Publications 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 My Bibliography Google Scholar 2025 146. Gao, M.-J., Chen, Q., Coutu, C., Fu, F., Yu, B., Li, X., Chen, Z.J., Hegedus, D. (2025) SCL15 Regulates the Release of Seed Dormancy in Arabidopsis thaliana by Integrating the Circadian Clock, Hormonal Signals and Cell Wall Remodelling. Physiologia Plantarum OpenAccess 145. Chen, Z. J. (2025) Empowering plant epigenetics to breed resilience of crops: From nucleolar dominance to transgenerational epigenetic inheritance. The Plant Genome 18(2):e70064. PubMed 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 10:1039-1051. OpenAccess 143. Cao, S., Chen, Z. J. (2024) Transgenerational epigenetic inheritance during plant evolution and breeding. Trends in Plant Science 29:2023-2023. Feature Review (Cover) 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 effect 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 119:2450-2463. 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 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. 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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. 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