Publications

Profession Academic Profiles:

• Google Scholar

• ResearchGate

• ORCID ID: 0000-0001-6849-6493

Refereed Journal Articles

Note: Bold indicates the author’s name. Asterisk (*) stands for the equal-first author or the corresponding author.

1. Yanghua He, Robert L. Taylor Jr., Hao Bai, Christopher M. Ashwell, Keji Zhao, Yaokun Li, Guirong Sun, Huanmin Zhang, Jiuzhou Song. Transgenerational epigenetic inheritance and immunity in chickens that vary in Marek's disease resistance. Poultry Science. August 2023. https://doi.org/10.1016/j.psj.2023.103036.

2. Guanjue Xiang, Xi He, Belinda M. Giardine, Kathryn J. Weaver, Dylan J. Taylor, Rajiv C. McCoy, Camden Jansen, Cheryl A. Keller, Alexander Q. Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F. Heuston, Stacie M. Anderson, Jing Luan, Marit W. Vermunt, Feng Yue, Michael E.G. Sauria, Michael C. Schatz, James Taylor, Berthold Gottgens, Jim R. Hughes, Douglas R. Higgs, Mitchell J. Weiss, Yong Cheng, Gerd A. Blobel, David Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross C. Hardison. Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. bioRxiv: MS ID#: BIORXIV/2023/535219. doi: https://doi.org/10.1101/2023.04.02.535219. Genome Research. Accepted.

3. Mandeep Adhikari, Michael B. Kantar, Ryan J. Longman, Christopher Aguirre, Melelani Oshiro, Kyle Caires, C. N. Lee, Yanghua He*. Genome-wide association study for carcass weight in pasture finished beef cattle in Hawaii. Frontiers in Genetics. Volume 14. 2023. doi: 10.3389/fgene.2023.1168150

4. Jingyue Ellie Duan, Jicai Jiang, Yanghua He*. Editorial: Bridging (Epi-) Genomics and Environmental Changes: The Livestock Research. Front. Genet. 2022, 13:961232. doi: 10.3389/fgene.2022.961232

5. Mandeep Adhikari, Ryan J Longman, Thomas W Giambelluca, C.N. Lee, Yanghua He*. Climate change impacts shifting landscape of the dairy industry in Hawai`i. Translational Animal Science, 2022. https://doi.org/10.1093/tas/txac064. PubMed Central PMID: 35755135

6. Jose Carrillo; Ying Bai; Yanghua He; Yaokun Li; Wentao Cai; Derek M. Bickhart; George Liu; Scott M. Barao; Tad Sonstegard; Jiuzhou Song. Growth curve, blood parameters and carcass traits of grass-fed Angus steers. Animal. 2021 Oct 29;15(11):100381. PubMed Central PMID: 34757288

7. Cunling Jia, Ying Bai, Jianan Liu, Wentao Cai, Lei Liu, Yanghua He, and Jiuzhou Song. Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef Cattle. Front. Genet., 04 March 2021. PubMed Central PMCID: PMC7969984

8. Xi Wang, Xi Li, Sujun Wu, Kerong Shi, Yanghua He. DNA methylation and transcriptome comparative analysis for Lvliang Black goats in distinct feeding pattern reveals epigenetic basis for environment adaptation. Biotechnology & Biotechnological Equipment 2021 v.35 no.1, pp. 788-795. Catalog7770408

9. Qian Qi, Li Cheng, Xing Tang, Yanghua He, Yichao Li, Tiffany Yee, Dewan Shrestha, Ruopeng Feng, Peng Xu, Xin Zhou, Shondra M Pruett-Miller, Ross C. Hardison, Mitchell J. Weiss, Yong Cheng. Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis. Blood (IF 22.113). DECEMBER 9, 2020. PubMed Central PMCID: PMC7955410

10. Jianan Liu, Fang Liu, Wentao Cai, Cunling Jia, Ying Bai, Yanghua He, Weiyun Zhu, Robert W. Li, Jiuzhou Song. Diet-induced changes in bacterial communities in the jejunum and their associations with bile acids in Angus beef cattle. Animal Microbiome 2020; 2: 33. PubMed Central PMCID: PMC7807434

