi Chen, Elizabeth Luscher, Lei Gao, Chunyan Liu, Xiaofeng Cao, Beixin Mo, Jinbiao Ma, Blake C. Meyers, and Xuemei Chen*. (2017). ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis. PLoS Biology 15(2): e2001272. PMCID: PMC5322904.

109. Kaeli C. M. Johnson, Yu Yu, Lei Gao, Ryan C. Eng, Geoffrey O. Wasteneys, Xuemei Chen, and Xin Li*. (2016). A partial loss-of-function mutation in an Arabidopsis RNA polymerase III subunit leads to pleiotropic defects. Journal of Experimental Botany 67, 2219-2230. PMCID: PMC4809280.

108. Shengben Li, Brandon Le, Xuan Ma, Shaofang Li, Chenjiang You, Lin Liu, Lei Gao,Ting Shi, Yonghui Zhao, Beixin Mo, Xiaofeng Cao, and Xuemei Chen*. (2016). Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis. eLife 2016;5:e22750. PMCID: PMC5207768.

107. Yun Ju Kim*, Ruozhong Wang, Lei Gao, Dongming Li, Chi Xu, Hyunggon Mang,
Jien Jeon, June M Kwak, Beixin Mo, Langtao Xiao, and Xuemei Chen*. (2016). POWERDRESS and HDA9 interact and promote histone H3 deacetylation at specific genomic sites in Arabidopsis. PNAS 113, 14858–14863. PMCID: PMC3547843.

106. Zhigang Huang, Ting Shi, Binglian Zheng, Rae Eden Yumul, Xigang Liu, Chenjiang You, Zhihong Gao, Langtao Xiao*, and Xuemei Chen*. (2016). APETALA2 antagonizes the transcriptional activity of AGAMOUS in regulating floral stem cells in Arabidopsis. New Phytologist 15(3): 1197–1209. PMCID: PMC5342953.

105. Chenlong Li, Lianfeng Gu, Lei Gao, Chen Chen, Chuang-Qi Wei, Qi Qiu, Chih-Wei Chien, Suikang Wang, Lihua Jiang, Lian-feng Ai, Chia-Yang Chen, Songguang Yang, Vi Nguyen, Yanhua Qi, Michael P. Snyder, Alma L. Burlingame, Susanne E. Kohalmi, Shangzhi Huang, Xiaofeng Cao, Zhi-Yong Wang, Keqiang Wu, Xuemei Chen, & Yuhai Cui*. (2016). Concerted genomic targeting of histone H3 lysine 27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis. Nature Genetics 48(6), 687-693. PMCID: PMC5134324.

104. Lin Liu and Xuemei Chen* (2016). RNA quality control as a key to suppressing RNA silencing of endogenous genes in plants. Mol. Plant 9(6), 826-36. PMCID: PMC5123867.

103. Shaofang Li, Lin Liu, Shengben Li, Lei Gao, Yuanyuan Zhao, Yun Ju Kim, and Xuemei Chen*. (2016). SUVH1, a Su(var)3-9 family member, promotes the expression of genes targeted by DNA methylation, Nucleic Acids Res. 44 (2), 608-620. PMCID: PMC4737185

102. Jianbo Song, Beixin Mo*, and Xuemei Chen*. (2015). Uridylation and adenylation of RNA. Science China Life Science 58 (11), 1057–1066. PMCID: PMC5089844.

101. Maryam Sanei and Xuemei Chen*. (2015). Mechanisms of microRNA turnover. Curr. Opion. Plant Biol. 27, 199-206. PMCID: PMC4618239.

100. Qiong Zhao, Caiji Gao, PoShing Lee, Lin Liu, Shaofang Li, Tangjin Hu, Jinbo Shen, Shuying Pan, Hao Ye, Yunru Chen, Wenhan Cao, Yong Cui, Peng Zeng, Sheng Yu, Yangbin Gao, Liang Chen, Beixin Mo, Xin Liu, Shi Xiao, Yunde Zhao, Silin Zhong, Xuemei Chen, Liwen Jiang*. (2015). Fast-suppressor screening for new components in protein trafficking, organelle biogenesis and silencing pathway in Arabidopsis thaliana using dominant DEX-inducible FREE1-RNAi plants. Journal of Genetics and Genomics 42, 319-330. PMCID: PMC4686145.

