2020

Dan Wang, Hui Tang, Jian-Feng Liu, Shizhong Xu, Qin Zhang* and Chao Ning*. Rapid Epistatic Mixed Model Association Studies by Controlling Multiple Polygenic Effects. Bioinformatics, 2020. [preprint] [software]

Dan Wang, Chao Ning, Jianfeng Liu, Xingbo Zhao. Relationship between mitochondrial DNA haplogroup and litter size in the pig. Reproduction, Fertility and Development, 2020, 32(3): 267-273.

Kerong Shi, Fugui Niu, Qin Zhang, Chao Ning, Shujian Yue, Chengzhang Hu, Zhongjin Xu, Shengxuan Wang, Ranran Li, Qiuling Hou and Zhonghua Wang. Identification of Whole-Genome Significant Single Nucleotide Polymorphisms in Candidate Genes Associated With Serum Biochemical Traits in Chinese Holstein Cattle. Frontiers in Genetics, 2020, 11: 163.

2019

Chao Ning, Dan Wang, Lei Zhou, Julong Wei, Yuanxin Liu, Huimin Kang, Shengli Zhang, Xiang Zhou, Shizhong Xu and Jian-Feng Liu. Efficient Multivariate Analysis Algorithms for Longitudinal Genome-wide Association Studies. Bioinformatics, 2019, 35(23): 4879-4885. [preprint] [pdf] [software]

Dan Wang†, Chao Ning†, Jian-Feng Liu, Qin Zhang, Li Jiang. Short communication: Replication of genome-wide association studies for milk production traits in Chinese Holstein by an efficient rotated linear mixed model. Journal of Dairy Science, 2019, 102(3): 2378-2383. [pdf]

Yanping Wang†, Chao Ning†, Cheng Wang, Jianfeng Guo, Jiying Wang, Ying Wu. Genome-wide association study for intramuscular fat content in Chinese Lulai black pigs. Asian-Australasian Journal of Animal Sciences, 2019, 32(5): 607-613. [pdf]

Dan Wang†, Hai Xiang†, Chao Ning, Hao Liu, Jian-Feng Liu and Xingbo Zhao. Mitochondrial DNA enrichment reduced NUMT contamination in porcine NGS analyses. Briefings in Bioinformatics, 2019. [pdf]

Xianrui Zheng†, Li Jiang†, Chao Ning, Zhengzheng Hu, Lei Zhou, Ying Yu, Shengli Zhang and Jianfeng Liu. A novel mutation in the promoter region of RPL8 regulates milk fat traits in dairy cattle by binding transcription factor Pax6. Biochimica et Biophysica Acta, 2019, 1864(12).

Hao Fan, Zengpeng Lv, Liping Gan, Chao Ning, Zhui Li, Minghui Yang, Beibei Zhang, Bochen Song, Guang Li, Dazhi Tang, Jinxin Gao, Shaojia Yan, Youli Wang, Jianfeng Liu and Yuming Guo. A Novel lncRNA Regulates the Toll-Like Receptor Signaling Pathway and Related Immune Function by Stabilizing FOS mRNA as a Competitive Endogenous RNA. Frontiers in Immunology, 2019, 10. [pdf]

Zengpeng Lv, Jingle Jiang, Chao Ning, Hongjian Dai, Song Jin, Xihui Wei, Debing Yu, Fangxiong Shi. RNA Expression Profile and Alternative Splicing Signatures of Genistein-Treated Breeder Hens Revealed by Hepatic Transcriptomic Analysis. Oxidative Medicine and Cellular Longevity, 2019: 1-19.

2018

Chao Ning, Dan Wang, Huimin Kang, Raphael Mrode, Lei Zhou, Shizhong Xu, Jian-Feng Liu. A rapid epistatic mixed-model association analysis by linear retransformations of genomic estimated values. Bioinformatics, 2018, 34(11): 1817-1825. [pdf] [software]

Chao Ning†, Dan Wang†, Xianrui Zheng†, Qin Zhang, Shengli Zhang, Raphael Mrode, Jian-Feng Liu. Eigen decomposition expedites longitudinal genome-wide association studies for milk production traits in Chinese Holstein. Genetics Selection Evolution, 2018, 50(1): 12. [pdf]

Xianrui, Zheng†, Chao Ning†, Pengju Zhao, Wen Feng, Yuxi Jin, Lei Zhou, Ying Yu, Jian-Feng Liu. Integrated analysis of lncRNAs and mRNA expression profiles reveals the potential role of lncRNAs in different bovine lactation stages. Journal of Dairy Science, 2018, 101(12): 11061-11073. [pdf]