11. Hao Bai, Yanghua He, Yanli Lin, Qixin Leng, José A Carrillo, Jianan Liu, Feng Jiang, Jilan Chen, Jiuzhou Song. Identification of a novel differentially methylated region adjacent to ATG16L2 in lung cancer cells using methyl-CpG binding domain protein enriched genome sequencing. Genome. 2020 Oct 28. PubMed Central PMID: 33113339

12. Hao Bai, Yanghua He, Yi Ding, Qin Chu, Ling Lian, Eliyahu M Heifetz, Ning Yang, Hans H Cheng, Huanmin Zhang, Jilan Chen, Jiuzhou Song. Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing. BMC Genetics. 2020 Jul 16; 21(1):77. PubMed Central PMCID: PMC7364486

13. Ying Bai, José A. Carrillo, Yaokun Li, Yanghua He, Jiuzhou Song. Diet induced the change of mtDNA copy number and metabolism in Angus cattle. Journal of Animal Science and Biotechnology volume 11, Article number: 84 (2020). PubMed Central PMCID: PMC7372754

14. Cicera R. Lazzarotto, Nikolay L. Malinin, Yichao Li, Ruochi Zhang, Yang Yang, Yanghua He, Xin Lan, Kasey Jividen, Varun Katta1, Natalia G. Kolmakova, Christopher T. Petersen, Qian Qi, Evgheni Strelcov, Samantha Maragh, Giedre Krenciute, Jian Ma, Yong Cheng, Shengdar Q. Tsai. CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity. Nature Biotechnology (IF 68.164). volume 38, (2020) PubMed Central PMCID: PMC7652380

15. Yanghua He, Bo Han, Yi Ding, Huanmin Zhang, Li Zhang, Chunfang Zhao, Ning Yang, and Jiuzhou Song. LincGALMD1 regulates viral gene expression in the chicken. Frontiers in Genetics, 10:1122. 2019 doi: 10.3389/fgene.2019.01122. PubMed Central PMCID: PMC6868033

16. Hao Bai, Yanghua He*, Yi Ding, José A. Carrillo, Huanmin Zhang, Ramesh K. Selvaraj, Jilan Chen, Jiuzhou Song. Allele-Specific Expression (ASE) and Differential Expression (DE) of CD4+ T Cells in response to Marek’s Disease Virus Infection. Genes 2019, 10, 718; PubMed Central PMCID: PMC6770979

17. Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Jianan Liu, Linsen Zan, Jiuzhou Song. DNA methylation, microRNA expression profiles and their relationships with transcriptome in grass-fed and grain-fed Angus Cattle rumen tissue. PLoS One. 2019 Oct 17;14(10): e0214559. PubMed Central PMCID: PMC6797229

18. Hao Bai, Yanghua He, Yi Ding, Shuang Chang, Huanmin Zhang, Jilan Chen, Jiuzhou Song. Parent-of-origin has no detectable effect on survival days of Marek's disease virus infected White Leghorns. Poultry Science. 2019 Oct 1;98(10):4498-4503. PubMed Central PMID: 31076761

19. Lingyang Xu, Yanghua He*, Yi Ding, George E. Liu, Huanmin Zhang, Hans H. Cheng, Robert L. Taylor Jr, Jiuzhou Song. Genetic assessment of inbred chicken lines indicates genomic signatures of resistance Marek’s disease. Journal of Animal Science and Biotechnology. December 2018, 9:65. PubMed Central PMCID: PMC6136188

20. Yanghua He, Qisheng Zuo, John Edwards, Keji Zhao, Jinzhi Lei, Wentao Cai, Qing Nie, Bichun Li, and Jiuzhou Song. DNA Methylation and Regulatory Elements during Chicken Germline Stem Cell Differentiation. Stem Cell Reports (IF 7.34). Cell Press. 2018 Jun 5; 10(6): 1793–1806. PubMed Central PMCID: PMC5989647