99. Xiaoyan Wang, Shuxin Zhang, Yongchao Dou, Chi Zhang, Xuemei Chen, Bin Yu*, and Guodong Ren*. (2015). Synergistic and independent actions of multiple terminal nucleotidyl transferases in the 3’ tailing of small RNAs in Arabidopsis. PLoS Genetics 11(4): e1005091. PMCID: PMC4415790.

98. Bin Tu, Chi Xu, Li Liu, Jixian Zhai, Shengben Li, Miguel A. Lopez, Yuanyuan Zhao, Yu Yu, Vanitharani Ramachandran, Guodong Ren, Bin Yu, Shigui Li, Blake C. Meyers, Beixin Mo*, and Xuemei Chen*. (2015). Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis. PLoS Genetics 11 (4): e1005119. PMCID: PMC4415760.

97. Yi Huang, Timmy Kendall, Evan S. Forsythe, Ana Dorantes-Acosta, Shaofang Li, Juan Caballero-Perez, Xuemei Chen, Mario Arteaga-Vázquez, Mark A. Beilstein, and Rebecca A. Mosher*. (2015). Ancient origin and recent innovations of RNA Polymerase IV and V. Mol. Biol. and Evo. 32(7):1788-99. PMCID: PMC4476159

96. Chenlong Li, Chen Chen, Lei Gao, Songguang Yang, Vi Nguyen, Xuejiang Shi, Katherine Siminovitch, Susanne E. Kohalmi, Shangzhi Huang, Keqiang Wu, Xuemei Chen, and Yuhai Cui*. (2015). The Arabidopsis SWI2/SNF2 chromatin remodeler BRAHMA regulates Polycomb function during vegetative development and directly activates the flowering repressor gene SVP. PLoS Genetics 11 (1): e1004944. PMCID: PMC4304717.

95. Patricia Lam, Lifang Zhao, Nathan A Eveleigh, Yu Yu, Xuemei Chen, and Ljerka Kunst*. (2015). An exosomal ribonuclease and trans-acting siRNAs regulate cuticular wax biosynthesis during Arabidopsis inflorescence stem development. Plant Physiology 167, 323-336. PMCID: PMC4326755.

94. Shaofang Li, Lee Vandivier, Bin Tu, Lei Gao, So Youn Won, Shengben Li, Binglian Zheng, Brian Gregory, and Xuemei Chen*. (2015). Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis. Genome Research 25, 235-245. PMCID: PMC4315297

93. Thanh Theresa Dinh and Xuemei Chen*. (2015). Chemical genetic screens using Arabidopsis thaliana seedlings grown on solid media. Methods Mol. Biol. 1263, 111-125.

92. Guodong Ren, Xuemei Chen, and Bin Yu*. (2014). Small RNAs meet their targets: when methylation defends miRNAs from uridylation. RNA Biology 11, 1099-1104.

91. So Youn Won, Rae Eden Yumul, and Xuemei Chen*. (2014). Small RNAs in plants: metabolism and function. Molecular Biology, The Plant Sciences 2, 95-127. Springer Science+Business Media New York, S.H. Howell (ed.)

90. Xigang Liu*, Dongming Li, Thanh Theresa Dinh, Bihai Shi, Yongpeng Li, Xiuwei Cao, Lin Guo, Yanyun Pan, Yuling Jiao and Xuemei Chen*. (2014). AUXIN RESPONSE FACTOR 3 integrates the functions of AGAMOUS and APETALA2 in floral meristem determinacy. Plant Journal 80, 629-641. PMCID: PMC4215321.

89. Xigang Liu, Lei Gao, Thanh Theresa Dinh, Ting Shi, Dongming Li, Ruozhong Wang, Lin Guo, Langtao Xiao, and Xuemei Chen*. (2014). DNA topoisomerase I impacts Polycomb Group protein-mediated epigenetic regulation and plant development by reducing nucleosome density in Arabidopsis. Plant Cell 26, 2803-2817. PMCID: PMC4145115.

88. James Wong, Lei Gao, Yang Yang, Jixian Zhai, Siwaret Arikit, Yu Yu, Shuyi Duan, Qin Xiong, Jun Yan, Shengben Li, Renyi Liu, Yuanchao Wang, Guiliang Tang, Blake C. Meyers, Xuemei Chen, Wenbo Ma* (2014). Roles of small RNAs in soybean defense against Phytophthora sojae infection. Plant Journal 79, 928–940. PMCID: PMC5137376.

