孔艺萌课题组大合影

团队介绍：

采用计算科学与生物科学的交叉方法，利用高通量测序技术，深入探索遗传物质的表观遗传修饰。通过整合多组学数据，开发先进的生物信息学工具，实现人类疾病的精准检测，并深入解析致病机理。

负责人：

孔艺萌，东南大学青年首席教授，博士生导师

Email：kongyimeng@seu.edu.cn

办公地点：和燕路371号东南大学生命健康高等研究院105

师资队伍：

孔艺萌，东南大学青年首席教授，博士生导师。入选国家海外高层次引进人才。发表SCI论文15篇，以第一作者（含共同）发表包括Science、Nature Review Genetics、Nature Communications、Genome Biology在内的国际著名学术期刊7篇。

徐鹏，东南大学研究员，博士生导师。曾任西奈山伊坎医学院讲师，长期从事生物信息学、衰老生物学和肿瘤生物学研究，发表SCI论文22篇，以第一作者（含共同）发表包括Cell Systems、 Genome Research、Molecular Neurodegeneration、Aging Cell和Bioinformatics在内的国际著名学术期刊10篇。

研究方向：

高通量测序技术的算法开发和遗传调控研究

科研进展：

交叉运用计算科学和生物科学方法，基于前沿的高通量测序技术，对生物体内遗传调控进行了系统的研究。主要成果包括：（1）开展三代高通量测序技术的跨平台研究，利用机器学习和深度学习算法，开发面向表观组新工具，实现了基因组和转录组表观修饰信号的精确检测和定量；2）开发基于多维组学大数据的分析工具，探索遗传物质转录后修饰的动态性、进化机制以及功能；3）开发共表达网络分析新方法，构建人体组织的衰老调控网络，解析衰老基因的功能模块和关键的细胞类型，阐明衰老的代谢机制。这些高通量测序的检测和分析技术，为进一步探索人类疾病的遗传修饰致病机理，相关疾病的预防与转化医学研究提供了基础。

代表性文论：

1. 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).

2. Kong, Y, Mead, E.A, Fang, G: Navigating the pitfalls of mapping DNA and RNA modifications. Nature Review Genetics 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 editing events using nanopore direct RNA sequencing. Genome Biology (2023) 24, 75. (^# Equal contributors)

4. 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.

5. 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)

6. 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)

7. 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)

8. Xu, P. , Kong, Y.,Palmer, N., Ng, M., Zhang, B., and Das, S.K. (2024). Integrated Multi-OmicAnalyses Uncover the Effects of Aging on Cell-Type Regulation inGlucose-Responsive Tissues. AgingCell, 23(8): e14199.

9. Xu,P. andB. Zhang (2023). Multiscale network modeling reveals the gene regulatorylandscape driving cancer prognosis in 32 cancer types. Genome Research33(10): 1806-1817.

10. Xu, P. +, Wang, M.+, Sharma, N.K. +, Comeau, M.E., Wabitsch, M., Langefeld,C.D., Civelek, M., Zhang, B., and Das, S.K. (2023). Multi-omic integration reveals cell-type-specific regulatory networksof insulin resistance in distinct ancestry populations. Cell Systems 14, 41-57.e48. 

11. Xu, P., Wang, M., Song, W.M.,Wang, Q., Yuan, G.C., Sudmant, P.H., Zare, H., Tu, Z., Orr, M.E., and Zhang, B.(2022). The landscape of human tissue andcell type specific expression and co-regulation of senescence genes. Molecular Neurodegeneration 17, 5. 

12 Xu, P., Chen, Y., Gao, M.,Chong, Z. (2021). ClipSV: Improvingstructural variation detection by read extension, spliced alignment, andtree-based decision rules. NAR GenomBioinform 3, lqab003. 

13 Xu, P., Kennell Jr, T., Gao,M., Consortium, H.G.S.V., Kimberly, R.P., and Chong, Z. (2020). MRLR: unraveling high-resolution meioticrecombination by linked reads. Bioinformatics36, 10-16.

14 Wang,M. +, Song, W.M. +, Ming, C. +, Wang, Q.+, Zhou, X. +, Xu, P.+, Krek, A., Yoon, Y., Ho, L., Orr, M.E., et al. (2022). Guidelines for Bioinformatics of Single-CellSequencing Data Analysis in Alzheimer’s Disease: Review, Recommendation,Implementation and Application. MolecularNeurodegeneration 17, 17.

15 Xu,P.,Kong, Y., Li, X., and Li, L. (2013). Identificationof molecular processes needed for vascular formation through transcriptomeanalysis of different vascular systems. BMC Genomics 14, 1-11.