2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010
2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2001 | 1999 & Earlier
2024
144. Sreedasyam, A., Lovell, J. T., Mamidi, S., Khanal, S., Jenkins, J. W., Plott, C., Bryan, K. B., Li, Z., Shu, S., Carlson, J., Goodstein, D., De Santiago, L., Kirkbride, R. C., Calleja, S., Campbell, T., Koebernick, J. C., Dever, J. K., Scheffler, J. A., Pauli, D., Jenkins, J. N., McCarty, J. C., Williams, M., Boston, L. B., Webber, J., Udall, J. A, Chen, Z. J., Bourland, F., Stiller, W. N., Saski, C. A., Grimwood, J., Chee, P. W., Jones, D. C., Schmutz, J. (2024) Genome resources for three modern cotton lines guide future breeding efforts. Nature Plants OpenAccess
143. Cao, S., Chen, Z. J. (2024) Transgenerational epigenetic inheritance during plant evolution and breeding. Trends in Plant Science (DOI: 10.1016/j.tplants.2024.04.007) PubMed
142. Wang, F., Han, T., Chen, Z. J. (2024) Circadian and Photoperiodic Regulation of the Vegetative to Reproductive Transition in Plants. Communications Biology 7:579. OpenAccess
141. Cao, S., Zhang, H., Liu, Y., Sun, Y., and Chen, Z. J. (2024) Cytoplasmic genome contributions to domestication and improvement of modern maize. BMC Biology 22:64. OpenAccess
140. June, V., Song, X., Chen, Z. J. (2024) Imprinting but not cytonuclear interactions determines parent-of-origin effct on seed size heterosis in Arabidopsis hybrids. Plant Physiology 31:1214-1228. PubMed News & Views
139. Jiao, W., Lu, K., Wen, M., Mao, J., Ni, Z., Chen, Z. J., Wang, X., Song, Q., Yuan, J. (2024) Ploidy variation induces butterfly effect on chromatin topology in wheat. Plant Journal. PubMed
2023
138. 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. OpenAccess
137. 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) Asymmetrical variation in DNA methylation changes during domestication and de-domestication. The Plant Cell 35:3429-3443. PubMed
2022
136. 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 Arabidopsis. Genetics 223(2):iyac161. PubMed
135. Li, Z., Chen, Z.J. (2022) Nonadditive gene expression and epigenetic changes in polyploid plants and crops. Advances in Agronomy 176:179-208. ScienceDirect
134. 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 maize. Genome Biology 23:53. OpenAccess
2021
133. 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. OpenAccess
132. 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
131. 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
130. 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
129. 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. OpenAccess
128. Liu, Y., Yuan, J., 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
2020
127. 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
126. 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
125. 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
124. 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
123. 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 In a Nutshell
122. 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. OpenAccess
121. 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. OpenAccess
2019
120. 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 Arabidopsis. Proc. Natl. Acad. Sci. USA 116:2761-2766. PubMed Press Release
119. 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. OpenAccess
118. 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
117. Chen, Z. J., Mas, P. (2019) Interactive roles of chromatin regulation and circadian clock function in plants. Genome Biology 20:62. OpenAccess
2018
116. 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
115. 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
114. 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
113. 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
112. 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
111. 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
2017
110. 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. OpenAccess Press Release Research Highlight
109. 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. OpenAccess
108. 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
107. 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. OpenAccess
106. 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. OpenAccess
2016
105. 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
104. 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. OpenAccess Press Releasse
2015
103. 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
102. 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. OpenAccess
101. 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. OpenAccess
100. 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 Arabidopsis. Nature Communications 6:7453. OpenAccess
99. 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
98. 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
97. Song, Q. and Chen, Z. J. (2015) Epigenetic and developmental regulation in plant polyploids. Current Opinions in Plant Biology 24:101–109. PubMed
96. 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. OpenAccess
95. 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. OpenAccess
94. 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. OpenAccess
93. 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. OpenAccess
92. 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
2014
91. 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
90. 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
89. 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. OpenAccess
88. 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. OpenAccess
87. 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. OpenAccess
86. 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
85. 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
2013
84. Chen, Z. J. (2013) Genomic and epigenetic insights into the molecular bases of heterosis. Nature Reviews Genetics 14:471-482. PubMed
83. Chen, Z. J. and Birchler, J. A. (2013) Polyploid and Hybrid Genomics. Wiley-Blackwell, New York. pp. 363 (ISBN 978-0-470-96037-0)
82. 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)
81. 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)
2012
80. 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. OpenAccess
79. 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
78. 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. OpenAccess
77. 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
76. 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
75. 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
74. Sung, S., Huq, E., and Chen, Z. J. (2012) International plant molecular biology: a bright future for green science. Genome Biology 13:323. OpenAccess
73. 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)
2011
72. 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
71. 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
70. Chen, Z. J. and Guan, X. (2011) Auxin boost for cotton. Nature Biotechnology 29:407-409. PubMed
69. 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. OpenAccess
68. 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. OpenAccess
67. 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
66. 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)
2010
65. Chen, Z. J. (2010) Molecular mechanisms of polyploidy and hybrid vigor. Trends in Plant Science15:57-71. PubMed
64. Jackson, S. and Chen, Z. J. (2010) Genomic and expression plasticity of polyploidy. Current Opinions in Plant Biology 13:153-159. PubMed
63. 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
62. 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
61. 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
60. 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
59. 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
58. 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
57. 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
2009
56. 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
55. 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
54. 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
53. 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. OpenAccess
52. 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
51. 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. OpenAccess
2008
50. Ha, M., Pang, M., Agarwal, V., Chen, Z. J. (2008) Interspecies regulation of microRNAs and their targets. Biochim. Biophy. Acta 1779:735-742. PubMed
49. 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
2007
48. 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
47. 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
46. 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
45. 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
44. Chen, Z. J., Ha, M., and Soltis, D. E. (2007). Polyploidy: Genome obesity and its consequences. New Phytologist 174: 717-720. PubMed
43. 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
42. 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 in Brassica napus. Planta 227:13-24. PubMed
41. 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. OpenAccess
2006
40. Chen, Z. J. and Z. Ni (2006) Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. BioEssays 28:240-252. PubMed
39. 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
38. 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
37. 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
36. 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
35. 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
34. 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 vitro. Cell Research 16: 479-488. PubMed
33. 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
32. 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
2005
31. 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
30. 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
29. 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
28. Syed, N. H. and Z. J. Chen (2005). Molecular marker genotypes, hetrozygosity and genetic interactions explain heterosis in Arabidopsis thaliana. Heredity 94:295-304. PubMed
27. 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
26. 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
2004
25. 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
24. 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
23. 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
22. 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
21. 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
20. 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
19. 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
2003
18. 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
17. 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
16. 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
2001
15. 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
14. 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
13. 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
12. Pikaard, C. S., Chen, Z. J. (1998) Chapter 21: Nucleolar dominance. In: Paule, M. R. (ed.) Transcription of Ribosomal RNA Genes by Eukaryotic RNA Polymerase I. R. G. Landes Co., Georgetown, Texas, p. 275-293.
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.
