副教授、博士、博士生导师

研究领域：人工智能、机器学习、生物信息学

办公室＆实验室：中南大学计算机楼

电子邮件：hongdong@csu.edu.cn

联系电话：18229752015

教育背景

1. 2007/9–2012/6，中南大学，化学化工学院，博士

2. 2003/9–2007/6，中南大学，化学化工学院，本科

工作简历

1. 2016/12–至今，中南大学，计算机学院

2. 2015/5–2016/10，系统生物学研究所(西雅图)，研究员(Research Scientist)

3. 2012/8–2015/5，密歇根大学，博士后

学术成果

u 主持项目

1. 科技创新2030“脑科学与类脑研究”重大项目青年科学家项目，2022ZD0213700，基于基因可变剪接的阿尔茨海默病机制研究，2012/8-2027/7，500万，主持

2. 国家自然科学基金面上项目，62473382，基于转录组多尺度特征挖掘与知识整合的致病基因预测，2025/1-2028/12，50万，主持

3. 国家自然科学基金委员会联合基金项目，U22A2041，基于超算与多组学的智能医药大数据关键技术研究及应用，2023-01-01 至 2026-12-31，85万元(总257万元)，在研，参与（合作单位负责人）

4. 国家自然科学基金青年项目，61702556，内含子保留的多组学数据整合分析方法研究，2017/1-2019/12，21万，主持

5. 国家自然科学基金面上项目，61972185，基于异质属性网络表征学习的识别癌症驱动基因算法研究，2020/1-2023/12，60万（合作单位负责人）

u 期刊论文

1. Yunpei Xu#, Shaokai Wang#, Qilong Feng, Jiazhi Xia, Yaohang Li, Hong-Dong Li*, JianxinWang*, scCAD: Cluster decomposition-based anomaly detection for rare cell identification in single-cell expression data, Nature Communications, 2024, 15:7561

2. Yiwei Liu, Changhuo Yang, Hong-Dong Li*, Jianxin Wang*, IsoFrog: a reversible jump MarkovChain Monte Carlo feature selection-based method for predicting isoform functions, Bioinformatics,2023, 39(9),btad530

3. Chao Deng, Hong-Dong Li*, Li-Shen Zhang, Yi-Wei Liu, Yaohang Li, Jianxin Wang*, Identifyingnew cancer genes based on the integration of annotated gene sets via hypergraph neural networks, ISMB, 2024

4. Chao Zhang#, Zhi-Wei Duan#, Yun-Pei Xu, Jin Liu, Hong-Dong Li*, FEED: a feature selection method based on gene expression decomposition for single-cell clustering, Briefings in Bioinformatics, 2023, 24(6):bbad389

5. Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang*,CellBRF: a feature selection method for single-cell clustering using cell balance and random forest,Bioinformatics 39 (ISMB issue), i368-i376

6. Hong-Dong Li*, Chao Deng, Xiao-Qi Zhang, Cui-Xiang Lin, A Gene Set-Integrated Approach for Predicting Disease-Associated Genes，IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023, 3440-3450

7. Jiashu Liu, Cui-Xiang Lin, Xiaoqi Zhang, Zongxuan Li,Wenkui Huang, Jin Liu, Y Guan, Hong-Dong Li*, Computational approaches for detecting disease-associated alternative splicing events, Brief Bioinform, 2023, 24(3), doi: 10.1093/bib/bbad106.

8. Hong-Dong Li*, Cui-Xiang Lin, Jiantao Zheng, GTFtools: a software package for analyzing various features of gene models, Bioinformatics, 2022, 38(20)4806-4808

9. Cui-Xiang Lin, Hong-Dong Li, Chao Deng, Weisheng Liu, Shannon Erhardt, Fang-Xiang Wu,Xing-Ming Zhao, Yuanfang Guan, Jianxin Wang*, An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer’s disease, Briefings in Bioinformatics, 2022, 23(1),bbab522.

10. Zhenpeng Wu# , Jiantao Zheng#, Jiashu Liu, Cuixiang Lin, Hong-Dong Li*, DeepRetention: A Deep Learning Approach for Intron Retention Detection, Big Data Mining and Analytics, 2022,DOI: 10.26599/BDMA.2022.9020023.

11. Cui-Xiang Lin, Hong-Dong Li, Chao Deng, Yuanfang Guan, Jianxin Wang*, TissueNexus: A Database of Human Tissue Functional Gene Networks Built with A Large Compendium of Curated RNA-seq Data, Nucleic Acids Research, 2022, 50(D1):D710-D718.

12. Cui-Xiang Lin#, Hong-Dong Li#, Chao Deng, Shannon Erhardt, Jun Wang, Xiaoqing Peng*,Jianxin Wang*, AlzCode: a Platform for Multiview Analysis of Genes Related to Alzheimer’sDisease, Bioinformatics, 2022, 38(7): 2030-2032

13. Yingyi Liu#, Hong-Dong Li#, Yunpei Xu, Yiwei Liu, Xiaoqing Peng, Jianxin Wang*, IsoCell:An Approach to Enhance Single Cell Clustering by Integrating Isoform-level Expression through Orthogonal Projection, IEEE/ACM Transactions on Computational Biology and Bioinformatics,2022, doi:10.1109/TCBB.2022.3147193.

