（1）深入挖掘三代测序底层信息，建立基于机器学习的表观组学新方法；

（2）肠道菌群宏表观组的精确重构和解析，研究肠道菌群宏表观组对人类疾病的调控机制；

（3）基于高通量测序技术、单细胞及空间转录组技术，探索人类功能基因组和致病机制。

代表性论文

1.     Kong Y, Cao L, Deikus G, Fan Y, MeadE, Lai W, Zhang Y, Yong R, Sebra R, Wang H, Zhang X, Fang G: Criticalassessment of DNA adenine methylation in eukaryotes using quantitativedeconvolution. Science 2022, 375(6850).

2.     Kong, Y, Mead, E.A, Fang, G: Navigatingthe pitfalls of mapping DNA and RNA modifications. Nature ReviewGenetics 24, 363–381 (2023).

3.    Chen, L#, Ou, L#, Jing,X#, Kong Y#, Xie B, Zhang N, Shi H, Qin H, Li X,Hao P: DeepEdit: single-molecule detection and phasing of A-to-I RNA editingevents using nanopore direct RNA sequencing. Genome Biology (2023)24, 75. (# Equal contributors)

4.     KongY, Zhou H, Yu Y, Chen L, Hao P, Li X: The evolutionary landscape ofintergenic trans-splicing events in insects. Nature Communications2015, 6:8734-8734.

5.     Kong Y#, Xu P#, Jing X, Chen L, Li L, LiX: Decipher the ancestry of the plant-specific LBD gene family. BMCgenomics 2017, 18(1):951. (# Equal contributors)

6.     Xu P#, Kong Y#, Song D, Huang C, Li X, Li L: Conservationand functional influence of alternative splicing in wood formation of Populusand Eucalyptus. BMC Genomics 2014, 15(1):780. (# Equalcontributors)

7.     Yang J#, Kong Y#, Li X, Yang S: A novel transposable Mu-like prophagein Bacillus alcalophilus CGMCC 1.3604 (ATCC 27647). Virol Sin 2015,30(1):63-65. (# Equal contributors)

8.    Cao, L., Kong, Y., Fan, Y. et al. mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome. Nat Methods 21, 236–246 (2024). https://doi.org/10.1038/s41592-023-02125-1

9.     Li X, KongY, Zhao Q-Y, Li Y-Y, Hao P: De novo assembly of transcriptome fromnext-generation sequencing data. Quantitative Biology 2016,4(2):94-105.  

10.     Yu Y, Zhou H, Kong Y, Pan B, Chen L, Wang H, Hao P, Li X: The landscape ofA-to-I RNA editome is shaped by both positive and purifying selection. PLoSGenetics 2016, 12(7):e1006191.

11.   Yang J, Nie L, Chen B, Liu Y, Kong Y,Wang H, Diao L: Hygromycin-resistance vectors for gene expression inPichiapastoris. Yeast 2014, 31(4):115-125.

12.   Wang X-C, Zhao Q-Y, Ma C-L, Zhang Z-H, CaoH-L, Kong Y, Yue C, Hao X-Y, Chen L,Ma J-Q et al: Global transcriptome profiles of Camellia sinensis during coldacclimation. BMC genomics 2013, 14:415-415.

13.   Cao Z, Yu Y, Wu Y, Hao P, …, Kong Y, et al: The genome of Mesobuthus martensii reveals aunique adaptation model of arthropods. Nat Communications2013, 4:2602.

14.   Xu P, KongY, Li X, Li L: Identification of molecular processes needed for vascularformation through transcriptome analysis of different vascular systems. BMCGenomics 2013, 14(1):217.

15.   Zhao Q-Y, Wang Y, Kong Y, Luo D, Li X, Hao P: Optimizing de novo transcriptomeassembly from short-read RNA-Seq data: a comparative study. BMCBioinformatics 2011, 12(Suppl 14):S2.