教育经历

2008.09~2012.07 中国农业大学理学院  博士
2001.09~2003.07 吉林大学数学所        硕士
1997.09~2001.07 吉林大学数学系        本科

工作经历

2003.07-至今        北京科技大学数学系
2016.03-2017.03   美国加州大学洛杉矶分校访问
2018.07-2019.08   美国蒙特克莱尔州立大学统计系访问
2019.07-2019.07   英国邓迪大学数学系访问

学术兼职：

中国运筹学会第十二届理事兼副秘书长

中国运筹学会青年工作委员会秘书长
中国运筹学会计算生物学分会理事

科研业绩

1. 2024.05-2025.09 新一代重型燃气轮机高性能低排放燃烧室全尺寸试验数据数学方法分析（第二阶段），中国联合重型燃气轮机技术有限公司，负责人

2. 2023.10-2024.07 非公经济核心企业挖掘主题库和非公经济企业信用评价主题库建设，中国电子科技集团第十五研究所，负责人

3. 2023.03-2023.09 先进重型燃机燃烧室全尺寸试验数据数学方法分析, 中国联合重型燃气轮机技术有限公司，负责人

4. 2021.01-2024.12蛋白质翻译后修饰的深度特征学习及预测  国家自然科学基金面上项目 负责人  项目编号: 12071024
5. 2020.08-2023.07基于大数据智能的非公经济群体感知与服务辅助技术研究与应用 科技部重大项目2030计划“新一代人工智能（2030）” 子课题负责人，项目编号：2020AAA0105100
6. 2019.10-2020.06 基于机器学习的****软件   负责人
7. 2017.01-2020.12基于多标签学习的蛋白质翻译后修饰位点预测  国家自然科学基金面上项目 负责人   项目编号: 11671032
8. 2018.01-2018.12 深度学习前言与应用 引智项目，负责人  项目编号：C2018033
9. 2017.12-2018.11多示例多标签学习在蛋白质组学中的研究与应用，基础科研业务费 负责人 项目编号： FRF-TP-17-024A2
10. 2016.01-2016.12整合成多标签学习问题的蛋白质修饰研究，基础科研业务费  负责人  项目编号: FRF-BR-15-075A
11. 2014.01-2016.12 基于机器学习的蛋白质翻译后修饰位点预测的研究 国家自然科学青年基金 负责人  项目编号:11301024
12. 2017.01-2017.12计算生物学的若干问题研究，引智项目，负责人  项目编号：C2017021

出版教材:
2014.05 《大学文科数学》(上、下册), 主编, 科学出版社

发表论文：

1.Qingchun Liu, Yan Xu*. transCAE: Enhancing cell type annotation in single-cell RNA-seq data with transfer learning and convolutional autoencoder. Journal of Molecular Biology. 2025.February 15. Vol.437(4):168936.  

2.Yang Gui, Chao Li*, Yan Xu*. Spatial domains identification in spatial transcriptomics using modality-aware and subspace-enhanced graph contrastive learning. Computational and Structural Biotechnology. 2024. December. Vol. 23: 3703–3713.

3.Leqi Chen, Liwen Liu, Haiyan Su, Yan Xu*. KbhbXG: A Machine Learning Architecture Based on XGBoost for Prediction of Lysine β-Hydroxybutyrylation (Kbhb) Modification Sites. Methods. 2024.5. vol.227:27-34.

4.Shiqi Fan, Yan Xu*. DeepKPred: Prediction and Functional Analysis of Lysine 2-Hydroxyisobutyrylation Sites Based on Deep Learning. Annals of Data Science. 2024.April. Vol.11:693-707.

5.Jing Cao, Yan Xu*. Predicting Cysteine Reactivity Changes Upon Phosphorylation Using XGBoost. FEBS Open Bio. 2024.14(1).51-62.

6.Yongqi Hu, Chunzhong Li*，Xiaobo Wang, Liwen Liu, Yan Xu*. Modulation Recognition of Optical and Electromagnetic Waves Based on Transfer Learning. Optik-International Journal for Light and Electron Optics. 2023, 291:171359.

7.Liwen Liu, Xiaobo Wang, Yongqi Hu, Chen Wang, Yan Xu*. Multi-label Deep Forest: Towards Automatic Modulation Recognition of Compound Wireless Signals at Low-SNR Environment. Circuits Systems & Signal Processing， 2023 vol42(5):3008-3037.

