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1.Changzhi Zhao1, 2*, Xiaoguo Zheng3, 4*, Wubin Qu5*, Guanglei Li1, Xinyun Li1, 2, Yi-Liang Miao1, 2, Xiaosong Han1, Xiangdong Liu1, 2, Zhenhua Li3, 4, Yunlong Ma1, Qianzhi Shao5, Haiwei Li5, Fei Sun, Shengsong Xie, and Shuhong Zhao. CRISPR-offinder: a CRISPR guide RNA design and off-target searching tool for user-defined protospacer adjacent motif. International Journal of Biological Sciences 2017; 13(11): 1470-1478. doi: 10.7150/ijbs.21312
2.Xinyi Liu, Yongliang Wang, Liming Hou, Yuanzhu Xiong, and Shuhong Zhao. Fibroblast Growth Factor 21 (FGF21) Promotes Formation of Aerobic Myofibers via the FGF21-SIRT1-AMPK-PGC1α Pathway. Journal of Cellular Physiology. J. Cell. Physiol. 232: 1893–1906, 2017
3.J. Zhang,* J. H. Chen,* X. D. Liu,* H. Y. Wang,*_x005f_x000b_X. L. Liu,* X. Y. Li,* Z. F. Wu,† M. J. Zhu,*‡2 and S. H. Zhao. Genomewide association studies for hematological traits and_x000b_T lymphocyte subpopulations in a Duroc × Erhualian F2 resource population. J. Anim. Sci. 2016.94:5028–5041
4.Liangliang Fu, Yueyuan Xu, Ye Hou, Xiaolong Qi, Lian Zhou, Huiying Liu, Yu Luan, Lu Jing, Yuanxin Miao, Shuhong Zhao, Huazhen Liu & Xinyun Li. Proteomic analysis indicates that mitochondrial energy metabolism in skeletal muscle tissue is negatively correlated with feed efficiency in pigs. Scientific Reports | 7:45291 | DOI: 10.1038/srep45291
5.Li C, He H, Liu A, Liu H, Huang H, Zhao C, Jing L, Ni J, Yin L, Hu S, Wu H, Li X, Zhao S. Natural Functional SNPs in miR-155 Alter Its Expression Level, Blood Cell Counts, and Immune Responses. Front Immunol. 2016 Aug 2;7:295. doi: 10.3389/fimmu.2016.00295.
6.Yunxia Zhao, Ye Hou, Fei Liu, An Liu, Lu Jing, Changzhi Zhao, Yu Luan, Yuanxin Miao, Shuhong Zhao and Xinyun Li. Transcriptome analysis reveals that vitamin A metabolism in _x000b_ the liver affects feed efficiency in pigs._x000b_ G3: GENES, GENOMES, GENETICS November 1, 2016 vol. 6 no. 11 3615-3624; https://doi.org/10.1534/g3.116.032839
7.H. Wang, Y. Hou, J. Guo, H. Chen, X. Liu, Z. Wu, S. Zhao, and M. Zhu Transcriptomic landscape for lymphocyte count variation in poly I:C-induced porcine peripheral blood. Animal Genetics, 26 NOV 2015 . DOI: 10.1111/age.12379
8.Wei W, Zhang WY, Bai JB, Zhang HX, Zhao YY, Li XY, Zhao SH. The NF-ҡB modulated miR-195/497 inhibit myoblast proliferation by targeting Igf1r/Insr and cyclin genes. J Cell Sci. (2016) 129, 39-50 doi:10.1242/jcs.174235
