2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 
2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2001 | 1999 & Earlier


My Bibliography

Google Scholar


138. June, V., Song, X., Chen, Z. J. (2023) Imprinting but not cytonuclear interactions affetcs parent-of-origin effct on seed size in Arabidopsis hybrids. bioRxiv

137. June, V., Xu, D., Papoulas, O., Boutz, D., Marcotte, E.D., Chen, Z. J. (2023) Protein nonadditive expression and solubility contribute to heteorisis in Arabidopsis hybrids and allotetraploids. Front. Plant Sci. 14:1252564. PubMed

136. Cao, S., Chen, K., Lu, K., Chen, S., Zhang, X., Shen, C., Zhu, S., Niu, Y., Fan, L., Chen, Z.J., Xu, J., Song, Q. (2023) Pan-epigenome of rice uncovers reversal of DNA methylation changes during domestication and de-domestication. The Plant Cell 35:3429-3443. PubMed


135. Ando, A., Kirkbride, R. C., Qiao, H., Chen, Z. J. (2022) Maternal-specific expression of EIN2 in the endosperm affects endosperm cellularization and seed size in ArabidopsisGenetics 223(2):iyac161. PubMed

134. Li, Z., Chen, Z.J. (2022) Nonadditive gene expression and epigenetic changes in polyploid plants and crops. Advances in Agronomy. ScienceDirect

133. Cao, S., Wang, L., Han, T., Ye, W., Liu, Y., Sun, Y., Moose, S. P., Song, Q., Chen, Z. (2022) Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maizeGenome Biology 23:53. PubMed


132. Han, T., Wang, F., Song. Q., Ye, W., Liu, D., Wang, L., Chen, Z. J. (2021) An epigenetic basis of inbreeding depression in maize. Science Advances 7(35): eabg5442. Pubmed

131. Jiang, X.Y., Song, Q. X., Ye, W. X., Chen, Z. J. (2021) Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids. Nature Ecology & Evolution 5(10):1382-1393. PubMed

130. Wang, L., Cao, S., Wang, P., Song, Q., Zhao, F.-J., Chen, Z. J. (2021) DNA hypomethylation in tetraploid rice potentiates stress-responsive gene expression for salt tolerance. Proc. Natl. Acad. Sci. U.S.A. 118(13):e2023981118. Pubmed

129. Wang, L., Jia, G., Jiang, X., Cao, S., Chen, Z. J., Song, Q. (2021) Altered chromatin architecture and gene expression during polyploidization and domestication of soybean. Plant Cell 33:1430-1446. PubMed

128. Ando, A., Ryan C. Kirkbride, R. C., Jones, D.C., Grimwood, J., Chen, Z. J. (2021) LCM and RNA-seq analysis revealed new roles of cell cycle and translational regulation in early stages of cotton fiber cell development. BMC Genomics 22:309. Pubmed

127. Liu, Y., YuanJ., Jia, G., Chen, Z. J., Song, Q. (2021) Histone H3K27 dimethylation landscapes contribute to genome stability and genetic recombination during wheat polyploidization. Plant Journal 105:678-690. PubMed


126. Chen, Z. J., Sreedasyam, A., Ando, A., Song, Q., De Santiago, L. M., Hulse-Kemp, A. M., Ding, M., Ye, W., Kirkbride, R. C., Jenkins, J., Plott, C., Lovell, J., Lin, Y.-M., Vaughn, R., Liu, B., Wen, L., Simpson, S., Scheffler, B. E., Saski, C. A., Grover, C. E., Hu, G., Conover, J., Carlson, J. W., Shu, S., Boston, L. B., Williams, M., Peterson, D. G., McGee, K., Jones, D. C., Wendel, J. F., Stelly, D. M., Grimwood, J., Schmutz, J. (2020) Genomic diversifications of five allopolyploid Gossypium species and their impact on cotton improvement. Nature Genetics 52:525-533. PubMed Press Release

125. McWhite, C. D., Papoulas, O., Drew, K., Cox, R. M., June, V., Dong, O. X., Kwon, T., Wan, C, Salmi , M. L., Roux, S. J., Browning, K. S., Chen, Z. J., Ronald, P. C., Marcotte, E. M. (2020) A pan-plant protein complex map reveals deep conservation and novel assemblies. Cell 181:460-474.e14. PubMed Press Release

124. Song, Q., Ando, A., Jiang, N., Ikeda, Y., Chen, Z. J. (2020) Single-cell analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes. Genome Biology 21:178. PubMed

123. Wang, F., Han, T., Song, Q., Ye, W., Song, X., Chu, J., Li., J., Chen, Z. J. (2020) The rice circadian clock regulates tiller growth and panicle development through strigolactone signaling and sugar sensing. Plant Cell 32:3124-3138. PubMed Editorial in Brief

122. Li, Z., Zhu, A., Song, Q., Chen, H. Y., Harmon, F. G., Chen, Z. J. (2020) Temporal regulation of metabolome and proteome in photosynthetic and photorespiratory pathways contributes to maize heterosis. Plant Cell 32:3706-3722. PubMed