14. Hong-Dong Li#, Cory C. Funk#, Karen McFarland, Eric B. Dammer, Mariet Allen, Minerva M.Carrasquillo, Yona Levties, Paramita Chakrabarty, Jeremy D. Burgess, Xue Wang, Dennis Dickson,Nicholas T. Seyfried, Duc M. Duong, James J. Lah, Steven G. Younkin, Allan I. Levey, Gilbert S.Omenn, Nilüfer Ertekin-Taner, Todd E. Golde, Nathan D. Price*, Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer’s disease. Alzheimer’s Dement, 2021, 17:984-1004 (IF=21.56).

15. Zhao-Yu Fang, Cui-Xiang Lin, Yun-Pei Xu, Hong-Dong Li*, Qing-Song Xu*, REBET: a method to determine the number of cell clusters based on batch effect removal, Briefings in Bioinformatics,2021,22(6): bbab204

16. Jiantao Zheng#, Cuixiang Lin#, Zhenpeng Wu, Hong-Dong Li*, A comparison of computational approaches for intron retention detection, Big Data Mining and Analytics, 2021: 15-31.

17. Hong-Dong Li, Changhuo Yang, Zhimin Zhang, Mengyun Yang, Fang-Xiang Wu, Gilbert S Omenn,Jianxin Wang*, IsoResolve: Predicting Splice Isoform Functions by Integrating Gene and Isoform-level Features with Domain Adaptation. Bioinformatics, 2021,37(4):522-530

18. Hong-Dong Li, Cory C. Funk, Nathan D. Price*, iREAD: a tool for intron retention detection from RNA-seq data. BMC Genomics, 2020, 14, 128.

19. Yunpei Xu, Hong-Dong Li (co-first), Yi Pan, Feng Luo, Jianxin Wang*, A gene rank based approach for single cell similarity assessment and clustering. IEEE/ACM T Comput Biol, 2019, doi:10.1109/TCBB.2019.2931582

20. Hong-Dong Li*, Qing-Song Xu, Yi-Zeng Liang, libPLS: an integrated library for partial least squares regression and discriminant analysis. Chemom. Intell. Lab. Syst, 2018, 176, 34-43 (Citation: 120).

21. Mariet Allen, Xue Wang, Jeremy D Burgess, ..., Hong-Dong Li, ..., Julia R. Crook, Yan W. Asmann,Nilufer Ertekin-Taner*, Conserved brain myelination networks are altered in Alzheimer’s and other neurodegenerative diseases. Alzheimer’s Dement, 2018, 14(3), 352-366.

22. Rebecca Sims, Sven J van der Lee, ... , Hong-Dong Li,... , Sudha Seshadri, Julie Williams, andGerard D. Schellenberg, Rare coding variants in PLCG2, ABI3 and TREM2 implicate microglial-mediated innate immunity in Alzheimer’s disease, Nat Genet. 2017, 49(9), 1373-1384 (Citation:225).

23. Hong-Dong Li, Gilbert S. Omenn, Yuanfang Guan. A proteogenomic approach to understand splice isoform functions through structure and expression-based computational approaches, Briefings inBioinformatics, 2016, 17, 1024-1031.

24. Hong-Dong Li, Rajasree Menon, Brandon Govindarajoo, Bharat Panwar, Yang Zhang, Gilbert S.Omenn, and Yuanfang Guan. Functional Networks of Highest-Connected Splice Isoforms: From the Chromosome 17 Human Proteome Project. J Proteome Res, 2015, 14, 3484-3491 (Selected into the 入选该期刊最近10年(2010–2020)发表的最具影响力的60篇文章特刊 to celebrate the 10^th Anniversary of the Human Proteome Project and near the 20th Anniversary of HUPO, available at:https://pubs.acs.org/page/jprobs/vi/humanproteome).

25. Hong-Dong Li, Gilbert S. Omenn, and Yuanfang Guan. Misomine: A Genome-Scale High-Resolution Data Portal of Expression, Function and Networks at the Splice Isoform Level in the Mouse. Database,2015, 2015, bav045.

26. Hong-Dong Li, Rajasree Menon, Gilbert S. Omenn, Yuanfang Guan, The Emerging Era of Genomic Data Integration for Analyzing Splice Isoform Functions, Trends Genet, 2014, 30, 340-347, 下载次数最多文章 (11/2/2014)(IF: 10.6; citation: 58)

27. Hong-Dong Li, Rajasree Menon, Gilbert S. Omenn, Yuanfang Guan. Revisiting the Identification of Canonical Splice Isoforms through Integration of Functional Genomics and Proteomics Evidence,Proteomics, 2014, 14, 2709-2718 (The 13th World Congress of the Human Proteome Organization Young Investigator Award, Spain, 2014).

28. Ridvan Eksi, Hong-Dong Li (co-first author), Rajasree Menon, Yuchen Wen, Gilbert S. Omenn,Yuanfang Guan. Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq data. PLoS Computational Biology, 2013, 9(11), e1003314 (citation: 43).