87. Thanh Theresa Dinh, Lei Gao, Xigang Liu, Dongming Li, Shengben Li, Yuanyuan Zhao, Michael O’Leary, Brandon Le, Robert J. Schmitz, Pablo Manavella, Shaofang Li, Detlef Weigel, Olga Pontes, Joseph R. Ecker, and Xuemei Chen*. (2014). DNA Topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis. PLoS Genet 10(7), e1004446. PMCID: PMC4080997.

86. Yuanyuan Zhao and Xuemei Chen*. (2014). Noncoding RNAs and DNA Methylation in Plants. Natl Sci Rev 1 (2): 219-229. PMCID: PMC4307843.

85. Guodong Ren, Meng Xie, Shuxin Zhang, Carissa Vinovskis, Xuemei Chen*, and Bin Yu*. (2014). Methylation protects microRNAs from an AGO1-associated activity that uridylates 5′ RNA fragments generated by AGO1 cleavage. PNAS 111, 6365-6370. PMCID: PMC4035956.

84. Yun Ju Kim, Alexis Maizel*, and Xuemei Chen*. (2014). Traffic into silence: endomembranes and post‐transcriptional RNA silencing. EMBO J. 33: 968–980. PMCID: PMC4193931.

83. Thanh Theresa Dinh, Elizabeth Luscher, Shaofang Li, Xigang Liu, So Youn Won and Xuemei Chen*. (2014). Genetic screens for floral mutants in Arabidopsis thaliana: enhancers and suppressors. Methods in Molecular Biology 1110, 127-156. PMCID: PMC4306286.

82. Xuan Ma, Xiaofeng Cao, Beixin Mo, and Xuemei Chen*. (2013). Trip to ER: microRNA-mediated translational repression in plants. RNA Biology 10, 1586-1592. PMCID: PMC3866237.

81. Jixian Zhai, Yuanyuan Zhao, Stacey Simon, Sheng Huang, Katherine Petsch, Siwaret Arikit, Manoj Pillay, Lijuan Ji, Meng Xie, XiaoFeng Cao, Bin Yu, Marja Timmermans, Bing Yang, Xuemei Chen, and Blake Meyers*. (2013). Plant microRNAs display differential 3′ truncation and tailing modifications that are ARGONAUTE1 dependent and conserved across species. Plant Cell 25: 2417-2428. PMCID: PMC3753374.

80. Kestrel Rogers and Xuemei Chen*. (2013). Biogenesis, turnover and mode of action of plant microRNAs. Plant Cell 25: 2383-2399. PMCID: PMC3753372.

79. Shengben Li, Lin Liu, Xiaohong Zhuang, Yu Yu, Xigang Liu, Xia Cui, Lijuan Ji, Zhiqiang Pan, Xiaofeng Cao, Beixin Mo, Fuchun Zhang, Natasha Raikhel, Liwen Jiang, and Xuemei Chen*. (2013). microRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell 153, 562-574. PMCID: PMC3694718.

78. Thanh Theresa Dinh, Michael O’Leary, So Youn Won, Shengben Li, Lorena Arroyo, Xigang Liu, Andrew Defries, Binglian Zheng, Sean R. Cutler, and Xuemei Chen*. (2013). Generation of a luciferase-based reporter for CHH and CG DNA methylation in Arabidopsis thaliana. Silence 4:1. PMCID: PMC3623655.

77. Lulu Wang, Xianwei Song, Liangfeng Gu, Xin Li, Shouyun Cao, Chengcai Chu, Xia Cui, Xuemei Chen and Xiaofeng Cao*. (2013). NOT2 proteins promote Pol II-dependent transcription and interact with multiple miRNA biogenesis factors in Arabidopsis. Plant Cell 25, 715-727. PMCID: PMC3608788.

76. Yongli Qiao, Lin Liu, Cristina Flores, James Wong, Xianbing Wang, Qijun Xiang, Xigang Liu, Shushu Jiang, Jinxia Shi, Fuchun Zhang, Howard S. Judelson, Xuemei Chen, Wenbo Ma*. (2013). Oomycete Pathogens Encode RNA Silencing Suppressors. Nature Genetics 45, 330–333. PMCID: PMC4049077.