8.Huanyu Ma, Yan Xu, Yulong Liu*. Prediction of listed company innovation ability based on Attention mechanism. Journal of the Operations Research Society of China. 2023. March.Vol.11(1):177-188.

9.Shizhao Wei, Shungang Wang, Siyi Sun, Yan Xu. Stock Ranking Prediction based on an Adversarial Game Neural Network. IEEE Access. 2022. June. 23.Vol.10:65028-65036.

10.Huanyu Ma, Yan Xu, Yulong Liu*. Prediction of Listed Company Growth in Non-public Economy. Annals of Data Science. 2022 August. Vol. 9(4), 847-861.

11.Wen Li, Xiaobo Wang,Yan Xu*. Recognition of CRISPR Off-Target Cleavage Sites with SeqGAN. Current Bioinformatics. 2022.Jan. Vol17(1), 101-107.

12.Jiansheng Zhang, Hongli Fu, Yan Xu*. Human Age prediction of human based on DNA methylation by blood tissues. Genes. 2021.June 6. Vol.12. 870.

13.Yingxi Yang#, Hui Wang#, Wen Li, Xiaobo Wang, Shizhao Wei, Yulong Liu, Yan Xu*. Prediction and analysis of multiple protein lysine modified sites based on conditional wasserstein generative adversarial networks. BMC Bioinformatics. 2021.April, Vol.22:171.