9.Ruiyi Lin1, Di Wu1, 2, Changzhi Zhao1, Shangshang Chen1, Qian Xiao1, Changchun Li1, Xinyun Li1, Shuhong Zhao.*Inducible overexpression of porcine Homeobox A10 in the endometrium of transgenic mice. Journal of Integrative Agriculture (JIA) , Doi: 10.1016/S2095-3119(15)61169-8
10.Lu Jing, Ye Hou, Hui Wu, Yuanxin Miao, Xinyun Li, Jianhua Cao, John Michael Brameld, Tim Parr & Shuhong Zhao. Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs. Scientific Reports, 2015, 5:11953(1-14). DOI: 10.1038/srep11953
11.Xiaoyong Du, Bertrand Servin2†, James E Womack3, Jianhua Cao1, Mei Yu1, Yang Dong4,5, Wen Wang, and Shuhong Zhao. An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae. Du et al. BMC Genomics, 2014, 15:625 (page 1-16)
12.Guanglei Li1, Qitao Jia2, Jianguo Zhao2, Xinyun Li1, Mei Yu1, Melissa S Samuel3, Shuhong Zhao, Randall S Prather. and Changchun Li. Dysregulation of genome-wide gene expression and DNA methylation in abnormal cloned piglets. BMC Genomics, 2014, 15:811(pages 1-14)
13.The FAANG Consortium*, Leif Andersson, Alan L. Archibald, Cynthia D. Bottema, Rudiger Brauning, Shane C. Burgess, Eduardo Casas, Hans H. Cheng, Laura Clarke, Christine Couldrey, Brian P. Dalrymple, Christine G. Elsik, Sylvain Foissac, Elisabetta Giuffra§, Martien A. Groenen, Ben J. Hayes, LuSheng S. Huang, Hassan Khatib, James W. Kijas, Heebal Kim,Joan K. Lunney, Fiona M. McCarthy, John C. McEwan, Stephen Moore, Bindu Nanduri, Cedric Notredame, Yniv Palti, Graham S. Plastow, James M. Reecy, Gary A. Rohrer, Elena Sarrapoulou, Carl J. Schmidt, Jeff Silverstein, Ross L. Tellam, Michele Tixier-Boichard, Gwenola Tosser-Klopp, Christopher K. Tuggle§, Johanna Vikki, Stephen White, Shuhong Zhao, Huaijun Zhou. Coordinated international action to accelerate Genome to Phenome- The Functional Annotation of ANimal Genomes (FAANG) Project. Genome Biol. 2015 Mar 25;16:57(pages 1-6). doi: 10.1186/s13059-015-0622-4.
14.Ting Gu1, Meng-jin Zhu1, Martine Schroyen2, Long Qu3, Dan Nettleton3, Dan Kuhar4, Joan K Lunney4, Jason W Ross2, Shu-hong Zhao (共同通讯作者) and Christopher K Tuggle2*. Endometrial gene expression profiling in pregnant Meishan and Yorkshire pigs on day 12 of gestation. BMC Genomics 2014, 15:156 (1-12)
15.Jing Huang a,b, Guojian Mac,1, Liangliang Fu a, Hao Jia a, Mengjin Zhu a, Xinyun Li a, Shuhong Zhao (通讯作者) Pseudorabies viral replication is inhibited by a novel target of miR-21. Virology 456-457 (2014) 319–328
16.Zhao M, Liu XD, Li XY, Chen HB, Jin H, Zhou R, Zhu MJ, Zhao SH. Systems infection biology: a compartmentalized immune network of pig spleen challenged with Haemophilus parasuis. BMC Genomics. 2013 Jan 22;14:46. doi: 10.1186/1471-2164-14-46.