75. Rae Eden Yumul, Yun Ju Kim, Xigang Liu, Ruozhong Wang, Junhui Ding, Langtao Xiao, and Xuemei Chen*. (2013). POWERDRESS and diversified expression of the MIR172 gene family bolster the floral stem cell network. Plos Genetics 9(1): e1003218. PMCID: PMC3547843.

74. Kestrel Rogers and Xuemei Chen*. (2012). MicroRNA biogenesis and turnover in plants. Cold Spring Harbor Symposia on Quantitative Biology 77, 183-194. PMCID: PMC5127710.

73. Xurong Tang, Shaomin Bian, Mingjuan Tang, Qing Lu, Shengben Li, Xigang Liu, Gang Tian, Vi Nguyen, Edward W.T. Tsang, Aiming Wang, Steven J. Rothstein, Xuemei Chen*, and Yuhai Cui*. (2012). MicroRNA-mediated repression of the seed maturation program during vegetative development in Arabidopsis. Plos Genetics 8(11): e1003091. PMCID: PMC3510056.

72. Yuanyuan Zhao, Beixin Mo*, and Xuemei Chen*. (2012). Mechanisms that impact microRNA stability in plants. RNA Biology 9, 1218-1223. PMCID: PMC3583851.

71. Xuemei Chen*. (2012). Small RNAs in development – insights from plants. Current Opinion in Genetics and Development 22, 361-367. PMCID: PMC3419802.

70. So Youn Won, Shengben Li, Binglian Zheng, Yuanyuan Zhao, Dongming Li, Xin Zhao, Huilan Yi, Lei Gao, Thanh T Dinh and Xuemei Chen*. (2012). Development of a luciferase-based reporter of transcriptional gene silencing that enables bidirectional mutant screening in Arabidopsis thaliana. Silence 2012, 3:6. PMCID: PMC3548752.

69. Tzuu-fen Lee, Sai Guna Ranjan Gurazada, Jixian Zhai, Shengben Li, Stacey A. Simon, Marjori A. Matzke, Xuemei Chen, and Blake C. Meyers*. (2012). RNA Polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics 7, 781-795. PMCID: PMC3679228.

68. Weiqiang Qian, Daisuke Miki, Heng Zhang, Yunhua Liu, Xi Zhang, Kai Tang, Yunchao Kan, Honggui La, Xiaojie Li, Shaofang Li, Xiaohong Zhu, Xiaobing Shi, Kangling Zhang, Olga Pontes, Xuemei Chen, Renyi Liu, Zhizhong Gong, and Jian-Kang Zhu*. (2012). A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 336, 1445-1448. PMCID: PMC3575687.

67. Manassawe Lertpanyasampatha, Lei Gao , Panida Kongsawadworakul, Unchera Viboonjun, Hervé Chrestin, Renyi Liu, Xuemei Chen*, and Jarunya Narangajavana*. (2012). Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high throughput sequencing. Planta 236, 437-445. PMCID: PMC3405184.

66. Thanh Theresa Dinh, Thomas Girke, Xigang Liu, Levi Yant, Markus Schmid and Xuemei Chen*. (2012). The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element. Development 139, 1978-1986. PMCID: PMC3347690.

65. Guodong Ren, Xuemei Chen and Bin Yu*. (2012). Uridylation of miRNAs by HEN1 SUPPRESSOR1 in Arabidopsis. Current Biology 22, 695-700. PMCID: PMC3582666.

64. Yuanyuan Zhao, Yu Yu, Jixian Zhai, Vanitharani Ramachandran, Thanh Theresa Dinh, Blake C. Meyers, Beixin Mo*, and Xuemei Chen*. (2012). The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Current Biology 22, 689-694. PMCID: PMC3350747.

63. Jun Yan, Yiyou Gu, Xiaoyun Jia, Wenjun Kang, Shanjin Pan, Xiaoqing Tang, Xuemei Chen, and Guiliang Tang*. (2012). Effective small RNA destruction by the expression of short tandem target mimic in Arabidopsis thaliana. Plant Cell 24, 415-427. PMCID: PMC3315224.

