Publication List

• Yu-Xiang Huang, Rong Liu*. Improved prediction of post-translational modification crosstalk within proteins using DeepPCT. Bioinformatics. 2024, doi: 10.1093/bioinformatics/btae675

 

• Si-Rui Xiao, Yao-Kun Zhang, Kai-Yu Liu, Yu-Xiang Huang, Rong Liu*. PNBACE: an ensemble algorithm to predict the effects of mutations on protein-nucleic acid binding affinity. BMC Biology. 2024, 11;22(1):203.

 

• Zheng Jiang, Yue-Yue Shen, Rong Liu*. Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches. PLoS Computational Biology. 2023, 6;19(9):e1011428

 

• Yao Jiang, Jia-Xuan Zhang, Rong Liu*. Systematic comparison of differential expression networks in MTB mono-, HIV mono- and MTB/HIV co-infections for drug repurposing. PLoS Computational Biology. 2022, 18(12):e1010744

 

• Zheng Jiang, Si-Rui Xiao, Rong Liu*. Dissecting and predicting different types of binding sites in nucleic acids based on structural information. Briefings in Bioinformatics. 2021, doi：10.1093/bib/bbab411

 

• Yao Jiang, Hui-Fang Liu, Rong Liu*. Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions. PLoS Computational Biology. 2021, doi：10.1371/journal.pcbi.1008951

 

• Bingliang Fan, Zheng Jiang, Jun Sun, Rong Liu*. Systematic characterization and prediction of coenzyme A-associated proteins using sequence and network information. Briefings in Bioinformatics. 2020, doi：10.1093/bib/bbaa308

 

• Jun Sun, Qianqian Shi, Xi Chen, Rong Liu*. Decoding the similarities and specific differences between latent and active tuberculosis infections based on consistently differential expression networks. Briefings in Bioinformatics. 2019, doi: 10.1093/bib/bbz127

 

• Hui-Fang Liu and Rong Liu*. Structure-based prediction of post-translational modification cross-talk within proteins using complementary residue- and residue pair-based features. Briefings in Bioinformatics. 2019, doi: 10.1093/bib/bby123

 

• Jun Sun, Lingli Yang, Xi Chen, Dexing Kong, Rong Liu*. Integrating multifaceted information to predict Mycobacterium tuberculosis-human protein-protein interactions. Journal of Proteome Research. 2018, 17(11):3810-3823

• Jian Hu, Huifang Liu, Jun Sun, Jia Wang, Rong Liu*. Integrating co-evolutionary signals and other properties of residue pairs to distinguish biological interfaces from crystal contacts. Protein Science. 2018, 27(9):1723-1735

 

• Jing Chen, Jun Sun, Xiangming Liu, Feng Liu, Rong Liu*, Jia Wang*. Structure-based prediction of West Nile virus-human protein-protein interactions. Journal of Biomolecular Structure and Dynamics. 2018, 25:1-24

 

• Jun Sun, Jia Wang, Dan Xiong, Jian Hu, Rong Liu*. CRHunter: integrating multifaceted information to predict catalytic residues in enzymes. Scientific Reports. 2016, 6:34044

 

• Hao Zhang, Jun Sun, Jing Ye, Usama Ashraf, Zheng Chen, Bibo Zhu, Wen He, Qiuping Xu, Yanming Wei, Huanchun Chen, Zhen F. Fu, Rong Liu*, Shengbo Cao*. Quantitative label-free phosphoproteomics reveals differentially regulated protein phosphorylation involved in West Nile virus-induced host inflammatory response. Journal of Proteome Research. 2015, 14(12):5157-5168

 

• Xiaoxia Yang, Jia Wang, Jun Sun, Rong Liu*. SNBRFinder: A sequence-based hybrid algorithm for enhanced prediction of nucleic acid-binding residues. PLoS ONE. 2015, 10(7): e0133260

 

• Xiaoxia Yang, Zhiluo Deng, Rong Liu*. RBRDetector: Improved prediction of binding residues on RNA-binding protein structures using complementary feature- and template-based strategies. Proteins: Structure, Function, and Bioinformatics. 2014, 82(10):2455-71

 

• Rong Liu, Jianjun Hu. DNABind: A hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning and template-based approaches. Proteins: Structure, Function, and Bioinformatics. 2013, 81(11):1885-99

 

• Rong Liu, Jianjun Hu. Computational prediction of heme-binding residues by exploiting residue interaction network. PLoS ONE. 2011, 6(10):e25560

 

• Rong Liu, Jianjun Hu. HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information. BMC Bioinformatics. 2011, 12:207

 

Rong Liu, Jianjun Hu. Prediction of discontinuous B-cell epitopes using logistic regression and structural information. Journal of Proteomics & Bioinformatics. 2011, 4:010-015

 

• Rong Liu, Wenchao Jiang, Yanhong Zhou. Identifying protein-protein interaction sites in transient complexes with temperature factor, sequence profile and accessible surface area. Amino Acids. 2010, 38(1):263-270

 

• Rong Liu, Yanhong Zhou. Using support vector machine combined with post-processing procedure to improve prediction of interface residues in transient complexes. The Protein Journal. 2009, 28(7-8):369-374