17.Y Feng, L-L Niu, W Wei, W-Y Zhang, X-Y Li, J-H Cao and S-H Zhao (通讯作者). A feedback circuit between miR-133 and the ERK1/2 pathway involving an exquisite mechanism for regulating myoblast proliferation and differentiation Cell Death and Disease (2013) 4, e934; doi:10.1038/cddis.2013.462
18.W Wei, H-B He, W-Y Zhang, H-X Zhang, J-B Bai, H-Z Liu, J-H Cao, K-C Chang, X-Y Li and S-H Zhao. miR-29 targets Akt3 to reduce proliferation and facilitate differentiation of myoblasts in skeletal muscle development. Cell Death and Disease (2013) 4, e668; doi:10.1038/cddis.2013.184
19.Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H, Mann KM, Sang Y, Zhang J, Carvalho-Silva D, Hunt T, Hardy M, Hu Z, Zhao SH, Anselmo A, Shinkai H, Chen C, Badaoui B, Berman D, Amid C, Kay M, Lloyd D, Snow C, Morozumi T, Cheng RP, Bystrom M, Kapetanovic R, Schwartz JC, Kataria R, Astley M, Fritz E, Steward C, Thomas M, Wilming L, Toki D, Archibald AL, Bed'Hom B, Beraldi D, Huang TH, Ait-Ali T, Blecha F, Botti S, Freeman TC, Giuffra E, Hume DA, Lunney JK, Murtaugh MP, Reecy JM, Harrow JL, Rogel-Gaillard C*, Tuggle CK*.Structural and functional annotation of the porcine immunome. BMC Genomics. 2013 May 15;14:332. doi: 10.1186/1471-2164-14-332.
20.Liu G, Liu R, Li Q, Tang X, Yu M, Li X, Cao J, Zhao S (共同通讯作者). Identification of microRNAs in Wool Follicles during Anagen, Catagen, and Telogen Phases in Tibetan Sheep, PLOS ONE, 2013，DOI: 10.1371/journal.pone.0077801
21.Shuhong Zhao, Mengjin Zhu, and Hongbo Chen. Immunogenomics for identification of disease resistance genes in pigs: a review focusing on Gram-negative bacilli. Journal of Animal Science and Biotechnology 2012, 3:34
22.Yang S, He M, Liu X, Li X, Fan B, Zhao S (共同通讯作者). Japanese encephalitis virus infects porcine kidney epithelial PK15 cells via clathrin- and cholesterol-dependent endocytosis. Virol J. 2013 Aug 12;10:258. doi: 10.1186/1743-422X-10-258.
23.Yang S, Liu X, Li X, Sun S, Sun F, Fan B, Zhao S (共同通讯作者) MicroRNA-124 reduces caveolar density by targeting caveolin-1 in porcine kidney epithelial PK15 cells. Mol Cell Biochem. 2013 Dec;384(1-2):213-9. doi: 10.1007/s11010-013-1800-x
24.Di Wu, Dechao Song, Xinyun Li, Mei Yu, Changchun Li & Shuhong Zhao. Molecular characterization and identification of the E2/P4 response element in the porcine HOXA10 gene. Mol Cell Biochem. 2013 Feb;374(1-2):213-22. DOI 10.1007/s11010-012-1522-5
25.Congcong Li, Huabin He, Mengjin Zhu, Shuhong Zhao, Xinyun Li. Molecular characterisation of porcine miR-155 and its regulatory roles in the TLR3/TLR4 pathways. Dev Comp Immunol. Volume 39, Issues 1–2, January–February 2013, Pages 110–116
26.Yang Dong, Min Xie, Yu Jiang, Nianqing Xiao, Xiaoyong Du, Wenguang Zhang, Gwenola Tosser-Klopp, Jinhuan Wang, Shuang Yang, Jie Liang, Wenbin Chen, Jing Chen, Peng Zeng, Yong Hou, Chao Bian, Shengkai Pan, Yuxiang Li, Xin Liu, Wenliang Wang, Bertrand Servin, Brian Sayre, Bin Zhu, Deacon Sweeney, Rich Moore, Wenhui Nie, Yongyi Shen, Ruoping Zhao, Guojie Zhang, Jinquan Li, Thomas Faraut, James Womack, Yaping Zhang, James Kijas, Noelle Cockett, Xun Xu, Shuhong Zhao（共同通讯作者）, Jun Wang & Wen Wang. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)，Nature Biotechnology，(2012) doi:10.1038/nbt.2478
27.Groenen MA*, Archibald AL*, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Za
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