University of Hawai‘i at Manoa
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Last updated on Tuesday, August 29, 2023    Make updates ->

Yanghua  He

Name :

Yanghua He

Title :

Assistant Professor of Genomics and Epigenomics

Unit :

Department of Human Nutrition, Food & Animal Sciences

Address :

1955 East-West Road
                  Honolulu, HI 96822

Room :

Ag Sciences Building 314I

Phone :

(808) 956-7090

Fax :

(808) 956-4024

E-mail :

Website :

Specialties :

1. Benchwork: Sequencing platforms: Illumina HiSeq; Mi-seq; 10*Genomics; Nanopore sequencing. Library constructions for sequencing: DNA-seq; RNA-seq; ChIP-seq and CUT&RUN; MBD-seq; MeDIP-seq; WGBS; RRBS; Bisulfite cloning sequencing; pyrosequencing; HiC; PLAC-seq; ATAC-seq. CRISPR-based technologies (Genome-editing and Epigenome-editing). sgRNA Library Screening. 2. Data analysis: Bioinformatics in Genetic and Epigenetic data analysis; Galaxy platform; Linux Operating System; Computational languages: Perl, Python, R, Matlab, SAS, C++

Professional Prep/Appointments :

Assistant Professor
of Animal Genomics, HNFAS, CTAHR, University of Hawaii at Manoa (2019.08 - present)
Graduate Faculty (Concurrent Position): Animal Science Program, University of Hawaii at Manoa (2019.08 - present)
Graduate Faculty (Concurrent Position): Nutritional Sciences Program, University of Hawaii at Manoa (2019.08 - present)
Graduate Faculty (Concurrent Position): Molecular Biosciences and Bioengineering Program, University of Hawaii at Manoa (2019.08 - present)
Postdoctoral Research Associate
, Department of Hematology, St. Jude Children's Research Hospital, Tennessee, USA (2017-2019), Epigenome Editing in Children's Sickle Cell Disease
Postdoctoral Research Associate, Department of Animal and Avian Sciences, University of Maryland, Maryland, USA (2012-2017), Epigenomics in Animal Diseases and Production Traits
Ph.D., Animal Genetics and Breeding, China Agricultural University, Beijing, China (2012), Epigenetic Mechanisms in Mastitis of Dairy Cattle 


Projects :

1) applying Genome-Wide Association Study (GWAS) and Genomic Selection (GS) to improve economically important traits of Hawaii beef cattle under diverse climatic conditions;
2) combining with over 100-year Hawaiian climate data to study the impacts of climate changes on livestock production;
3) using epigenetic strategy to study muscle development and related disorders during embryonic development stages utilizing Myostatin transgenic mouse model.

Courses Taught:

Spring semester:
ANSC 201 Principal and Practice of Animal Science II (50-60 undergraduate students) as a primary instructor
ANSC 445 Genetics and Animal Breeding (~40 undergraduate students) as a primary instructor

Fall semester:
ANSC 200 Humans, Animals & Agriculture (50-60 undergraduate students) as a primary instructor
ANSC 387 Lab Skills in Animal Science (~20 undergraduate students) as a co-instructor
ANSC/FSHN/MBBE 650 DNA and Genetic Analysis (~25 graduate students) as a primary instructor

Research interests:

Animal Genomics and Epigenomics; Environmental genome-wide association studies (GWAS); Genomics Selection; Impacts of climate changes on livestock production; Nutrigenomics; Metagenomics; Gut health and microbiome diversity; CRISPR-Cas9.

Lab members: 

Past graduate students:
1. Huong Thanh Vu, M.S.; currently working in a Bio-tech company located in San Francisco

 Graduate students:

1. Mandeep Adhikari, Ph.D. Department of Molecular Biosciences and Bioengineering
2. Natalie Deans, M.S. Department of Human Nutrition, Food and Animal Sciences

Undergraduate students:
1. Christopher Aguirre, Molecular Biosciences and Bioengineering
2. Jacey Mitchell, Molecular Cell Biology, School of Life Sciences
3. Angela Camino, Molecular Biosciences and Bioengineering
4. Casey Ku, Molecular Cell Biology, School of Life Sciences

Selected Publications :

Google Scholar Profile
ResearchGate Profile

Star (*) stands for the equal-first author or corresponding author

Book Chapter

  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.

