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My Bibliography

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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

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

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

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. The Plant Cell 32:3124-3138. PubMed Editorial in Brief

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. The Plant Cell 32:3706-3722. PubMed

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

Liu, Y., YuanJ., Jia, G., Chen, Z. J., Song, Q. (2020) Histone H3K27 dimethylation landscapes contribute to genome stability and genetic recombination during wheat polyploidization. Plant Journal (doi: 10.1111/tpj.15063) PubMed

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


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

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

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

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


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

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

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

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

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

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. The Plant Cell 30:2006-2019. PubMed 


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

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

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

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

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 


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

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


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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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


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

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

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)

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)


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

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

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

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

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

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

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

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)


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

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

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

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

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

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

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)


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

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

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

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

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

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

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

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

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


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

Ha, M., Lu, J., Tian, L., Ramachandran, V., Kasschau, K. D., Chapman, E. J., Carrington, J. C., Chen, X., Li, W.-H., 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

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

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

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

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


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

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


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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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


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

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

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

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

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

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


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

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

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

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

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

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

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


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

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

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


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

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

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

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

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

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

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

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

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

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

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