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Zhang M, Zhang X, Jiang X, Qiu L, Jia G, Wang L, Ye W, Song Q*. (2022) iSoybean: a database for the mutational fingerprints of soybean. Plant Biotechnology Journal. doi: 10.1111/pbi.13844
Cao S, Wang L, Han T, Ye W, Liu Y, Sun Y, Moose SP, Song Q*, Chen ZJ*. (2022) Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize. Genome Biology, 23:53
Yuan J, Sun H, Wang Y, Li L, Chen S, Jiao W, Jia G, Wang L, Mao J, Ni Z, Wang X, Song Q*. (2022) Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution. Genome Biology, 23:34
Wang L, Jia G, Jiang X, Cao S, Chen ZJ, Song Q*. (2021) Altered chromatin architecture and gene expression during polyploidization and domestication of soybean. The Plant Cell. 33: 1430-1446
Liu Y, Yuan J*, Jia G, Ye W, Chen ZJ*, Song Q*. (2021) Histone H3K27 dimethylation landscapes contribute to genome stability and genetic recombination during wheat polyploidization. Plant Journal. 105:678-690
Yuan J, Jiao W, Liu Y, Ye W, Wang X, Liu B, Song Q*, Chen ZJ*. (2020) Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat. BMC Biology. 18:171
Chen ZJ#*, Sreedasyam A#, Ando A#, Song Q#, De Santiago LM#, Hulse-Kemp AM, Ding M, Ye W, Kirkbride RC, Jenkins J, Plott C, Lovell J, Lin YM, Vaughn R, Liu B, Simpson S, Scheffler BE, Wen L, Saski CA, Grover CE, Hu G, Conover JL, Carlson JW, Shu S, Boston LB, Williams M, Peterson DG, McGee K, Jones DC, Wendel JF, Stelly DM, Grimwood J* and Schmutz J. (2020) Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nature Genetics. 52:525-533
Song Q#, Ando A#, Jiang N, Ikeda Y and Chen ZJ*. (2020) Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes. Genome Biology. 21:178
Yin D#*, Ji C#, Song Q#, Zhang W#, Zhang X, Zhao K, Chen CY, Wang C, He G, Liang Z, Ma X, Li Z, Tang Y, Wang Y, Li K, Ning L, Zhang H, Zhao K, Li X, Yu H, Lei Y, Wang M, Ma L, Zheng H, Zhang Y, Zhang J*, Hu W* and Chen ZJ*. (2020) Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut. Advanced Science. 7:1901672
Han T, Wang F, Song Q, Ye W, Liu T, Wang L, Chen ZJ*. (2021) An epigenetic basis of inbreeding depression in maize. Science Advances. 7 : eabg5442
Jiang X, Song Q, Ye W, Chen ZJ*. (2021) Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids. Nature Ecology & Evolution. 5:1382-1393
Wang L, Cao S, Wang P, Lu K, Song Q, Zhao FJ, Chen ZJ* (2021) DNA hypomethylation in tetraploid rice potentiates stress-responsive gene expression for salt tolerance. PNAS. 118:e2023981118
2019年之前
Song Q#, Huang TY#, Yu HH, Ando A, Mas P, Ha M, Chen ZJ*. (2019) Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis. Genome Biology. 20:170
Song Q, Ando A, Xu D, Fang L, Zhang T, Huq E, Qiao H, Deng XW*, Chen ZJ*. (2018) Diurnal down-regulation of ethylene biosynthesis mediates biomass heterosis. PNAS. 115: 5606-5611.
Song Q, Zhang T, Stelly D and Chen ZJ*. (2017) Epigenomic and functional analyses revealed roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons. Genome Biology. 18:99.
Song Q, Guan X and Chen ZJ*. (2015) Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton. PLoS Genetics 11:e1005724.
Miller M#, Song Q#, Shi X, Juenger TE and Chen, ZJ*. (2015) Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis. Nature Communications 6:7453.
Song Q and Chen, ZJ*. (2015) Epigenetic and developmental regulation in plant polyploids. Current Opinion Plant Biology 24:101-109.
Song QX#, Li QT#, Liu YF, Zhang FX, Ma B, Zhang WK, Man WQ, Du WG, Wang GD, Chen SY* and Zhang JS*. (2013) Soybean GmbZIP123 gene enhances lipid content in the seeds of transgenic Arabidopsis plants. Journal of Experimental Botany 64:4329-4341.
