2020年

1)          Bi, Y., Zhao, Q., Yan, W., Li, M., Liu, Y., Cheng, C., Zhang, L., Yu, X., Li, J., Qian, C., Wu, Y., Chen, J., and Lou, Q. (2020). Flexible chromosome painting based on multiplex PCR of oligonucleotides and its application for comparative chromosome analyses in Cucumis. Plant J. 102, 178-186.

2)          Dang, X., Yang, Y., Zhang, Y., Chen, X., Fan, Z., Liu, Q., Ji, J., Li, D., Li, Y., Fang, B., Wu, Z., Liu, E., Hu, X., Zhu, S., She, D., Wang, H., Li, Y., Chen, S., Wu, Y., and Hong, D. (2020). OsSYL2(AA), an allele identified by gene-based association, increases style length in rice (Oryza sativa L.). Plant J.

3)          Fan, X., Chen, J., Wu, Y., Teo, C., Xu, G., and Fan, X. (2020). Genetic and Global Epigenetic Modification, Which Determines the Phenotype of Transgenic Rice? International Journal Of Molecular Sciences 21.

4)          Liu, C., Shen, Y., Qin, B., Wen, H., Cheng, J., Mao, F., Shi, W., Tang, D., Du, G., Li, Y., Wu, Y., and Cheng, Z. (2020). Oryza sativa RNA-Dependent RNA Polymerase 6 Contributes to Double-Strand Break Formation in Meiosis. The Plant cell 32, 3273-3289.

5)          Lu, Y., Dai, J., Yang, L., La, Y., Zhou, S., Qiang, S., Wang, Q., Tan, F., Wu, Y., Kong, W., and La, H. (2020). Involvement of MEM1 in DNA demethylation in Arabidopsis. Plant Molecular Biology 102, 307-322.

6)          Song, X., Song, R., Zhou, J., Yan, W., Zhang, T., Sun, H., Xiao, J., Wu, Y., Xi, M., Lou, Q., Wang, H., and Wang, X. (2020). Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L. Chromosome Research 28, 171-182.

7)          Wang, L., Deng, L., Bai, X., Jiao, Y., Cao, Y., and Wu, Y. (2020). Regulation of nodule number by GmNORK is dependent on expression of GmNIC in soybean. Agroforestry Systems 94, 221-230.

8)          Xin, H., Zhang, T., Wu, Y., Zhang, W., Zhang, P., Xi, M., and Jiang, J. (2020). An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting. Plant J. 101, 253-264.

9)          Yang, Y., Sun, Y., Li, Q., Wu, Y., and Wang, D. (2020). First report of Plum bark necrosis stem pitting-associated virus infecting grapevine in China. Virology Journal 17.

10)      Zhu, D., Mao, F., Tian, Y., Lin, X., Gu, L., Gu, H., Qu, L.-j., Wu, Y., and Wu, Z. (2020). The Features and Regulation of Co-transcriptional Splicing in Arabidopsis. Molecular Plant 13, 278-294.

11)      1. Zhang Aq#, Wang S#, Kim J, et al. Nuclear pore complex components have temperature-influenced roles in plant growth and immunity, Plant, Cell & Environment, 2020, 43(6): 1452-1466.

 

2019年

1)          Fang, Y., Chen, L., Lin, K., Feng, Y., Zhang, P., Pan, X., Sanders, J., Wu, Y., Wang, X.-e., Su, Z., Chen, C., Wei, H., and Zhang, W. (2019). Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice. Genome Res 29, 1287-1297.

2)          Liu, J., Wang, D., Su, Y., Lang, K., Duan, R., Wu, Y., Ma, F., and Huang, S. (2019). FairBase: a comprehensive database of fungal A-to-I RNA editing. Database-the Journal Of Biological Databases And Curation.

3)          Wang, Q., Liu, S., Lu, C., La, Y., Dai, J., Ma, H., Zhou, S., Tan, F., Wang, X., Wu, Y., Kong, W., and La, H. (2019). Roles of CRWN-family proteins in protecting genomic DNA against oxidative damage. Journal of plant physiology 233, 20-30.

