- 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..
- 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..
- 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..
- 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..
- 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..
- 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..
- 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..
- 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..
- 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..
- Yan Xu*, Kuo-Chen Chou. Recent progress in predicting posttranslational modification sites in proteins. Current Topics in Medicinal Chemistry. 2016.16(6), 591-603..