121. Yuan, J., Jiao, W., Liu, Y., Ye, W., Wang, X., Liu, B., Song, Q., Chen, Z. J. (2020) Dynamic DNA methylation changes in response to genome merger and separation during hexaploid wheat evolution. BMC Biology 18:171. Pubmed

120. Luo, J., Chai, J., Wen, Y., Tao, M., Lin, G., Liu, X., Ren, L., Chen, Z., Wu, S., Li, S., Wang, Y., Qin, Q., Wang, S., Gao, Y., Huang, F., Wang, L., Ai, C., Wang, X., Li, L., Ye, C., Yang, H., Luo, M., Chen, J., Hu, H., Yuan, L., Zhong, L., Wang, J., Xu, J., Du, Z., Ma, Z. (S.), Murphy, R. W., Meyer, A., Gui, J., Xu, P., Ruan, J., Chen, Z. J., Liu, S., Lu, X., Zhang, Y. (2020) From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish. Science Advances 6: eaaz7677. PubMed


119. Kirkbride, R. C., Lu, J., Zhang, C., C., Mosher, R. A., Baulcombe, D. C., Chen, Z. J. (2019) Maternal small RNAs mediate spatial and temporal regulation of gene expression, imprinting, and seed development in ArabidopsisProc. Natl. Acad. Sci. USA 116:2761-2766. PubMed Press Release

118. Song, Q., Huang, T.-Y., Yu, H. H., Ando, A., Mas, P., Ha, M., Chen, Z. J. (2019) Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis. Genome Biology 20:170. PubMed

117. Yin, D., Ji, C., Song, Q.*, Zhang, W., Zhang, X., Zhao, K., Chen, C. Y., Wang, C., He, G., Liang, Z., Ma, X., Li, Z., Tang, Y., Wang, Y., Li, K., Ning, L., Zhang, H., Zhu, W., Li, X., Yu, H., Lei, Y., Wang, M., Ma, L., Zheng, H., Zhang, Y., Zhang, J., Hu, W., Chen, Z. J. (2019) Comparison of Arachis monticola with diploid and cultivated tetraploid genomes reveals asymmetric subgenome evolution and improvement of peanut. Advanced Science 7:1901672. PubMed

116. Chen, Z. J., Mas, P. (2019) Interactive roles of chromatin regulation and circadian clock function in plants. Genome Biology 20:62. PubMed


115. Song, Q., Ando, A., Xu, D., Fang, L., Zhang, T., Huq, E., Qiao, H., Deng, X. W., Chen, Z. J. (2018) Diurnal down-regulation of ethylene biosynthesis mediates biomass heterosis. Proc. Natl. Acad. Sci. USA 115:5606-5611. PubMed Press Release

114. Zhao, X., Jiang, Y., Li, J., Huq, E., Chen, Z. J., Xu, D., Deng, X. W. (2018) COP1 SUPPRESSOR 4 promotes seedling photomorphogenesis by repressing CCA1and PIF4 expression in Arabidopsis. Proc. Natl. Acad. Sci. USA 115:11631-11636. PubMed

113. Ding, M., Chen, Z. J. (2018) Epigenetic perspectives on the evolution and domestication of polyploid plants and crops. Current Opinions in Plant Biology 42:37-48. PubMed

112. Jiao, W., Yuan, J., Jiang, S., Liu, Y., Wang, L., Liu, M., Zheng, D., Ye, W., Wang, X., Chen, Z.J. (2018) Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids. Plant Journal 93:828-842 PubMed

111. Wang, L., Yuan, J., Ma, Y., Jiao, W., Ye, W., Yang, D.L., Yi, C., Chen, Z.J. (2018) Rice interploidy crosses disrupt epigenetic regulation, gene expression, and seed development. Molecular Plant 11:300-314. PubMed

110. Lin, F., Yan Jiang, Y., Jian Li, J., Yan, T., Fan, L., Liang, J., Chen, Z. J., Xu, D., Deng, X. W. (2018) BOX DOMAIN PROTEIN28 Negatively Regulates Photomorphogenesis by Repressing the Activity of Transcription Factor HY5 and Undergoes COP1-mediated Degradation. Plant Cell 30:2006-2019. PubMed 


109. Song, Q., Zhang, T., Stelly, D. M., and Chen, Z. J. (2017) Epigenomic and functional analyses reveal roles for epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons. Genome Biology 18:99. PubMed Press Release

108. Fang, L., Gong, H., Hu, Y., Liu, C., Zhou, B., Huang, T., Wang, Y., Chen, S., Fang, D. D., Du, X., Chen, H., Chen, J., Wang, S., Wang, Q., Wan, Q., Liu, B., Pan, M., Chang, L., Wu, H., Mei, G., Xiang, D., Li, X., Cai, C., Zhu, X., Chen, Z. J., Han, H., Chen, X., Guo, W., Zhang, T., and Huang, X. (2017) Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons. Genome Biology 18:33. PubMed