4)           Song, X.,  Qing Sang, Q., Wang, H., Pei, H., Gan, X.*, Wang F.*, (2019) Complement genome annotation lift over using a weighted sequence alignment strategy. Frontiers in genetics, doi:10.3389/fgene.2019.01046. 

5)          Hong Shen, Zhihui Xu, Zanming Shen & Zhongyan Lu (2019). The regulation of ruminal short-chain fatty acids on the functions of rumen barriers. Frontiers in Physiology, 10:1305.

6)          Zhongyan Lu, Zhihui Xu, Zanming Shen, Hong Shen* & Jörg R. Aschenbach* (2019). Transcriptomic analyses suggest a dominate role of insulin in the coordinated control of energy metabolism and ureagenesis in goat liver. BMC genomics, 20:854.

7)          Zhongyan Lu, Zhihui Xu, Zanming Shen, Yuanchun Tian & Hong Shen (2019). Dietary Energy Level Promotes Rumen Microbial Protein Synthesis by Improving the Energy Productivity of the Ruminal Microbiome. Frontiers in Microbiology, 10:847.

8)          Zhongyan Lu, Hong Shen* & Zanming Shen* (2019). Effects of Dietary-SCFA on Microbial Protein Synthesis and Urinal Urea-N Excretion Are Related to Microbiota Diversity in Rumen. Frontiers in Physiology, 10:1079.

 

2018年

1)          Chen, H., Shu, H., Wang, L., Zhang, F., Li, X., Ochola, S.O., Mao, F., Ma, H., Ye, W., Gu, T., Jiang, L., Wu, Y., Wang, Y., Kamoun, S., and Dong, S. (2018). Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions. Genome Biology 19.

2)          Xin, H., Zhang, T., Han, Y., Wu, Y., Shi, J., Xi, M., and Jiang, J. (2018). Chromosome painting and comparative physical mapping of the sex chromosomes in Populus tomentosa and Populus deltoides. Chromosoma 127, 313-321.

3)          Wang, Q., Guo, Q., Guo, Y., Yang, J., Wang, M., Duan, X., Niu, J., Liu, S., Zhang, J., Lu, Y., Hou, Z., Miao, W., Wang, X., Kong, W., Xu, X., Wu, Y., Rui, Q., and La, H. (2018). Arabidopsis subtilase SASP is involved in the regulation of ABA signaling and drought tolerance by interacting with OPEN STOMATA 1. Journal Of Experimental Botany 69, 4403-4417.

4)          Xing, L., Hu, P., Liu, J., Witek, K., Zhou, S., Xu, J., Zhou, W., Gao, L., Huang, Z., Zhang, R., Wang, X., Chen, P., Wang, H., Jones, J.D.G., Karafiatova, M., Vrana, J., Bartos, J., Dolezel, J., Tian, Y., Wu, Y., and Cao, A. (2018). Pm21 from Haynaldia villosa Encodes a CC-NBS-LRR Protein Conferring Powdery Mildew Resistance in Wheat. Molecular Plant 11, 874-878.

5)          Liu, S., Xue, C., Fang, Y., Chen, G., Peng, X., Zhou, Y., Chen, C., Liu, G., Gu, M., Wang, K., Zhang, W., Wu, Y., and Gong, Z. (2018). Global Involvement of Lysine Crotonylation in Protein Modification and Transcription Regulation in Rice. Molecular & Cellular Proteomics 17, 1922-1936.

6)          Zhao, H., Zhang, W., Chen, L., Wang, L., Marand, A.P., Wu, Y., and Jiang, J. (2018). Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome. Plant Physiol 176, 2789-2803.

7)           Song, B., Mott R., Gan, X*. (2018) Recovery of novel association loci in Arabidopsis thaliana and Drosophila melanogaster through leveraging INDELs association and integrated burden test. PLOS Genetics. 14(10): e1007699 

8)          Zhongyan Lu#, Hong Shen# & Zanming Shen (2018). High-concentrate diet-induced change of cellular metabolism leads to decreases of immunity and imbalance of cellular activities in rumen epithelium. Cellular Physiology and Biochemistry 45: 2145-2157.

