Research
Our lab employs an interdisciplinary approach, integrating computational science and biological science methodologies, to conduct systematic research on epigenetic and post-transcriptional modifications of genetic material using cutting-edge high-throughput sequencing technologies. Key achievements include:
- Cross-Platform Study of Third-Generation High-Throughput Sequencing Technologies: Leveraging machine learning and deep learning algorithms, we have developed novel tools for epigenomics, enabling precise detection and quantification of epigenetic and transcriptomic modification signals.
- Development of Multi-Omics Data Analysis Tools: We have created advanced analytical tools for multi-dimensional omics data to explore the dynamics, evolutionary mechanisms, and functional roles of post-transcriptional modifications in genetic material.
These high-throughput sequencing detection and analysis technologies provide a foundation for further exploration of the genetic modification mechanisms underlying human diseases, as well as for preventive and translational medical research related to these diseases.
Team
Meet our team members:
- Yimeng Kong - Professor
- Linyu Hu - Research Assistant
- Hantao Zhang - PhD Student
- Yaopan Hu - PhD Student
- Shujie Yin - Master Student
- Yingying Zhan - Master Student
Publications
Our recent publications:
- Kong Y, Cao L, Deikus G, Fan Y, Mead E, Lai W, Zhang Y, Yong R, Sebra R, Wang H, Zhang X, Fang G: Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution. Science 2022, 375(6850).
- Kong Y, Mead E.A, Fang G: Navigating the pitfalls of mapping DNA and RNA modifications. Nature Review Genetics 24, 363–381 (2023).
- 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 editing events using nanopore direct RNA sequencing. Genome Biology (2023) 24, 75. (# Equal contributors)
- Kong Y, Zhou H, Yu Y, Chen L, Hao P, Li X: The evolutionary landscape of intergenic trans-splicing events in insects. Nature Communications 2015, 6:8734-8734.
- Kong Y#, Xu P#, Jing X, Chen L, Li L, Li X: Decipher the ancestry of the plant-specific LBD gene family. BMC Genomics 2017, 18(1):951. (# Equal contributors)
- Xu P#, Kong Y#, Song D, Huang C, Li X, Li L: Conservation and functional influence of alternative splicing in wood formation of Populus and Eucalyptus. BMC Genomics 2014, 15(1):780. (# Equal contributors)
- Yang J#, Kong Y#, Li X, Yang S: A novel transposable Mu-like prophage in Bacillus alcalophilus CGMCC 1.3604 (ATCC 27647). Virol Sin 2015, 30(1):63-65. (# Equal contributors)
- 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
- Li X, Kong Y, Zhao Q-Y, Li Y-Y, Hao P: De novo assembly of transcriptome from next-generation sequencing data. Quantitative Biology 2016, 4(2):94-105.
- Yu Y, Zhou H, Kong Y, Pan B, Chen L, Wang H, Hao P, Li X: The landscape of A-to-I RNA editome is shaped by both positive and purifying selection. PLoS Genetics 2016, 12(7):e1006191.
- Yang J, Nie L, Chen B, Liu Y, Kong Y, Wang H, Diao L: Hygromycin-resistance vectors for gene expression in Pichia pastoris. Yeast 2014, 31(4):115-125.
- Wang X-C, Zhao Q-Y, Ma C-L, Zhang Z-H, Cao H-L, Kong Y, Yue C, Hao X-Y, Chen L, Ma J-Q et al: Global transcriptome profiles of Camellia sinensis during cold acclimation. BMC Genomics 2013, 14:415-415.
- Cao Z, Yu Y, Wu Y, Hao P, …, Kong Y, et al: The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods. Nat Communications 2013, 4:2602.
- Xu P, Kong Y, Li X, Li L: Identification of molecular processes needed for vascular formation through transcriptome analysis of different vascular systems. BMC Genomics 2013, 14(1):217.
- Zhao Q-Y, Wang Y, Kong Y, Luo D, Li X, Hao P: Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 2011, 12(Suppl 14):S2.
News
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