107. Yuan, J., Jiao, W., Wang, L., Ma, Y., Ye, W., Jin, Z., Lu, J., Hong, D., You, S., Cheng, Z., and Chen, Z. J. (2017) Both maternally and paternally imprinted genes regulate seed development in rice. New Phytologist 216:373-387. PubMed

106. Ng, D. W-K., Chen, H. H. Y., and Chen, Z. J. (2017) Heterologous protein-DNA interactions lead to biased allelic expression of circadian clock genes in interspecific hybrids. Scientific Reports 7:45087. PubMed

105. Saski, C. A., Scheffler, B. E., Hulse-Kemp, A. M., Liu, B., Song, Q., Ando, A., Stelly, D. M., Scheffler, J. A., Grimwood, J., Jones, D. C., Peterson, D. G., Schmutz, J., and Chen, Z. J. (2017) Subgenome anchored physical frameworks and an approach toward reference-grade assemblies of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome. Scientific Reports 7(1):15274. PubMed 


104. Zheng, D., Ye, W., Song, Q., Han, F., Zhang, T., and Chen, Z. J. (2016) Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton. Plant Physiology 172:1760-1771. PubMed

103. Ko, D. K., Rohozinski, D., Song, Q., Taylor, S. H., Juenger, T. E., Harmon, F. G., Chen, Z. J. (2016) Temporal shift of circadian-mediated gene expression and carbon fixation contributes to biomass heterosis in maize hybrids. PLoS Genetics 12(7): e1006197. PubMed Press Releasse


102. Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, C. A., Scheffler, B. E., Stelly, D. M., Hulse-Kemp, A. M., Wan, Q., Liu, B., Liu, C., Wang, S., Pan, M., Wang, Y., Wang, D., Ye, W., Chang, L., Zhang, W., Song, Q., Kirkbride, R. C., Chen, X., Dennis, E., Llewellyn, D. J., Peterson, D. G., Thaxton, P., Jones, D. C., Wang, Q., Xu, X., Zhang, H., Wu, H., Zhou, L., Mei, G., Chen, S., Tian, Y., Xiang, D., Li, X., Ding, J., Zuo, Q., Tao, L., Liu, Y., Li, J., Lin, Y., Hui, Y., Cao, Z., Cai, C., Zhu, X., Jiang, Z., Zhou, B., Guo, W., Li, R., and Chen, Z. J. (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology 33:531-537. PubMed Press Release

101. Liu, X., Zhao, B., Zheng, H.-J., Hu, Y., Lu, G., Yang, C.-Q., Chen, J.-D., Chen, J.-J., Chen, D.-Y., Zhang, L., Zhou, Y., Wang, L.-J., Guo, W.-Z., Bai, Y.-L.; Ruan, J.-X., Shangguan, X.-X., Mao, Y.-B., Shan, C.-M., Jiang, J.-P., Zhu, Y.-Q., Jin, L., Kang, H., Chen, S.-T., He, X.-L., Wang, R., Wang, Y.-Z., Chen, J., Wang, L.-J., Yu, S.-T., Wang, B.-Y., Wei, J., Song, S.-C., Lu, X.-Y., Gao, Z.-C., Gu, W.-Y., Deng, X., Ma, D., Wang, S., Liang, W.-H., Fang, L., Cai, C.-P., Zhu, X.-F., Zhou, B.-L., Chen, Z. J., Xu, S.-H., Xu, S.-H., Zhang, Y.-G., Wang, S.-Y., Zhang, T.-Z., Zhao, G.-P., and Chen, X.-Y. (2015) Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites. Scientific Reports 5:14139. PubMed

100. Song, Q., Guan, X., and Chen, Z. J. (2015) Dynamic roles for small RNAs and DNA methylation during ovule and fiber development in allotetraploid cotton. PLoS Genetics 11(12):e1005724. PubMed

99. Miller, M., Song, Q., Shi, X., Juenger, T. E., and Chen, Z. J. (2015) Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of ArabidopsisNature Communications 6:7453. PubMed

98. Shi, X., Zhang, C., Ko, D.-K., and Chen, Z. J. (2015) Genome-wide dosage-dependent and -independent regulation contributes to gene expression and evolutionary novelty in plant polyploids.Molecular Biology and Evolution 32:2351-2366. PubMed

97. Kirkbride, R. C., Yu, H. H., Nah, G., Zhang, C., Shi, X., and Chen, Z. J. (2015) An epigenetic role for disrupted paternal gene expression in postzygotic seed abortion in Arabidopsis interspecific hybrids. Molecular Plant 8:1766-1775. PubMed

96. Song, Q. and Chen, Z. J. (2015) Epigenetic and developmental regulation in plant polyploids. Current Opinions in Plant Biology 24:101–109. PubMed

95. Gao, M.-J., Li, X., Huang, J., Gropp, G. M., Gjetvaj, B., Lindsay, D. L., Wei, S., Coutu, C., Chen, Z., Wan, X. C., Hannoufa, A., Lydiate, D. J., Gruber, M. Y., Chen, Z. J., Hegedus, D. D. (2015) SCARECROW-LIKE15 interacts with HISTONE DEACETYLASE19 and is essential for repressing the seed maturation program. Nature Communications 6:7243. PubMed