62. Xuemei Chen and Thomas Laux. (2012). Plant development — a snapshot in 2012. Current Opinion in Plant Biology 15, 1-3.

61. Lijuan Ji and Xuemei Chen*. (2012). Regulation of small RNA stability: Methylation and beyond. Cell Research 22, 624-636. PMCID: PMC3317568.

60. Xigang Liu, Yun Ju Kim, Ralf Müller, Rae Eden Yumul, Chunyan Liu, Yanyun Pan, Xiaofeng Cao, Justin Goodrich, and Xuemei Chen*. (2011). AGAMOUS terminates floral stem cell maintenance in Arabidopsis by directly repressing WUSCHEL through recruitment of Polycomb Group proteins. Plant Cell 23 3654-3670. PMCID: PMC3229141.

59. Boyana Grigorova, Chloe Mara, Courtney Hollender, Paja Sijacic, Xuemei Chen, and Zhongchi Liu*. (2011). LEUNIG and SEUSS co-repressors regulate miR172 expression in Arabidopsis flowers. Development 138, 2451-2456. PMCID: PMC4074289.

58. Binglian Zheng, Xuemei Chen, and Sheila McCormick*. (2011). Dual regulation of Cyclin B1 by the Anaphase-Promoting Complex/Cyclosome during Arabidopsis male gametophyte development. Plant Cell 23, 1033-1046. PMCID: PMC3082252.

57. Lijuan Ji, Xigang Liu, Jun Yan, Wenming Wang, Rae Eden Yumul, Yu Ju Kim, Thanh Theresa Dinh, Jun Liu, Xia Cui, Binglian Zheng, Manu Agarwal, Chunyan Liu, Xiaofeng Cao, Guiliang Tang, and Xuemei Chen*. (2011). ARGONAUTE10 and ARGONAUTE1 regulate the termination of floral stem cells through two microRNAs in Arabidopsis. PLoS Genet 7(3): e1001358. doi:10.1371/journal.pgen.1001358. PMCID: PMC3069122.

56. Yun Ju Kim and Xuemei Chen*. (2011). The plant Mediator and its role in noncoding RNA production. Frontiers in Biology 6(2), 125-132. PMCID: PMC3049218.

55. Binglian Zheng and Xuemei Chen*. (2011). Dynamics of histone H3 lysine 27 trimethylation in plant development. Current Opinion in Plant Biology 14, 123-129. PMCID: PMC3081887.

54. Yun Ju Kim, Binglian Zheng, Yu Yu, So Youn Won, Beixin Mo, and Xuemei Chen*. (2011). The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana. EMBO J. 30, 814-822. PMCID: PMC3049218.

53. Sizolwenkosi Mlotshwa*, Gail Pruss, Zhihuan Gao, Nomathamsanqa Mgutshini, Junjie Li, Xuemei Chen, Lewis Bowman, and Vicki Vance. (2010). Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing. Plant Journal 64, 699-704. PMCID: PMC3059090.

Editorial:.Xuemei Chen. Plant microRNAs at a glance. Seminars in Cell and Developmental Biology. available online: 29-JUL-2010; DOI information: 10.1016/j.semcdb.2010.07.005

52. Levi Yant, Johannes Mathieu, Thanh Theresa Dinh, Felix Ott, Christa Lanz, Heike Wollmann, Xuemei Chen, and Markus Schmid*. (2010). Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2. Plant Cell 22, 2156-2170. PMCID: PMC2929098.

51. Bin Yu, Liu Bi, Jixian Zhai, Manu Agarwal, Shengben Li, Qingfa Wu, Shou-Wei Ding, Blake C. Meyers, Hervé Vaucheret, and Xuemei Chen*. (2010). siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acids Res. 38, 5844-50. PMCID: PMC2943618.

50. Xuemei Chen. (2010). Small RNAs – secrets and surprises of the genome. Plant Journal 61, 941-958. PMCID: PMC3062250.

49. Xian-Bing Wang, Qingfa Wu, Takao Ito, Fabrizio Cillo, Wang-Xiang Li, Xuemei Chen, Jia-Lin Yu, and Shou-Wei Ding*. (2010). Essential role and specificity of viral siRNA amplification by host RNA-directed RNA polymerase in viral immunity against a positive-strand RNA virus. PNAS 107, 484-489. PMCID: PMC2806737.