Peer-reviewed manuscripts:

  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.
  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. PubMed Central PMCID: PMC10103973. bioRxiv: MS ID#: BIORXIV/2023/535219. doi: Accepted by Genome Research.
  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. PubMed Central PMCID: PMC10203587. 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. 6(2).
  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. 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, 35:1, 788-795, DOI: 10.1080/13102818.2021.1914164 
  8. 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.
  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 17.543). DECEMBER 9, 2020. 
  10. Jianan Liu, Fang Liu, Wentao Cai, Cunling Jia, Ying Bai, Yanghua He, Weiyun Zhu, Robert W. Li, Jiuzhou Song. Jejunal Microbiome and Bile Acids Induced by Diets in Angus Beef Cattle. Animal Microbiome volume 2, Article number: 33 (2020) 
  11. Hao Bai, Yanghua He, Yanli Lin, Qixin Leng, José 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. doi: 10.1139/gen-2020-0071.
  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. doi: 10.1186/s12863-020-00884-w.
  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) 
  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 36.558). volume 38, pages1317–1327(2020)
  15. Yanghua He, Bo Han, Yi Ding, Huanmin Zhang, Li Zhang, Chunfang Zhao, Ning Yang, and Jiuzhou Song. Linc-GALMD1 regulates viral gene expression in the chicken. 2019. Frontiers in Genetics, 10:1122. doi: 10.3389/fgene.2019.01122
  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; doi:10.3390/genes10090718
  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. Cold Spring Harbor Laboratory, 2019, doi:
  18. Hao Bao, 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 May 10. pii: pez209. doi: 10.3382/ps/pez209.
  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. (Equal-first author)
  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. Published Online: April 19, 2018. DOI:
  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. (Equal-first author)
  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; doi:10.3390/ijms18051020.(Equal-first author)
  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. doi: 10.1186/s40104-016-0137-1
  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. 2016. doi: 10.1111/age.12510.
  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(1): 565. doi: 10.1186/s12864-016-2947-0.
  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 6, Article number: 29390 (2016) doi:10.1038/srep29390
  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 6, Article number: 25948 (2016) doi:10.1038/srep25948
  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, 5, 15184; doi: 10.1038/srep15184 (2015).
  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. doi: 10.4238/2015.February.6.12.
  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. doi: 10.1371/journal.pone.0135670. eCollection 2015.
  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. Published: June 24, 2015DOI: 10.1371/journal.pone.0100476.
  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. Published: June 19, 2015DOI: 10.1371/journal.pone.0116437.
  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, 16:311.doi: 10.1186/s12864-015-1492-6.
  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. 13 October 2014 | doi: 10.3389/fgene.2014.00308
  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 May 22
  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, 12(4): 6228-6239.
  37. Yanghua He, Ying Yu, Yuan Zhang, Jiuzhou Song, Apratim Mitra, Yachun Wang, Dongxiao Sun, Yi Zhang, Shengli Zhang. The genomic landscape of H3K27me3 modification in bovine lymphocytes. Plos One. Published: June 28, 2012 DOI: 10.1371/journal.pone.0039094
  38. Jian Gao, Han-qi Zhang, Jian-zhong He, Yanghua He, Shu-mei Li, Rong-guang Hou, Qiao-xing Wu, Yang Gao and Bo Han. Characterization of Prototheca zopfii Associated with Outbreak of Bovine Clinical Mastitis in Herd of Beijing, China. Mycopathologia Online First™, 9 December 2011. DOI 10.1007/s11046-011-9510-y
  39. Yanghua He, Qin Chu, Peipei Ma, Yachun Wang, Qin Zhang, Dongxiao Sun, Yi Zhang, Ying Yu and 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 2011.78: 242-249.
  40. Yanghua He, Ning Yang, and Jiuzhou Song. The current and future of epigenetics in poultry health. Proceeding paper. THE XXV WORLD'S POULTRY CONGRESS. Beijing, China. 2016.
  41. Yanghua He and Jiuzhou Song. The Current and Future of Epigenetics of Marek’s Disease in Chickens. The 62nd Annual National Breeders Roundtable. Breeders Roundtable, 2013 Pages 19-25
  42. Yanghua He, Ying Yu and Yuan Zhang. Relationships between copy number variations and human disease and its perspective in animal disease-resistant breeding. HEREDITAS (Beijing). November 2008. 30(11): 1385―1391 (in Chinese)

Languages :

English, Mandarin