94. Tuttle, J. R., Nah, G., Duke, M. V., Alexander, D. C., Guan, X., Song, Q., Chen, Z. J., Scheffler, B. E., and Haigler, C. H. (2015) Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation. BMC Genomics 16:477. PubMed

93. Hulse-Kemp, A. M., Ashrafi, H., Stoffel, K., Zheng, X., Saski, C., Scheffler, B. E., Fang, D. D., Chen, Z. J., Van Deynze, A., and Stelly D. M. (2015) BAC-end sequence-based SNP mining in allotetraploid cotton (Gossypium) utilizing resequencing data, phylogenetic inferences and perspectives for genetic mapping. G3 5:1095-1105. PubMed

92. Kim, H. J., Hinchliffe, D. J., Barbara A. Triplett, B. A., Chen, Z. J., Stelly, D. M., Yeater, K. M., Moon, H., Gilbert, M. K., Thyssen, G., Turley, R. B., Fang, D. D. (2015) Phytohormonal networks promote differentiation of fiber initials on preanthesis cotton ovules grown in culture and in planta. PLoS One 10:e0125046. PubMed

91. Ashrafi, H., Hulse-Kemp, A. M, Wang, F., Yang, S. S., Guan, X., Jones, D. C., Matvienko, M., Mockaitis, K., Chen, Z. J., Stelly, D. M., and Van Deynze, A. (2015) A long-read transcriptome assembly of cotton (Gossypium hirsutum L.) and intraspecific single nucleotide polymorphism discovery. Plant Genome 8(2) 1-14. Article


90. Ng, D. W-K., Miller, M., Yu, H. H., Huang, T-.Y., Kim, E-D., Lu, J., Xie, Q., McClung, C. R., and Chen, Z. J. (2014) A role for CHH methylation in the parent-of-origin effect on circadian rhythms and biomass heterosis in plant hybrids. Plant Cell 26:2430-2440. PubMed

89. Guan, X., Song, Q., Chen, Z. J. (2014) Polyploidy and small RNA regulation of cotton fiber development. Trends in Plant Science 19:516-528. PubMed

88. Guan, X., Pang, M., Nah, G., Shi, X., Ye, W., Stelly, D. M., and Chen, Z. J. (2014) miR828 and miR858 regulate homoeologous MYB2 gene functions in Arabidopsis trichome and cotton fibre development. Nature Communications 5:3050. PubMed

87. Guan, X., Nah, G., Song, Q., Udall, J. A., Stelly, D. M., Chen, Z. J. (2014) Transcriptome analysis of extant cotton progenitors revealed tetraploidization and identified genome-specific single nucleotide polymorphism in diploid and allotetraploid cotton. BMC Research Notes 7:493. PubMed

86. Shan, C.-M., Shangguan X.-X., Zhao, B., Zhang, X.-F., Chao, L.-M., Yang, C.-Q., Wang, L.-J., Zhu, H.-Y., Zeng, Y.-D., Guo, W.-Z., Zhou, B.-L., Hu, G.-J., Guan, X.-Y., Chen, Z. J., Wendel, J. F., Zhang, T.-Z., and Chen, X.-Y. (2014) Control of cotton fiber elongation by a homeodomian transcription factor GhHOX3.Nature Communications 5:5519. PubMed

85. Tian, L., Li, X. W., Ha, M., Zhang, C., and Chen, Z. J. (2014) Genetic and epigenetic changes in a genomic region containing MIR172 in Arabidopsis allopolyploids and their progenitors. Heredity 112: 207–214. PubMed

84. Ng, D. W.-K., Shi, X., Nah, G., Chen, Z. J. (2014) High-throughput RNA-seq for allelic or locus-specific expression analysis in Arabidopsis related species, hybrids, and allotetraploids. In Spillane, C. and Mckeown, P. C. (eds.) Plant Epigenetics and Epigenomics. Springer, New York (doi: 10.1007/978-1-62703-773-0_3). Methods in Molecular Biology 1112:33-48. PubMed


83. Chen, Z. J. (2013) Genomic and epigenetic insights into the molecular bases of heterosis. Nature Reviews Genetics 14:471-482. PubMed

82. Chen, Z. J. and Birchler, J. A. (2013) Polyploid and Hybrid Genomics. Wiley-Blackwell, New York. pp. 363 (ISBN 978-0-470-96037-0)

81. Chen, Z. J. and Yu, H. H. (2013) Chapter 21. Genetic and epigenetic mechanisms for polyploidy and hybridity. In Chen, Z. J. and Birchler, J. A. (eds.) Chapter 21. Polyploid and Hybrid Genomics. p335-354. Wiley-Blackwell, New York. (DOI: 10.1002/9781118552872.ch21)

80. Guan, X. and Chen, Z. J. (2013) Chapter 11. Cotton fiber genomics. In Becraft, P. W. (ed.) Seed Genomics. p203-216. Wiley-Blackwell, New York. (DOI: 10.1002/9781118525524.ch11)