48. Binglian Zheng, Zhengming Wang, Shengben Li, Bin Yu, Jin-Yuan Liu, and Xuemei Chen*. (2009). Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes & Dev. 23, 2850-2860. PMCID: PMC2800093.

47. Mingxiong Pang, Andrew W Woodward, Vikram Agarwal, Xueying Guan, Misook Ha, Vanitharani Ramachandran, Xuemei Chen, Barbara A Triplett, David M Stelly, and Z Jeffrey Chen*. (2009). Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L). Genome Biology 10: R122. PMCID: PMC3091316.

46. Misook Ha, Jie Lu, Lu Tian, Vanitharani Ramachandran, Kristin D. Kasschau, Elisabeth J. Chapman, James C. Carrington, Xuemei Chen, Xiu-Jie Wang, and Z. Jeffrey Chen*. (2009). Small RNAs serve as a genetic buffer against genomic shock in interspecies hybrids and allopolyploids. PNAS 106, 17835-17840. PMCID: PMC2757398.

45. Bin Yu and Xuemei Chen*. (2010). Analysis of miRNA Modifications. Methods Mol Biol. 592, 137-148. PMCID: PMC5134323.

44. Xuemei Chen*. Small RNAs and their roles in plant development. (2009). Annu. Rev. Cell Dev. Biol. 25, 45-69. PMCID: PMC5135726.

43. Ying Huang, Lijuan Ji, Qichen Huang, Dmitry G. Vassylyev, Xuemei Chen, Jin-Biao Ma*. (2009). Structural insights into the molecular mechanism of the small RNA methyltransferase HEN1. Nature 461, 823-827. PMCID: PMC5125239.

42. Manu Agarwal, Julien Curaba, and Xuemei Chen*. (2009). Endogenous small RNA pathways in Arabidopsis. Chapter 11 in “Regulation of Gene Expression by Small RNAs”, edited by J. Rossi and J. Gaur, published by CRC press.

41. Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen*, and Tao Jiang*. (2009). Computational prediction of novel non-coding RNAs in Arabidopsis thaliana. BMC Bioinformatics 10(Suppl 1):S36. PMCID: PMC2648795.

40. Blake C. Meyersa, Michael J. Axtell, Bonnie Bartel, David P. Bartel, David Baulcombe, John L. Bowman, Xiaofeng Cao, James C. Carrington, Xuemei Chen, Pamela J. Green, Sam Griffiths-Jones, Steven E. Jacobsen, Allison C. Mallory, Robert A. Martienssen, R. Scott Poethig, Yijun Qi, Herve Vaucheret, Olivier Voinnet, Yuichiro Watanabe, Detlef Weigel and Jian-Kang Zhu. (2008). Criteria for Annotation of Plant MicroRNAs. Plant Cell 20, 3186-3190. PMCID: PMC2630443.

39. Vanitharani Ramachandran and Xuemei Chen*. (2008). Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 321, 1490-1492. PMCID: PMC2570778.

38. Bin Yu, Liu Bi, Binglian Zheng, Lijuan Ji, David Chevalier, Manu Agarwal, Vanitharani Ramachandran, Wanxiang Li, Thierry Lagrange, John C Walker, and Xuemei Chen*. (2008). The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. PNAS 105, 10073-10078. PMCID: PMC2481372.

37. Vanitharani Ramachandran and Xuemei Chen*. (2008). Small RNA metabolism in Arabidopsis. Trends in Plant Science 13, 368-374. PMCID: PMC2569976.

36. Xuemei Chen*. (2008). A silencing safeguard: links between RNA silencing and mRNA processing in Arabidopsis. Dev. Cell 14, 811-812. PMCID: PMC2570776.

35. Jixian Zhai, Jun Liu, Bin Liu, Pingchuan Li, Blake C. Meyers, Xuemei Chen and Xiaofeng Cao*. (2008). Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. Plos Genetics 4(4):e1000056. Doi: 10.1371/journal.pgen.1000056; PMCID: PMC2289841.

34. Sizolwenkosi Mlotshwa, Gail J. Pruss, Angela Peragine, Matthew W. Endres, Junjie Li, Xuemei Chen, R. Scott Poethig, Lewis H. Bowman, and Vicki Vance*. (2008). DICER-LIKE2 plays a primary role in transitive silencing of transgenes in Arabidopsis. Plos One 3(3), e1755. doi:10.1371/journal.pone.0001755; PMCID: PMC2262140.

