One of my research focuses on the use of comparative genomics method to understand the complex relationships between genome sequences and phenotypes of rice (Oryza sativa L.). In my laboratory, we not only analyze the comparative genome and proteome data, but also have a biochemical aim on the function of genes and proteins. Another research interest in my group focuses on rice biological breeding. 60 papers had been published in refereed journals with over 3000 citations, including Briefings in Bioinformatics, Planta, BBA-Protein and Proteomics, BMC Genomics, Agricultural Water Management, Plant Growth and Regulation, etc. H index is 32. The specific research interests include:

Rice comparative genomics                             

Rice biological breeding                       

    Plant genomics                   

(1) Spring term  Bioinformatics   Undergraduate students.

(2) Fall term    New preogress in bioinformatics    Graduate students.  

2024-2028: A 500,000 RMB grant awarded by Biological Breeding-National Science and Technology Major Project of China.

2023-2027: A 500,000 RMB grant awarded by Natural Science Foundation of China.

2021-2024: A 300,000 RMB grant awarded by Fujian Natural Science Foundation.

2013-2016: A 770,000 RMB grant awarded by Natural Science Foundation of China.

2011-2012: A 80,000 RMB grant awarded by Natural Science Foundation of China.

1. Ma S^#., Xu S^#., Tao H^#., Huang Y., Feng C., Huang G., Lin S., Sun Y., Chen X., Fabrice Kabore M.A., Tareke Woldegiorgis S., Ai Y., Zhang L., Liu W., He H*. OsBRW1, a novel blast-resistant gene, coded a NBS-LRR protein to interact with OsSRFP1 to balance rice growth and resistance. Plant Biotechnol. J. 2025, 23 (1): 250-267. 

2. Tao H^#., Xu S^#., Shen H., Yang J., Xu Y., Huang G., Feng C., Wan W., Tareke Woldegiorgis S., Liu W., He H*. Genome-wide characterization and functional analysis of heat shock transcription factors in wild and cultivated rice (Oryza sativa L.). Plant Stress 2024, 12: 100505

3. Ma S., Sun Y., Chen X., Guo J., Wu S., Wu G., Huang G., Kabore M.A.F., Woldegiorgis S.T., Ai Y., Zhang L., Liu W., He H*. Gα solicits OsNYC4 and GW2-WG1- OsbZIP47 modules to regulate grain size in rice (Oryza sativa L.). Agronomy 2024, 14, 1514.

4. Qiu F., Zheng Y., Lin Y., Woldegiorgis ST, Xu S., Feng C., Huang G., Shen H., Xu Y., Kabore MAF, Ai Y., Liu W., He H*. Integrated ATAC-seq and RNA-seq data analysis to reveal OsbZIP14 function in rice in response to heat stress. Int. J. Mol. Sci. 2023, 24 (6): 5619.

5. Woldegiorgis ST, Wu T., Gao L, Huang Y., Zheng Y., Qiu F., Xu S., Tao H., Harrison A., Liu W., He H*. Identification of heat-tolerant genes in non-reference sequences in rice by integrating pan-genome, transcriptomics, and QTLs. Genes (Basel) 2022, 13 (8): 1353.

6. Tian T., Chen L., Ai Y., He H*. Selection of candidate genes conferring blast resistance and heat tolerance in rice through integration of meta-QTLs and RNA-seq. Genes (Basel) 2022, 13 (2): 224. 

7. Chen L., Wan L., Wei X., Wan L*., He H*. Adaptive synchronization of reaction diffusion neural networks with infinite distributed delays and stochastic disturbance. IEEE Access 2020, 8: 180411-180421

8. Ma S., Song Q., Tao H., Harrison A., Wang S., Liu W., Lin S., Zhang Z., Ai Y*., He H*. Prediction of protein-protein interactions between fungus (Magnaporthe grisea) and rice (Oryza sativa L.). Briefings in Bioinformatics 2019, 20 (2): 448-456.

9. Woldegiorgis ST ^#., Wang S^#., He Y., Xu Z., Chen L., Tao H., Zhang Y., Zou Y., Harrison A., Zhang L., Ai Y., Liu W*., He H*. Rice stress-resistant SNP database. Rice (N Y) 2019, 12 (1):97.

10. Ma S^#., Lin S^#., Wang M., Zou Y., Tao H., Liu W., Zhang L., Liang K., Ai Y*., He H*. Differential expression proteins contribute to race-specific resistant ability in rice (Oryza sativa L.). Plants 2019, 8(2): 0-29. 

11. Liu W., Li L., Long X., You W., Zhong Y., Wang M., Tao H., Lin S., He H*. Construction and analysis of gene co-expression networks in Escherichia coli. Cells 2018, 7 (3), 19.

12. Li K^#., Xu C^#., Huang J^#., Liu W., Zhang L., Wan W., Tao H., Li L., Lin S., Harrison A., He H*. Prediction and identification of the effectors of heterotrimeric G proteins in rice (Oryza sativa L.). Briefings in Bioinformatics 2017, 18 (2): 270-278.

13. Liu W*., Lin L., Zhang L., Liu S., Gao K., Lv Y., Tao H., He H*. Gene co-expression network analysis identifies trait-related modules in Arabidopsis thaliana. Planta 2019, 249 (5): 1487-1501.