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教育經歷

2008.09~2012.07 中國農業大學理學院  博士
2001.09~2003.07 吉林大學數學所        碩士
1997.09~2001.07 吉林大學數學系        本科

工作經歷

2003.07-至今        永利集團3044am官方入口數學系
2016.03-2017.03   美國加州大學洛杉磯分校訪問
2018.07-2019.08   美國蒙特克萊爾州立大學統計系訪問
2019.07-2019.07   英國鄧迪大學數學系訪問

學術兼職：

中國運籌學會第十二屆理事兼副秘書長

中國運籌學會青年工作委員會秘書長
中國運籌學會計算生物學分會理事

科研業績

1. 2024.05-2025.09 新一代重型燃氣輪機高性能低排放燃燒室全尺寸試驗數據數學方法分析（第二階段），中國聯合重型燃氣輪機技術有限公司，負責人

2. 2023.10-2024.07 非公經濟核心企業挖掘主題庫和非公經濟企業信用評價主題庫建設，中國電子科技集團第十五研究所，負責人

3. 2023.03-2023.09 先進重型燃機燃燒室全尺寸試驗數據數學方法分析, 中國聯合重型燃氣輪機技術有限公司，負責人

4. 2021.01-2024.12蛋白質翻譯后修飾的深度特征學習及預測  國家自然科學基金面上項目 負責人  項目編號: 12071024
5. 2020.08-2023.07基于大數據智能的非公經濟群體感知與服務輔助技術研究與應用 科技部重大項目2030計劃“新一代人工智能（2030）” 子課題負責人，項目編號：2020AAA0105100
6. 2019.10-2020.06 基于機器學習的****軟件   負責人
7. 2017.01-2020.12基于多標簽學習的蛋白質翻譯后修飾位點預測  國家自然科學基金面上項目 負責人   項目編號: 11671032
8. 2018.01-2018.12 深度學習前言與應用 引智項目，負責人  項目編號：C2018033
9. 2017.12-2018.11多示例多標簽學習在蛋白質組學中的研究與應用，基礎科研業務費 負責人 項目編號： FRF-TP-17-024A2
10. 2016.01-2016.12整合成多標簽學習問題的蛋白質修飾研究，基礎科研業務費  負責人  項目編號: FRF-BR-15-075A
11. 2014.01-2016.12 基于機器學習的蛋白質翻譯后修飾位點預測的研究 國家自然科學青年基金 負責人  項目編號:11301024
12. 2017.01-2017.12計算生物學的若干問題研究，引智項目，負責人  項目編號：C2017021

出版教材:
2014.05 《大學文科數學》(上、下冊), 主編, 科學出版社

發表論文：

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.