33. Julien Curaba and Xuemei Chen*. (2008). Biochemical activities of Arabidopsis RNA-dependent RNA polymerase 6. Journal of Biological Chemistry 283, 3059-3066. PMCID: PMC2629599.

32. Xuemei Chen. (2008). MicroRNA metabolism in plants. Current Topics in Microbiology and Immunology 320, 117-136. PMCID: PMC2570777.

31. Li Zhao, YunJu Kim, Theresa Dinh, and Xuemei Chen*. (2007). miR172 regulates stem cell fate and defines the inner boundary of APETALA3 and PISTILLATA expression domain in Arabidopsis floral meristems. Plant Journal 51, 840-849. PMCID: PMC2629596.

30. Zhiyong Yang, Giedrius Vilkaitis, Bin Yu, Saulius Klimašauskas, and Xuemei Chen*. (2007). Approaches for studying microRNA and small interfering RNA methylation in vitro and in vivo. Methods in Enzymology 427, 139-154. PMCID: PMC3574582.

29. Victor Ambros and Xuemei Chen. (2007). The regulation of genes and genomes by small RNAs. Development 134, 1635-1641.

28. Xuemei Chen*. (2007). A marked end. Nature Structural and Molecular Biology 14, 259-260. PMCID: PMC3578389.

27. Sizolwenkosi Mlotshwa, Zhiyong Yang, YunJu Kim, and Xuemei Chen*. (2006). Floral patterning defects induced by Arabidopsis APETALA2 and microRNA172 expression in Nicotiana benthamiana. (2006). Plant Molecular Biology 61, 781-793. PMCID: PMC3574581.

26. Bin Yu, Elisabeth J. Chapman, Zhiyong Yang, James C. Carrington, and Xuemei Chen*. (2006). Transgenically expressed viral RNA silencing suppressors interfere with microRNA methylation in Arabidopsis. FEBS Letters 580, 3117-3120. PMCID: PMC5136478.

25. Zhiyong Yang, Yon W. Ebright, Bin Yu, and Xuemei Chen*. (2006). HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2’ OH of the 3’ terminal nucleotide. Nuclei Acids Res. 34, 667-675. PMCID: PMC1356533.

24. Xuemei Chen*. (2005). microRNA biogenesis and function in plants. FEBS Letters 579, 5923-5931. PMCID: PMC5127707.

23. Junjie Li, Zhiyong Yang, Bin Yu, Jun Liu, and Xuemei Chen*. (2005). Methylation protects miRNAs and siRNAs from a 3’ end uridylation activity in Arabidopsis. Current Biology 15, 1501-1507. PMCID: PMC5127709.
--- Featured in “Editors' Choice: Highlights of the recent literature”. Science 309, 1651.

22. Xuemei Chen*. (2005). Post-transcriptional processes and floral patterning. Flowering newsletter 39, 19-22.

21. Bin Yu, Zhiyong Yang, Junjie Li, Svetlana Minakhina, Maocheng Yang, Richard W. Padgett, Ruth Steward, and Xuemei Chen*. (2005). Methylation as a crucial step in plant microRNA biogenesis. Science 307, 932-935. PMCID: PMC5137370.

20. Jun Liu, Yuehui He, Rick Amasino, and Xuemei Chen*. (2004). SiRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis. Genes Dev., 18, 2873-2878. PMCID: PMC534648.

19. Wenming Wang and Xuemei Chen*. (2004). HUA ENHANCER3 reveals a role for a cyclin-dependent protein kinase in the specification of floral organ identity in Arabidopsis. Development 131, 3147-3156. PMCID: PMC5142244.

18. Xuemei Chen*. (2004). A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303, 2022-2025. PMCID: PMC5127708.

17. Yulan Cheng and Xuemei Chen*. (2004). Post-transcriptional control in plant development. Current Opinion in Plant Biology 7, 20-25. PMCID: PMC5125221.

16. Junjie Li and Xuemei Chen*. (2003). PAUSED, a putative exportin-t, acts in multiple developmental processes but is dispensable for viability in Arabidopsis. Plant Physiology 132, 1913-1924. PMCID: PMC181277.