79. Shi, X., Ng, D. W-K., Zhang, C., Comai, L. Ye, W., and Chen, Z. J. (2012) Cis- and trans-regulatroy divergence between progenitor species determines gene expression novelty in Arabidopsis allopolyploids. Nature Communications 3:950. PubMed

78. Lu, J., Zhang, C., Baulcombe, D. C., and Chen, Z. J. (2012) Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds. Proc. Natl. Acad. Sci. USA 109:5529-5534. PubMed

77. Miller, M., Zhang, C., and Chen, Z. J. (2012) Ploidy and hybridity effects on growth vigor and gene expression in Arabidopsis thaliana hybrids and their parents. G3: Genes, Genomes, Genetics 2:505-513. PubMed

76. Ng, D. W-K., Zhang, C., Miller, M., Shen. Z., Briggs, S. P., and Chen, Z. J. (2012) Proteomic divergence in Arabidopsis auto- and allopolyploids and their progenitors. Heredity 108:419-430. PubMed

75. Zhang, C., Ng, D. W.-K., Lu, J. and Chen, Z. J. (2012) Roles of target site location and sequence complementarity in trans-acting siRNA formation in Arabidopsis. Plant Journal 69:217-226. PubMed

74. Ng, D. W-K., Lu, J. and Chen, Z. J. (2012) Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility. Current Opinions in Plant Biology 15:154-161. PubMed

73. Sung, S., Huq, E., and Chen, Z. J. (2012) International plant molecular biology: a bright future for green science. Genome Biology 13:323. PubMed

72. Chen, Z. J. (2012) Plant Hybrid Vigor. McGraw-Hill Yearbook of Science & Technology 2012. p.188-191. McGraw-Hill Professional Publishing, New York. (9780071774031 • 0071774033)


71. Ng, D. W., Zhang, C., Miller, M., Palmer, G., Whiteley, M., Tholl, D., and Chen, Z. J. (2011) Cis- andtrans-regulation of miR163 and target genes confers natural variation of secondary metabolites in twoArabidopsis species and their allopolyploids. Plant Cell 23:1729-1740. PubMed

70. Ha, M., Ng, D. W.-K., Li, W.-H., and Chen, Z. J. (2011) Coordinated histone modifications are associated with gene expression variation within and between species. Genome Research 21:590-598. PubMed

69. Chen, Z. J. and Guan, X. (2011) Auxin boost for cotton. Nature Biotechnology 29:407-409. PubMed

68. Guan X., Lee, J.J., Pang, M., Shi, X., Stelly, D.M., and Chen, Z.J. (2011) Activation of Arabidopsis seed hair development by cotton fiber-related genes. PLoS One 6(7): e21301. PubMed

67. Kim, E. D. and Chen, Z. J. (2011) Unstable transcripts in Arabidopsis allotetraploids are associated with nonadditive gene expression in response to abiotic and biotic stresses PLoS One 6(8):e24251. PubMed

66. Mayfield, D., Chen, Z. J., and Pires, J. C. (2011) Epigenetic regulation of flowering time in polyploids. Current Opinions in Plant Biology 14:174–178. PubMed

65. Lu, J. and Chen, Z. J. (2011) Small RNA inheritance in hybrids and allopolyploids. In Erdmann, V. A. and Barciszewski, J. (eds.), Non-coding RNAs in Plants, RNA Technologies. Springer-Verlag Berlin Heidelberg. p.91-106. (DOI: 10.1007/978-3-642-19454-2_7)


64. Chen, Z. J. (2010) Molecular mechanisms of polyploidy and hybrid vigor. Trends in Plant Science15:57-71. PubMed

63. Jackson, S. and Chen, Z. J. (2010) Genomic and expression plasticity of polyploidy. Current Opinions in Plant Biology 13:153-159. PubMed

62. Nah, G. and Chen, Z. J. (2010) Tandem duplication of FLC locus and the origin of a new gene inArabidopsis related species. New Phytologist 186:228-238. PubMed

61. Lackey, E., Ng, D. W.-K. and Chen, Z. J. (2010) RNAi-mediated down-regulation of DCL1 and AGO1induces developmental changes in resynthesized Arabidopsis allotetraploids. New Phytologist 186:207-215. PubMed

60. Daniela Pignatta, D., Brian P. Dilkes, B. P., Yoo, S. Y., Isabelle M. Henry, I. M., Andreas Madlung, A., Doerge, R. W., Chen, Z. J., Comai, L. (2010) Differential sensitivity of the Arabidopsis thaliana transcriptome and enhancers to the effects of genome doubling. New Phytologist 186:194-206. PubMed

59. Clark, G., Torres, J., Finlayson, S., Guan, X., Handley, C., Lee, J., Kays, J. E., Chen, Z. J., and Roux, S. J. (2010) Apyrase (NTPDase) and extracellular nucleotides regulate cotton fiber elongation in cultured ovules. Plant Physiology 152:1073-1083. PubMed

58. Tseng, Y. Y., Chen, Z. J. and Li, W.-H. (2010) fPOP: Footprinting functional pockets of proteins by comparative spatial patterns. Nucleic Acids Research 38: D288-295. PubMed