 

2017年

1)          Li, H., Peng, T., Wang, Q., Wu, Y., Chang, J., Zhang, M., Tang, G., and Li, C. (2017). Development of Incompletely Fused Carpels in Maize Ovary Revealed by miRNA, Target Gene and Phytohormone Analysis. Frontiers In Plant Science 8.

2)          Wang, H., Dai, K., Xiao, J., Yuan, C., Zhao, R., Dolezel, J., Wu, Y., Cao, A., Chen, P., Zhang, S., and Wang, X. (2017). Development of intron targeting (IT) markers specific for chromosome arm 4VS of Haynaldia villosa by chromosome sorting and next-generation sequencing. Bmc Genomics 18.

3)          Xiao, J., Dai, K., Fu, L., Vrana, J., Kubalakova, M., Wan, W., Sun, H., Zhao, J., Yu, C., Wu, Y., Abrouk, M., Wang, H., Dolezel, J., and Wang, X. (2017). Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order. Bmc Genomics 18.

4)          Zhang, X., Wei, X., Xiao, J., Yuan, C., Wu, Y., Cao, A., Xing, L., Chen, P., Zhang, S., Wang, X., and Wang, H. (2017). Whole genome development of intron targeting (IT) markers specific for Dasypyrum villosum chromosomes based on next-generation sequencing technology. Molecular Breeding 37.

5)          Zhao, H., Han, Q., Zhang, L., Zhang, Z., Wu, Y., Shen, H., and Jiang, P. (2017). Emergence of mosaic recombinant strains potentially associated with vaccine JXA1-R and predominant circulating strains of porcine reproductive and respiratory syndrome virus in different provinces of China. Virology Journal 14.

6)          Hong Shen#, Zhongyan Lu#, Zhihui Xu, Zhan Chen & Zanming Shen (2017). Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats. Microbiome 5: 123.

7)          Hong Shen#, Zhongyan Lu#, Zhihui Xu & Zanming Shen (2017). Diet-induced reconstruction of mucosal microbiota associated with alterations of epithelium lectin expression and regulation in the maintenance of rumen homeostasis. Scientific Reports 7: 3941.

8)          Hong Shen#, Zhongyan Lu#, Zhihui Xu & Zanming Shen (2017). Antibiotic pretreatment minimizes dietary effects on reconstructure of rumen fluid and mucosal microbiota in goats. MicrobiologyOpen, e537.

9)           Wang S#, Wang S, Sun Q, et al. A Role of Cytokinin Transporter in Arabidopsis Immunity. Molecular Plant-Microbe Interactions, 2017, 30(4): 325-333.

 

2016年

1)          Bao, W., Jiang, J., Zhou, Y., Wu, Y., and Leung, F.C.-C. (2016). Screening and genomic analysis of a lignocellulose degrading bacterium. Weishengwu Xuebao 56, 765-777.

2)          Fang, Y., Wang, X., Wang, L., Pan, X., Xiao, J., Wang, X.-e., Wu, Y., and Zhang, W. (2016a). Functional characterization of open chromatin in bidirectional promoters of rice. Scientific Reports 6.

3)          Fang, Y., Wang, L., Wang, X., You, Q., Pan, X., Xiao, J., Wang, X.-e., Wu, Y., Su, Z., and Zhang, W. (2016b). Histone modifications facilitate the coexpression of bidirectional promoters in rice. Bmc Genomics 17.

4)          Han, J., Masonbrink, R.E., Shan, W., Song, F., Zhang, J., Yu, W., Wang, K., Wu, Y., Tang, H., Wendel, J.F., and Wang, K. (2016). Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton. Plant J. 88, 992-1005.

5)          Li, H., Wu, Y., Zhao, Y., Hu, X., Chang, J., Wang, Q., Dong, P., Zhang, M., and Li, C. (2016). Differential morphology and transcriptome profile between the incompletely fused carpels ovary and its wild-type in maize. Scientific Reports 6.