Dan Wang†, Chao Ning†, Hai Xiang, Xianrui Zheng, Minghua Kong, Tao Yin, Jian-Feng Liu, Xingbo Zhao. Polymorphism of mitochondrial tRNA genes associated with the number of pigs born alive. Journal of Animal Science and Biotechnology, 2018, 9(1): 86. [pdf]

Huimin Kang, Chao Ning, Lei Zhou, Shengli Zhang, Ning Yang, Jian-Feng Liu. PIBLUP: High-performance software for large-scale genetic evaluation of animals and plants. Frontiers in Genetics, 2018, 9: 226. [pdf]

Huimin Kang, Chao Ning, Lei Zhou, Shengli Zhang, Qingxia Yan, Jian-Feng Liu. Short communication: Single-step genomic evaluation of milk production traits using multiple-trait random regression model in Chinese Holsteins. Journal of Dairy Science, 2018, 101(12): 11143-11149. [pdf]

Zengpeng Lv, Hao Fan, Beibei Zhang, Chao Ning, Kun Xing, Yuming Guo. Dietary genistein supplementation in laying broiler breeder hens alters the development and metabolism of offspring embryos as revealed by hepatic transcriptome analysis. FASEB Journal, 2018, 32(8): 4214-4228. [pdf]

Ting Yang, Fengxia Zhang, Liwei Zhai, Weiyong He, Zhen Tan, Yangyang Sun, Yuan Wang, Lei Liu, Chao Ning, Weiliang Zhou, Hong Ao, Chuduan Wang, Ying Yu. Transcriptome of porcine PBMCs over two generations reveals key genes and pathways associated with variable antibody responses post PRRSV vaccination. Scientific Reports, 2018, 8:2460. [pdf]

Pengju Zhao, Xianrui Zheng, Wen Feng, Haifei Wang, Huimin Kang, Chao Ning, Heng Du, Ying Yu, Bugao Li, Yi Zhao, Jian-Feng Liu. Profiling long noncoding RNA of multi-tissue transcriptome enhances porcine noncoding genome annotation. Epigenomics, 2018, 10:301-320. [pdf]

2017

Chao Ning†, Huimin Kang†, Lei Zhou, Dan Wang, Haifei Wang, Aiguo Wang, Jinluan Fu, Shengli Zhang, Jian-Feng Liu. Performance gains in genome-wide association studies for longitudinal traits via modeling time-varied effects. Scientific Reports, 2017, 7(1): 590. [pdf]

Haifei Wang†, Jiying Wang†, Chao Ning†, Xianrui Zheng, Jinlian Fu, Aiguo Wang, Qin Zhang, Jian-Feng Liu. Genome-wide DNA methylation and transcriptome analyses reveal genes involved in immune responses of pig peripheral blood mononuclear cells to poly I: C. Scientific Reports, 2017, 7(1): 9709. [pdf]

Xianrui Zheng†, Chao Ning†, Yichun Dong, Pengju Zhao, Junhui Li, Ziyao Fan, Li Jiang, Ying Yu, Raphael Mrode, Jian-Feng Liu. Quantitative proteome analysis of bovine mammary gland reveals protein dynamic changes involved in peak and late lactation stages. Biochemical and Biophysical Research Communications, 2017, 494(1-2): 292-297. [pdf]

Yuan Wang, Xiangdong Ding, Zhen Tan, Chao Ning, Kai Xing, Ting Yang, Yongjie Pan, Dongxiao Sun, Chuduan Wang. Genome-wide association study of piglet uniformity and farrowing interval. Frontiers in Genetics, 2017, 8:194. [pdf]

Xiaotian Feng, Jicai Jiang, Abinash Padhi, Chao Ning, Jinluan Fu, Aiguo Wang, Raphael Mrode, Jian-Feng Liu. Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals. BMC Genomics, 2017, 18: 293. [pdf]

Jie Yang, Xuan Liu, Dan Wang, Chao Ning, Haifei Wang, Qin Zhang, Li Jiang. Functional validation of GPIHBP1 and identification of a functional mutation in GPIHBP1 for milk fat traits in dairy cattle. Scientific Reports, 2017, 7(1): 8546. [pdf]

H. Wang, J. Wang, S. Sun, Y. Wang, J. Guo, C. Ning, K. Yang and J.- F. Liu. Identification of reference microRNAs for quantitative expression analysis in porcine peripheral blood mononuclear cells treated with polyinosinic–polycytidylic acid. International Journal of Immunogenetics, 2015, 42, 217–225. [pdf]