57. Hinchliffe, D. J., Meredith, W. R., Yeater, K. M., Kim, H. J., Woodward, A. W., Chen, Z. J., and Triplett, B. A. (2010) Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression pattern as revealed by comparative high-throughput profiling.Theor. Appl. Genet. 120:1347-1366. PubMed

56. Wang, K., Guo, W, Yang, Z., Hu, Y., Zhang, W., Zhou, B., Stelly, D. M., Chen, Z. J., and Zhang, T. (2010) Structure and size variations between 12A and 12D homoeologous chromosomes based on high-resolution cytogenetic map in allotetraploid cotton. Chromosoma 119:255-266. PubMed


55. Ni, Z., Kim, E., Ha, M., Lackey, E., Liu, J., Zhang, Y., Sun, Q., and Chen, Z. J. (2009) Altered circadian rhythms regulate growth vigor in hybrids and allopolyploids. Nature 457:327-331. PubMed Press Release

54. Ha, M., Lu, J., Tian, L., Ramachandran, V., Kasschau, K. D., Chapman, E. J., Carrington, J. C., Chen, X., Wang, X., and Chen, Z. J. (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc. Natl. Acad. Sci. USA 106:17835-17840. PubMed

53. Ha, M., Kim, E.-D., and Chen, Z. J. (2009) Duplicate genes increase expression diversity in related species and allopolyploids. Proc. Natl. Acad. Sci. USA 106:2295-2300. PubMed

52. Pang, M., Woodward, A. W., Agarwal, V., Ha, M., Guan, X., Vanitharani Ramachandran, V., Chen, X., Triplett, B. A., Stelly, D. M., and Chen, Z. J. (2009) Genome-wide analysis revealed 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. PubMed

51. Tseng, Y. Y., Craig Dupree, C., Chen, Z. J. and Li, W.-H. (2009) SplitPocket: Identification of protein functional surfaces and characterization of their spatial patterns. Nucleic Acids Research 37: W384–389. PubMed

50. Gaeta, R. T., Suk-Young Yoo, S.-Y., Pires, J. C., Doerge, R. W., Chen, Z. J., and Osborn, T. C. (2009) Analysis of gene expression inresynthesized Brassica napus allopolyploids using Arabidopsis 70-mer oligo microarrays. PLoS One 4: e4760. PubMed


49. Ha, M., Pang, M., Agarwal, V., Chen, Z. J. (2008) Interspecies regulation of microRNAs and their targets. Biochim. Biophy. Acta 1779:735-742. PubMed

48. Chen, M., Ha, M., Lackey, E., Wang, J., and Chen, Z. J. (2008) RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics 178:1845-1858. PubMed


47. Chen, Z. J., Scheffler, B. E., Dennis, E., Triplett, B. A., Zhang, T., Chen, X., Stelly, D. M., Rabinowicz, P. D., Town, C. D., Arioli, T., Brubaker, C., Cantrell, R. G., Lacape, J. M., Ulloa, M., Chee, P., Gingle, A. R., Haigler, C. H., Percy, R., Saha, S., Wilkins, T., Wright, R. J., Van Deynze, A., Zhu, Y., Yu, S., Guo, W., Abdurakhmonov, I., Katageri, I., Ananda-Kumar, P., Rahman, M., Yusuf Zafar, Y., Yu, J. Z., Kohel, R. J., Wendel, J. F., and Paterson, A. H. (2007) Toward sequencing cotton (Gossypium) genomes. Plant Physiol. 145:1303-1310. PubMed

46. Lee, J., Woodward, A. W., and Chen, Z. J. (2007) Gene expression changes and early events in cotton fiber development. Annals of Botany 100:1391-1401. PubMed

45. Ha, M., Li, W.-H., and Z. J. Chen (2007). External factors accelerate expression divergence between duplicate genes. Trends in Genet. 23:162-166. PubMed

44. Chen, Z. J. (2007). Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Ann Rev. Plant Biol. 58:377-406. PubMed

43. Chen, Z. J., Ha, M., and Soltis, D. E. (2007). Polyploidy: Genome obesity and its consequences. New Phytologist 174: 717-720. PubMed

42. Chen, Z. J. and Tian, L. (2007). Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochim. Biophy. Acta 1769:295-307. PubMed

41. Zhao, J., Wang, J., An, L., Doerge, R. W., Chen, Z. J., Grau, C. R., Meng, J., and Osborn, T. C. (2007). Arabidopsis microarray combined with comparative mapping identify candidate resistance genes inBrassica napusPlanta 227:13-24. PubMed

40. Udall, J. A., Cheung, F., Woodward, A. W., Swanson, J. M., Flagel, L., Hovav, R., Ryan A. Rapp, R. A., Nettleton, D., Lee, J. J., Gingle, A. R., Town, C., Chen, Z. J., Wendel, J. F. (2007). Spotted cotton oligonucleotide microarrays for gene expression analysis. BMC Genomics 8:81. PubMed