6)          Shen, H., Lu, Z., Chen, Z., Wu, Y., and Shen, Z. (2016). Rapid Fermentable Substance Modulates Interactions between Ruminal Commensals and Toll-Like Receptors in Promotion of Immune Tolerance of Goat Rumen. Frontiers In Microbiology 7.

7)          Sun, Y., Xiao, J., Jia, X., Ke, P., He, L., Cao, A., Wang, H., Wu, Y., Gao, X., and Wang, X. (2016). The role of wheat jasmonic acid and ethylene pathways in response to Fusarium graminearum infection. Plant Growth Regulation 80, 69-77.

8)           Gan, X.*, Hay A., Kwantes, M., Harberer, G., Hallab, A., Dello Ioio, R., Hofhuis, H., Pieper, B., Cartolano, M., Neumann, U.,  Nikolov, L. A.,  Song, B., Hajheidari, M., Briskine, R., Kougioumoutzi, E., Vlad, D., Broholm, S., Hein, J.,  Meksem, K.,  Lightfoot, D., Shimizu, K. K., Shimizu-Inatsugi, R., Imprialou, M.,  Kudrna, D., Wing, R., Sato, S., Huijser, P., Filatov, D., Mayer, K. F. X., Mott, R., Tsiantis, M. (2016) The Cardamine hirsuta genome highlights the pervasive role of transcription factors and tandem gene duplications in generating morphological diversity. Nature Plants, 2(11)

9)          The 1001 Genomes Consortium. (2016). 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 166, 481-91.

10)      Hong Shen#, Zhongyan Lu#, Zhan Chen, Yufeng Wu & Zanming Shen (2016). Rapid Fermentable Substance Modulates Interactions between Ruminal Commensals and Toll-Like Receptors in Promotion of Immune Tolerance of Goat Rumen. Frontiers in Microbiology 7: 1812.

11)      Hong Shen, Zhan Chen, Zanming Shen & Zhongyan Lu (2016). Maintaining stability of the rumen ecosystem is associated with changes of microbial composition and epithelial TLR signaling. MicrobiologyOpen, e436.

12)      Wang S#, Bai G#, Wang S, et al. Chloroplast RNA-Binding Protein RBD1 Promotes Chilling Tolerance through 23S rRNA Processing in Arabidopsis. PLOS Genet, 2016, 12(5): e1006027.

 

2015年及以前

1)          Hong Shen, Yonghua Gai, Daxiang Song, Hongying Sun, Ulf Scheller & Kaiya Zhou (2007). New species of Pauropodidae (Myriapoda: Pauropoda) from Nanjing, China. Journal of Natural History 41: 37 - 40.

2)           Gan, X., Stegle, O., Behr, J., Steffen, J.G., Drewe, P., Hildebrand, K.L., Lyngsoe, R., Schultheiss, S.J., Osborne, E.J., Sreedharan, V.T., Kahles, A., Bohnert, R., Jean, G., Derwent, P., Kersey, P., Belfield, E.J., Harberd, N.P., Kemen, E., Toomajian, C., Kover, P.X., Clark, R.M., Ratsch, G., and Mott, R. (2011). Multiple Reference Genomes and Transcriptomes for Arabidopsis Thaliana. Nature 477, 419-423.

3)          Hong Shen, Anke Braband & Gerhard Scholtz (2013). Mitogenomic analysis of decapod crustacean phylogeny confirms largely more traditional views on their relationships. Mol Phylogenet Evol 66: 776-789.

4)          CONVERGE Consortium. (2015). Sparse whole-genome sequencing identifies two loci for major depressive disorder. Nature 523, 588-91.

5)          Hong Shen, Anke Braband & Gerhard Scholtz (2015). The complete mitogenomes of lobsters and crayfish (Crustacea: Decapoda: Astacidea) reveal surprising differences in closely related taxa and convergences to Priapulida. J Zoolog Syst Evol Res 53(4): 273-281

6)          Wang S#, Su S Z#, Wu Y, et al. Overexpression of maize chloride channel gene ZmCLC-d in Arabidopsis thaliana improved its stress resistance. Biologia Plantarum, 2015, 59(1): 55-64.