Song QX, Lu X, Li QT, Chen H, Hu XY, Ma B, Zhang WK, Chen SY* and Zhang JS*. (2013) Genome-wide analysis of DNA methylation in soybean. Molecular Plant 6:1961-1974.
Song QX, Liu YF, Hu XY, Zhang WK, Ma B, Chen SY* and Zhang JS*. (2011) Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biology 11:5.
Li QT, Lu X, Song QX, Chen HW, Wei W, Tao JJ, Bian XH, Shen M, Ma B, Zhang WK, Bi YD, Li W, Lai YC, Lam SM, Shui GH, Chen SY* and Zhang JS*. (2017) Selection for a Zinc-Finger Protein Contributes to Seed Oil Increase during Soybean Domestication. Plant Physiology 173:2208-2224.
Saski CA*, Scheffler BE, Hulse-Kemp AM, Liu B, Song Q, Ando A, Stelly DM, Scheffler JA, Grimwood J, Jones DC, Peterson DG, Schmutz J and Chen ZJ. (2017) Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. Scientific Reports 7:15274.
Zheng D, Ye W, Song Q, Han F, Zhang T and Chen ZJ*. (2016) Histone Modifications Define Expression Bias of Homoeologous Genomes in Allotetraploid Cotton. Plant Physiology 172:1760-1771.
Ko DK, Rohozinski D, Song Q, Taylor SH, Juenger TE, Harmon FG and Chen ZJ*. (2016) Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids. PLoS Genetics 12:e1006197.
Zhang T*, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, Scheffler BE, Stelly DM, Hulse-Kemp AM, Wan Q, Liu B, Liu C, Wang S, Pan M, Wang Y, Wang D, Ye W, Chang L, Zhang W, Song Q, Kirkbride RC, Chen X, Dennis E, Llewellyn DJ, Peterson DG0, Thaxton P, Jones DC, 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 ZJ*. (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology 33:531-537.
Tuttle JR, Nah G, Duke MV, Alexander DC, Guan X, Song Q, Chen ZJ, Scheffler BE and Haigler CH*. (2015) Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation. BMC Genomics 16:477.
Guan X, Song Q and Chen ZJ*. (2014) Polyploidy and small RNA regulation of cotton fiber development. Trends Plant Science 19:516-528.
Guan X, Nah G, Song Q, Udall JA, Stelly DM and Chen ZJ*. (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.
Liu YF, Li QT, Lu X, Song QX, Lam SM, Zhang WK, Ma B, Lin Q, Man WQ, Du WG, Shui GH, Chen SY* and Zhang JS*. (2014) Soybean GmMYB73 promotes lipid accumulation in transgenic plants. BMC Plant Biolology 14:73.
Zou HF, Zhang YQ, Wei W, Chen HW, Song QX, Liu YF, Zhao MY, Wang F, Zhang BC, Lin Q, Zhang WK, Ma B, Zhou YH, Zhang JS* and Chen SY*. (2013) The transcription factor AtDOF4.2 regulates shoot branching and seed coat formation in Arabidopsis. Biochemical Journal 449:373-378.
Ma B, He SJ, Duan KX, Yin CC, Chen H, Yang C, Xiong Q, Song QX, Lu X, Chen HW, Zhang WK, Lu TG, Chen SY* and Zhang JS*. (2013) Identification of rice ethylene-response mutants and characterization of MHZ7/OsEIN2 in distinct ethylene response and yield trait regulation. Molecular Plant 6:1830-1848.
Hao YJ, Wei W, Song QX, Chen HW, Zhang YQ, Wang F, Zou HF, Lei G, Tian AG, Zhang WK, Ma B, Zhang JS* and Chen SY*. (2011) Soybean NAC transcription factors promote abiotic stress tolerance and lateral root formation in transgenic plants. Plant Journal 68:302-313.
Hao YJ, Song QX, Chen HW, Zou HF, Wei W, Kang XS, Ma B, Zhang WK, Zhang JS* and Chen SY*. (2010) Plant NAC-type transcription factor proteins contain a NARD domain for repression of transcriptional activation. Planta 232:1033-1043.
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