39. Chen, Z. J. and Z. Ni (2006) Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. BioEssays 28:240-252. PubMed

38. Wang, J., L Tian, H.-S. Lee, N. E. Wei, H. Jiang, B. Watson, A. Madlung, T. C. Osborn, R.W. Doerge, L. Comai, and Z. J. Chen (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172:507-517. PubMed

37. Wang, J., Tian, L., Lee, H.-S., and Chen, Z. J. (2006). Nonadditive regulation of FRI and FLC mediates flowering-time variation in Arabidopsis allopolyploids. Genetics 173:965-974. PubMed

36. Yang, S. S., Foo Cheung, J. J. Lee, Misook Ha, N. E. Wei, S.-H. Sze, D. M. Stelly, P. Thaxton, B. Triplett, C. D. Town, Z. J. Chen (2006) Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. Plant Journal 47:761-775. PubMed

35. Lee, J. J., O. S. Hassan, W. Gao, J. J. Wang, N. E. Wei, R. J. Kohel, P. Payton, X.-Y. Chen, D. M. Stelly, and Z. J. Chen (2006) Developmental and gene expression analyses of a cotton naked seed mutant using cotton oligo-gene microarrays. Planta 223: 418-432. PubMed

34. Gao, W., Z. J. Chen, J. Z. Yu, R. J. Kohel, J. E. Womack, D. M. Stelly (2006) Wide-cross whole-genome radiation hybrid mapping of the cotton (Gossypium barbadense L.) genome, Mol. Genet. & Genomics 275:105-113. PubMed

33. Fong, P. M., L. Tian, and Z. J. Chen (2006) Arabidopsis thaliana histone deacetylase 1 (AtHD1) is localized in euchromatic regions and demonstrates histone deacetylase activity in vitroCell Research 16: 479-488. PubMed

32. Tate, J. A., Z. Ni, A.-C. Scheen, J. Koh, C. A. Gilbert, Z. J. Chen, P. S. Soltis, and D. E. Soltis (2006) Evolution and expression of homoeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics 173:1599-1611. PubMed

31. Wang, N., Lu, S.E., Wang. J., Chen, Z. J., Gross, D. C. (2006) The expression of genes encoding lipodepsipeptide phytotoxins by Pseudomonas syringae pv. syringae is coordinated in response to plant signal molecules. Mol. Plant Microbe Interact. 19:257-69. PubMed


30. Wang J, Lee JJ, Tian L, Lee HS, Chen M, Rao S, Wei EN, Doerge RW, Comai L, Chen ZJ (2005) Methods for genome-wide analysis of gene expression changes in polyploids. Methods Enzymol. 395:570-596. PubMed

29. Pikaard, C. S., Preuss, S. Earley, K., Lewis, M. S., Lawrence, R. J., and Chen, Z. J. (2005). Detecting differential expression of parental or progenitor alleles in genetic hybrids and allopolyploids. Methods Enzymol. 395:554-569. PubMed

28. Tian, L., M. P. Fong, J. J. Wang, N. E. Wei, H. Jiang, R. W. Doerge, and Z. J. Chen (2005). Reversible histone acetylation and deacetylation mediate dynamic changes in plant gene regulation and development. Genetics 169:337-345. PubMed

27. Syed, N. H. and Z. J. Chen (2005). Molecular marker genotypes, hetrozygosity and genetic interactions explain heterosis in Arabidopsis thalianaHeredity 94:295-304. PubMed

26. Lu, S.-E., Wang, N., Wang, J., Chen, Z. J., and Gross, D. C. (2005). Oligonucleotide microarray analysis of the salA regulon controlling phytotoxin production by Pseudomonas syringae pv. syringae.Mol. Plant Microbe Interact. 18:324-333. PubMed

25. Johnston, J. S., A. Pepper, A. E. Hall, Z. J. Chen, G. Hodnett, J. Drabek, R. Lopez, and H. J. Price (2005). Evolution of genome size in the Brassicaceae. Ann. Bot. 95: 229-235. PubMed


24. Wang, J., H.-S. Lee, L. Tian, M. Chen, J. J. Lee, A. Madlung, L. Comai, and Z. J. Chen (2004) Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167: 1961-1973. PubMed

23. Chen, Z. J., J. Wang, L. Tian, H.-S. Lee, J. J. Wang, M. Chen, J. J. Lee, C. Josefsson, A. Madlung, B. Watson, J. C. Pires, Z. Lippman, M. Vaughn, V. Colot, R.W. Doerge, R. A. Martienssen, L. Comai, and T. C. Osborn (2004) The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biol. J. Linn. Soc. 82:689-700. PubMed

22. Lawrence, R. J., K. Earley, M. Silva, O. Pontes, Z. J. Chen, N. Neves, W. Viegas and C. S. Pikaard (2004) A concerted DNA methylation/histone methylation switch regulating rRNA gene dosage control and nucleolar dominance requires nucleolar histone deacetylase, HDT1 . Mol. Cell 13:599-609. PubMed