21. Bo Han, Yanghua He*, Li Zhang, Yi Ding, Ling Lian, Chunfang Zhao, Jiuzhou Song, and Ning Yang. Long intergenic non-coding RNA GALMD3 in chicken Marek’s disease. Scientific Reports. 2017 Aug 31;7(1):10294. PubMed Central PMCID: PMC6868033

22. Lingyang Xu, Yanghua He*, Yi Ding, Guirong Sun, Jose Carrillo, Yaokun Li, Mona Ghaly, Li Ma, Huanmin Zhang, George Liu, Jiuzhou Song. Characterization of copy number variation's potential role in Marek’s Disease. International Journal of Molecular Sciences. 2017, 18(5), 1020; PubMed Central PMCID: PMC5454933

23. Tahir Usman, Yachun Wang, Chao Liu, Yanghua He, Xiao Wang, Yichun Dong, Hongjun Wu, Airong Liu, Ying Yu. Novel SNPs in IL-17F and IL-17A genes associated with somatic cell count in Chinese Holstein and Inner-Mongolia Sanhe cattle. Journal of Animal Science and Biotechnology. Journal of Animal Science and Biotechnology. 2017. 8:5. PubMed Central PMCID: PMC5237346

24. Dong Li, Yanghua He, Jiuzhou Song, Yani Zhang and Bichun Li. Regulation of crucial lncRNAs in differentiation of chicken embryonic stem cells to spermatogonia stem cells. Animal Genetics. 2017 Apr;48(2):191-204. PubMed Central PMID: 27862128

25. Yanghua He, Minyan Song, Yi Zhang, Xizhi Li, Jiuzhou Song, Yuan Zhang and Ying Yu. Whole-genome regulation analysis of histone H3 lysin 27 trimethylation in subclinical mastitis cows infected by Staphylococcus aureus. BMC Genomics. 2016 Aug 8; 17:565. PubMed Central PMCID: PMC4977872

26. Minyan Song, Yanghua He, Huangkai Zhou, Yi Zhang, Xizhi Li, Ying Yu. Combined analysis of DNA methylome and transcriptome reveal novel candidate genes relevant with susceptibility to bovine Staphylococcus aureus subclinical mastitis. Scientific Reports 2016 Jul 14; 6:29390. PubMed Central PMCID: PMC4944166

27. José A. Carrillo, Yanghua He, Yaokun Li, Richard A. Erdman, Tad Sonstegard, Jiuzhou Song. Integrated metabolomic and transcriptome analyses reveal finishing forage affects metabolic pathways related to beef quality and animal welfare. Scientific Reports 2016 May 17; 6:25948. PubMed Central PMCID: PMC4869019  

28. Yanghua He, Yi Ding, Fei Zhan, Huanmin Zhang, Gangqing Hu, Keji Zhao, Ning Yang, Jiuzhou Song. The conservation and signatures of lincRNAs in Marek's disease of chicken. Scientific Reports, 2016 Jan 27;6:19422. PubMed Central PMCID: PMC4728745

29. Nan Liu, J. N. He, W. M. Yu, Kaidong Liu, Ming Cheng, Jifeng Liu, Yanghua He, Jinshan Zhao, X. X. Qu. Transcriptome analysis of skeletal muscle at prenatal stages in Polled Dorset versus Small-tailed Han sheep. Genet Mol Res. 2015 Feb 6;14(1):1085-95. PubMed Central PMID: 25730048

30. Yaokun Li, José A. Carrillo, Jianan Liu, George Liu, Yanghua He, Yi Ding, Chunping Zhao, Linsen Zan, and Jiuzhou Song. Transcriptomic profiling of spleen in grass-fed and grain-fed Angus cattle. PLoS One. 2015 Sep 14;10(9): e0135670. PubMed Central PMCID: PMC4569079

31. José A. Carrillo, Yanghua He, Juan Luo, Kimberly R. Menendez, Nathaniel L. Tablante, Keji Zhao, Joseph N. Paulson, Bichun Li, Jiuzhou Song. Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine, PLoS One. 2015 Jun 24;10(6): e0100476. PubMed Central PMCID: PMC4481310

32. Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Linsen Zan, and Jiuzhou Song. Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle. PLoS One. 2015 Jul 21;10(7): e0134067. PubMed Central PMCID: PMC4510587

33. Apratim Mitra, Juan Luo, Yanghua He, Yulan Gu, Huanmin Zhang, Keji Zhao, Kairong Cui and Jiuzhou Song. Histone modifications induced by MDV infection at early cytolytic and latency phases. BMC Genomics. 2015 Apr 18;16(1):311. PubMed Central PMCID: PMC4404578

34. Yanghua He, Jose A. Carrillo, Juan Luo, Yi Ding, Fei Tian and Jiuzhou Song. Genome-wide mapping of DNase I hypersensitive sites and association analysis with gene expression in MSB1 cells. Front Genet. 2014 Oct 13; 5:308. PubMed Central PMCID: PMC4195362

35. Nan Liu, Hegang Li, Kaidong Liu, Juanjuan Yu, Ming Cheng, Wei De, Jifeng Liu, Shuyan Shi, Yanghua He and Jinshan Zhao. Differential expression of genes and proteins associated with wool follicle cycling. Mol Biol Rep. 2014 Aug;41(8):5343-9. PubMed Central PMID: 24847760

36. Xiaoshuo Wang, Yuan Zhang, Yanghua He, Peipei Ma, Lijun Fan, Yachun Wang, Yi Zhang, Dongxiao Sun, Shengli Zhang, Chuduan Wang, Jiuzhou Song and Ying Yu. Aberrant promoter methylation of the CD4 gene in peripheral blood cells of mastitic dairy cows. Genetics and molecular research. 2013 Dec 4;12(4):6228-39. PubMed Central PMID: 24338418

37. Yanghua He, Ying Yu, Yuan Zhang, Jiuzhou Song, Apratim Mitra, Yi Zhang, Yachun Wang, Dongxiao Sun, Shengli Zhang. Genome-wide bovine H3K27me3 modifications and the regulatory effects on genes expressions in peripheral blood lymphocytes. Plos One. 2012;7(6): e39094. PubMed Central PMCID: PMC3386284

38. Jian Gao, Han-qi Zhang, Jian-zhong He, Yanghua He, Shu-mei Li, Rong-guang Hou, Qiao-xing Wu, Yang Gao, Bo Han. Characterization of Prototheca zopfii Associated with Outbreak of Bovine Clinical Mastitis in Herd of Beijing, China. Mycopathologia. 2012 Apr;173(4):275-81. PubMed Central PMID: 22160589

39. Yanghua He, Qin Chu, Peipei Ma, Yachun Wang, Qin Zhang, Dongxiao Sun, Yi Zhang, Ying Yu, Yuan Zhang. Association of bovine CD4 and STAT5b single nucleotide polymorphisms with somatic cell scores and milk production traits in Chinese Holsteins. Journal of Dairy Research. 2011 May;78(2):242-9. PubMed Central PMID: 21435309

40. Yanghua He, Ying Yu, Yuan Zhang. Relationships between copy number variations and human disease and its perspective in animal disease-resistant breeding. [Article in Chinese] HEREDITAS (Beijing). 2008 Nov;30(11):1385-91. PubMed Central PMID: 19073544

Extension Publications

1. Jinzeng Yang, Michael DuPonte, Douglas Vincent, Kyle Caires, Yanghua He, Nicole Correa, Lehua Wall, Keala Cowell, Marla Fergerstrom. DNA-Based Bull Selection and Artificial Insemination for Grass-Fed Beef Cattle Production. 2020 June. http://www.ctahr.hawaii.edu/oc/freepubs/pdf/AAS-1.pdf

Book Chapters

1.   Yanghua He* and Jiuzhou Song. 2016. Book Chapter 15 Bioinformatics Analysis of Epigenetics. In: Bioinformatics in Aquaculture (edited by John Liu), Blackwell Publishing, Ames, IA. ISBN10: 1118782356. ISBN13: 9781118782354. Publication date: 03 February 2017. Publication City/Country New York, United States.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781118782392.ch15