15. Stéphanie Boutet, Franck Vazquez, Jun Liu, Christophe Béclin, Mathilde Fagard, Ariane Gratias, Jean-Benoit Morel, Patrice Crété, Xuemei Chen, and Hervé Vaucheret. (2003). Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling post-transcriptional gene silencing and virus resistance. Current Biology 13, 843-848. PMCID: PMC5137371.

14. Victor Ambros, Bonie Bartel, David P. Bartel, Christopher B. Burge, James C. Carrington, Xuemei Chen, Gideon Dreyfuss, Dean Eddy, Sam Griffiths-Jones, Marjori Matzke, Gary Ruvkun, and Thomas Tuschl. (2003). A uniform system for microRNA annotation. RNA 9, 277-279. PMCID: PMC1370393.

13. Yulan Cheng, Naohiro Kato, Wenming Wang, Junjie Li, and Xuemei Chen*. (2003). Two RNA-binding proteins, HEN4 and HUA1, act in the processing of AGAMOUS pre-mRNA in Arabidopsis thaliana. Dev. Cell 4, 53-66. PMCID: PMC5135010.

12. Wonkeun Park, Junjie Li, Rentao Song, Joachim Messing, and Xuemei Chen*. (2002). CARPEL FACTORY, the Dicer homologue, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Current Biology 12, 1484-1495. PMCID: PMC5137372.

11. Tamara Western, Yulan Cheng, Jun Liu, and Xuemei Chen*. (2002). HUA ENANCER2, a putative DExH-box RNA helicase, maintains homeotic B and C gene expression in Arabidopsis. Development 129, 1569-1581. PMCID: PMC5136479.

10. Xuemei Chen*, Jun Liu, Yulan Cheng, and Dongxuan Jia. (2002). HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development 129, 1085-1094. PMCID: PMC5137379.

9. Junjie Li, and Dongxuan Jia, and Xuemei Chen*. (2001). HUA1, a regulator of stamen and carpel identities in Arabidopsis, codes for a nuclear zinc finger protein. Plant Cell 13, 2269-2281. PMCID: PMC139158.

8. Xuemei Chen, José Luis Riechmann, Dongxuan Jia and Elliot Meyerowitz. (2000). The minimal regulatory region of the floral homeotic gene PISTILLATA does not contain a CArG box. Sexual Plant Reproduction 13, 85-94.

7. Xuemei Chen, and Elliot M. Meyerowitz. (1999). HUA1 and HUA2 are two members of the floral homeotic AGAMOUS pathway. Mol. Cell 3, 349-360.

6. Joshua Z. Levin, Jennifer C. Fletcher, Xuemei Chen and Elliot M. Meyerowitz. (1998). A genetic screen for modifiers of UFO meristem activity identifies three novel FUSED FLORAL ORGANS genes required for early flower development in Arabidopsis. Genetics 149, 579-595. PMCID: PMC1460208.

5. Xuemei Chen, Clare L. Simpson, Karen Kindle and David Stern*. (1997). A dominant mutation in the Chlamydomonas reinhardtii nuclear gene SIM30 suppresses translational defects caused by initiation codon mutations in chloroplast genes. Genetics 145, 935-943. PMCID: PMC1207898.

4. Xuemei Chen, Karen Kindle and David Stern*. (1995). The initiation codon determines the efficiency but not the site of translation initiation in Chlamydomonas reinhardtii chloroplasts. Plant Cell 7, 1295-1305. PMCID: PMC160952.

3. Wataru Sakamoto, Xuemei Chen, Karen Kindle and David Stern (1994). Function of the Chlamydomonas reinhardtii petD 5' untranslated region in regulating the accumulation of subunit IV of the cytochrome b6/f complex. Plant Journal 6, 503-512.

2. Xuemei Chen, Karen Kindle and David Stern. (1993). Initiation codon mutations in the Chlamydomonas chloroplast petD gene result in temperature-sensitive photosynthetic growth. EMBO J. 12, 3627-3635.

1. Candace W. Collmer, Laura Stenzler, Xuemei Chen, Nicholas Fay, David Hacker, and Stephen H. Howell*. (1992). Single amino acid change in the helicase domain of the putative RNA replicase of turnip crinkle virus alters symptom intensification by virulent satellites. PNAS 89, 309-313. PMCID: PMC48226.