21. Lee, H.-S., J. Wang, L. Tian, M. Black, H. Jiang, A. Madlung, B. Watson, L. Lukens, J.C. Pires, J. J. Wang, L. Comai, T. Osborn, R. W. Doerge, and Z. J. Chen (2004) Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and Brassica .Plant Biotechnology J. 2:45-57. PubMed

20. Syed, N. H., H.S. Pooni, M. Mei, Z. J. Chen, and M. J. Kearsey (2004). Optimising the construction of a substitution library in Arabidopsis thaliana using computer simulations. Molecular Breeding 13:59-68. PubMed

19. Mei, M., N. H. Syed, W. Gao, P.M. Thaxton, D. M. Stelly, and Z. J. Chen (2004) Genetic mapping and QTL analysis of fiber related traits in cotton (Gossypium). Theor. Appl. Genet. 108:280-291. PubMed

18. Gao, W. Z. J. Chen, J. Yu, D. Raska, R. J. Kohel, C. W. Smith, J. E. Womack, and D. M. Stelly (2004) Wide-cross whole genome radiation hybrid (WWRH) mapping of cotton (Gossypium hirsutum L.).Genetics 167: 1317-1329. PubMed


17. Tian, L., J. Wang, M. K. Fong, M. Chen, H. Cao, S. B. Gelvin, and Z. J. Chen (2003) Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 ( AtHD1 ) expression. Genetics 165:399-409. PubMed

16. Osborn, T. C., J. C. Pires, J. A. Birchler, D. L. Auger, Z. J. Chen, H.-S. Lee, L. Comai, A. Madlung, R.W. Doerge, V. Colot, R. A. Martienssen (2003) Understanding mechanisms of novel gene expression in polyploids. Trends in Genetics 19:141-147. PubMed

15. Pontes, O., Lawrence, R. J., Neve, N., Silva, M., Lee, J.-H., Chen, Z. J, Viegas, W., and Pikaard, C. S. (2003). Nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis allopolyploids displaying natural variation in nucleolar dominance. Proc. Natl. Acad. Sci. USA 100:11418-11423. PubMed


14. Lee, H.-S. and Z. J. Chen (2001). Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc. Natl. Acad. Sci. USA 98:6753-6758. PubMed

13. Tian, L. and Z. J. Chen (2001). Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc. Natl. Acad. Sci. USA 98:200-205. PubMed

1999 & Earlier

12. Frieman, M. B., Z. J. Chen, A. L. Shen, J. Saez-Vasquez, and C. S. Pikaard (1999) RNA polymerase I transcription in an interspecific hybrid and its progenitors: tests of transcription factor involvement in uniparental rRNA gene silencing. Genetics 152:451-460. PubMed

11. Chen, Z. J., L. Comai, and C. S. Pikaard (1998) Gene dosage and stochastic effects determine direction and severity of uniparental rRNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids.  Proc. Natl. Acad. Sci. USA 95:14891-14896. PubMed

10. Chen, Z. J., R. L. Phillips and H. W. Rines (1998) Maize DNA enrichment by representational difference analysis in a maize chromosome addition line of oat.  Theor. Appl. Genet. 97:337-344. Link

9. Chen, Z. J. and C. S. Pikaard (1997a) Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes & Development 11:2124-2136. PubMed

8. Chen, Z. J. and C. S. Pikaard (1997b) Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica.  Proc. Natl. Acad. Sci. USA 94:3442-3447. PubMed

7. Chen, Z., K. F. Schertz, J. Mullet, A. DuBell, and G. E. Hart (1995) Characterization and expression of rpoC2 in CMS and fertile lines of sorghum.  Plant Mol. Biol. 28:799-80912. PubMed

6. Chen, Z., M. Devey, N. A. Tuleen, and G. E. Hart (1994) Use of recombinant substitution lines in construction of RFLP-based genetic maps of chromosomes 6A and 6B of tetraploid wheat (Triticum turgidum L.). Theor. Appl. Genet. 89:703-712. Link

5. Chen, Z., G. H. Liang, S. Muthukrishnan, K. F. Schertz, and G. E. Hart (1993). A chloroplast DNA deletion located in RNA polymerase gene rpoC2 in CMS lines of sorghum.  Mol. Gen. Genet.236:251-259. Link

4. Chen, Z., G. H. Liang, S. Muthukrishnan, K. D. Kofoid (1990) Chloroplast DNA polymorphism in fertile and male-sterile cytoplasms of sorghum [Sorghum bicolor (L.) Moench]. Theor. Appl. Genet. 80:4435-4439. Link

3. Chen, Z., Zhu, L. H. (1990) Karyotype analysis of Lu Dao: an indigenous rice germplasm of Jiangsu province. Acta Genetica Sinica 17(1):1-5.

2. Chen, Z., Zhu, L. H. (1990) A preliminary study on the relationship between Lu Dao and Yunnan land races of rice germplasm. Acta Agronomica Sinica 16(3):219-227.

1. Chen, Z., Yu, H. (1989) Comparative Studies on C-banded and N-banded Heterochromatin of Triticum timopheevi Zhuk. Acta Genetica Sinica 16(4):251-255.