14. Meiqi Wu, Yingxi Yang, Hui Wang, Jun Ding, Huan Zhu, Yan Xu*. IMPMD: an integrated method for predicting potential associations between miRNAs and diseases. Current Genomics. 2019.December. Vol.20, No.8. 581-591.
15. Yuan-Hai Shao, Chun-Na Li, Ling-Wei Huang, Zhen Wang, Nai-Yang Deng, Yan Xu*. Joint sample and feature selection via sparse primal and dual LSSVM. Knowledge-Based System. 2019. December. Vol:185. 104915.
16. Chun-Na Li，Meng-Qi Shang, Yuan-Hai Shao，Yan Xu*，Li-Ming Liu，Zhen Wang. Sparse L1-norm two dimensional linear discriminant analysis via the generalized elastic net regularization. Neurocomputing. 2019.April.14.Vol.337: 80-96.
17. Yan Xu, Xingyan Li, Yingxi Yang, Chunhui Li*, Xiaojian Shao. Human age prediction based on DNA methylation of non-blood tissues. Computer Methods and Programs in Biomedicine. 2019. April. Vol.171: 11-18.
18. Yan Xu, Yingxi Yang, Zu Wang, Yuanhai Shao*. Prediction of Acetylation and Succinylation in Proteins based on Multi-label Learning RankSVM. Letters in Organic Chemistry. 2019, March. Vol. 16(4): 275-282
19. Hongli Fu, Yingxi Yang, Hui Wang, Yan Xu*. DeepUbi：a deep learning framework for prediction of ubiquitination sites in proteins. BMC Bioinformatics. 2019, Feb.18. Vol.20(1):86.
20. Yan Xu, Yingxi Yang, Hui Wang, Yuanhai Shao*. Lysine Malonylation Identification in E.coli with Multiple Features. Current Proteomics. 2019. Feb.Vol.16(3). 166-174.
21. Meiqi Wu, Yingxi Yang, Hui Wang, Yan Xu*. A deep learning method to more accurately entall known lysine acetylation sites. BMC Bioinformatics. 2019, Jan. 23. Vol.20(1):49.
22. Yan Xu, Yingxi Yang, Zu Wang, Chunhui Li, Yuanhai Shao*. A systematic review on posttranslational modification in proteins: feature construction, algorithm and webserver. Protein and Peptide Letters. 2018, Dec. Vol. 25(9): 807-814.
23. Yan Xu, Yingxi Yang, Jun Ding, Chunhui Li*. iGlu-Lys: A Predictor for Lysine Glutarylation through Amino Acid Pair Order Features. IEEE Transactions on NanoBioscience. 2018, Oct. Vol.17(4):394-401.
24. Xingyan Li，Weidong Li, Yan Xu*. Human Age Prediction Based on DNA Methylation Using a Gradient Boosting Regressor. Genes, 2018, (August. 21) Vol. 9. 424.
25. Yingxi Yang, Hui Wang, Jun Ding, Yan Xu*. iAcet-Sumo: identification of lysine acetylation and sumoylation sites in proteins by multi-class transformation methods. Computers in Biology and Medicine. 2018, Sep.1 Vol.100:144-151.
26. Yan Xu, Zu Wang, Chunhui Li*, Kuo-Chen Chou. iPreny-PseAAC: Identify C-terminal Cysteine Prenylation Sites in Proteins by Incorporating Two Tiers of Sequence Couplings into PseAAC. Medicinal Chemistry. 2017, May.Vol.13(6), 544-551.
27. Li-Ming Liu, Yan Xu*, Kuo-Chen Chou. iPGK-PseAAC: identify lysine phosphoglycerylation sites in proteins by incorporating four different tiers of amino acid pairwise coupling information into the general PseAAC. Medicinal Chemistry. 2017, May.Vol 13(6), 552-559.
28. Yan Xu, Li Li, Jun Ding, Ling-Yun Wu, Guoqin Mai*, Fengfeng Zhou*. Gly-PseAAC: identifying protein lysine glycation through sequences. Gene. 2017 Feb.20.602:1-7.
29. Yan Xu, Ya-Xin Ding, Jun Ding, Ling-Yun Wu, Yu Xue*. Mal-Lys: prediction of lysine malonylation sites in proteins integrated sequence-based features with mRMR feature selection. Scientific Reports. 2016.12.02, Vol6.38318.
30. Yan Xu*, Jun Ding, Ling-Yun Wu. iSulf-Cys: prediction of S-sulfenylation sites in proteins with physicochemical properties of amino acids. PloS One. 2016.11(4): e0154237. 2016. April.
31. Yan Xu*, Kuo-Chen Chou. Recent progress in predicting posttranslational modification sites in proteins. Current Topics in Medicinal Chemistry. 2016.16(6), 591-603.
32. Yan Xu, Ya-Xin Ding, Nai-Yang Deng, Li-Ming Liu*. Prediction of Sumoylation Sites in Proteins Using Linear Discriminant Analysis. Gene. 2016. Jan.15 576:99-104.
33. Yan Xu*, Ya-Xin Ding, Jun Ding, Ling-Yun Wu, Nai-Yang Deng. Phogly-PseAAC: prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity. Journal of Theoretical Biology. 2015.08.21, (379)10-15.
34. Yan Xu*, Ya-Xin Ding, Jun Ding, Ya-Hui Lei, Nai-Yang Deng. iSuc-PseAAC: predicting lysine succinylation in proteins by incorporating peptide position-specific propensity. Scientific Reports. 2015.06.18 .Vol5.10184.
35. Yan Xu*, Xin Wen, Li-Shu Wen, Ling-Yun Wu, Nai-Yang Deng, Kuo-Chen Chou. iNitro-Tyr: Prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition. PLoS ONE 9(8), e105018.
36. Yan Xu*, Xin Wen, Xiao-Jian Shao, Nai-Yang Deng, Kuo-Chen Chou. iHyd-PseAAC: predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propensity into pseudo amino acid composition. International Journal of Molecular Sciences. 2014, May, 5. 15:7594-7610.
37. Yan Xu*, Xiao-Bo Wang, Yong-Cui Wang, Ying-Jie Tian, Xiao-Jian Shao, Ling-Yun Wu, Nai-Yang Deng. Prediction of Posttranslational Modification Sites from Sequences with Kernel Methods. Journal of Theoretical Biology. 2014. March 7. 7:344, 78-87.
38. Yan Xu*, Xiao-Jian Shao, Ling-Yun Wu, Nai-Yang Deng, Kuo-Chen Chou. iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins. PeerJ. 2013 Oct 3. 1:e171.
39. Yan Xu*, Jun Ding, Ling-Yun Wu, Kuo-Chen Chou. iSNO-PseAAC: Predict Cysteine S-nitrosylation Sites in Proteins by Incorporating Position Specific Amino Acid Propensity into Pseudo Amino Acid Composition, PLoS One, 2013.Feb. 8(2), e55844.
40. Yan Xu*, Jun Ding, Qiang Huang, Nai-Yang Deng. Prediction of Protein Methylation Sites using Conditional Random Field. Protein and Peptide Letters, 2013, 20(1), 71-77.