Academic Research
First Author(#),Corresponding Author(*),Joint First Authors/Equal contributions(†)
2025
(1) Jian Zhang#*, Jingjing Qian, Pei Wang, Xuan Liu, Fuhao Zhang, Haiting Chai, Quan Zou*. Explainable Deep Multilevel Attention Learning for Predicting Protein Carbonylation Sites, Advanced Science, 2025, 2500581. link
(2) Yubo Wang, Haoran Zhu, Yansong Wang, Yuning Yang, Yujian Huang*, Jian Zhang*, Ka-chun Wong, Xiangtao Li*. EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events, Bioinformatics, 2025, 41(1):btaf018. link
2024
(1) Jian Zhang#*, Sushmita Basu, Fuhao Zhang, Lukasz Kurgan*. MERIT: Accurate prediction of multi ligand-binding residues with hybrid deep transformer network, evolutionary couplings and transfer learning, Journal of Molecular Biology, 2024, 168872. link
(2) Jian Zhang#*, Feng Zhou, Xingchen Liang, Lukasz Kurgan*. Accurate Prediction of Protein-Binding Residues in Protein Sequences Using SCRIBER, Prediction of Protein Secondary Structure, 2024, 247-260. link
(3) Jian Zhang#*, Jingjing Qian, Quan Zou, Feng Zhou, Lukasz Kurgan*. Recent Advances in Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences, Protein Supersecondary Structures: Methods and Protocols, 2024, 1-19. link
(4) Jing Li, Shida He, Jian Zhang, Feng Zhang, Quan Zou, Fengming Ni*. T4Seeker: a hybrid model for type IV secretion effectors identification, BMC biology, 2024, 22:259. link
(5) Jian Zhang#*, Jingjing Qian. Advances in Computational Intelligence-Based Methods of Structure and Function Prediction of Proteins, Biomolecules, 2024, 14(9): 1083. link
2023
(1) Fuhao Zhang, Min Li, Jian Zhang, Wenbo Shi, Lukasz Kurgan*. DeepPRObind: Modular deep learner that accurately predicts structure and disorder-annotated protein binding residues, Journal of Molecular Biology, 2023, 167945. link
(2) Fuhao Zhang, Min Li, Jian Zhang, Lukasz Kurgan*. HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins, Nucleic Acids Research, 2023, 51(5):gkac1253. link
(3) Sushmita Basu†, Bi Zhao†, Bálint Biró, Eshel Faraggi, Jörg Gsponer, Gang Hu, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Johannes Söding, Martin Steinegger, Duolin Wang, Kui Wang, Dong Xu, Jian Zhang, Lukasz Kurgan*. DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options, Nucleic Acids Research, 2023, gkad985. link
(4) Jian Zhang#*, Sushmita Basu, Lukasz Kurgan*. HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins, Nucleic Acids Research, 2023, gkad1131. link
2022
(1) Jian Zhang#*, Feng Zhou, Xingchen Liang, Guifu Yang. SCAMPER: accurate type-specific prediction of calcium-binding residues using sequence-derived features, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023, 20(2): 1406-1416. link
(2) Nan Ye, Feng Zhou, Xingchen Liang, Haiting Chai, Jianwei Fan, Jian Zhang. A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level, BioMed Research International, 2022, 8965712: 1-19. link
2021
(1) Jian Zhang#*, Xingchen Liang, Feng Zhou, Bo Li, Yanling Li. TYLER, a fast method that accurately predicts cyclin-dependent proteins by using computation-based motifs and sequence-derived features, Mathematical Biosciences and Engineering, 2021, 18(5): 6410–6429. link
(2) Jian Zhang#*, Sina Ghadermarzi, Akila Katuwawala, Lukasz Kurgan*. DNAgenie: accurate prediction of DNA type specific binding residues in protein sequences, Briefings in Bioinformatics, 2021, 22(6), bbab336. link
2020
(1) Jian Zhang#, Lukasz Kurgan*. Prediction of protein-binding residues: dichoto-my of sequence-based methods developed using structured complexes vs. disordered proteins, Bioinformatics, 2020, 36(18), 4729-4738. link
(2) Fuhao Zhang#, Wenbo Shi, Jian Zhang, Min Zeng, Min Li, Lukasz Kurgan*. PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection, Bioinformatics, 2020, 36(2), i735-i744. link
(3) Jian Zhang#*, Yu Zhang, Yanlin Li, Song Guo, Guifu Yang. Identification of Cancer Biomarkers in Human Body Fluids by Using Enhanced Physicochemical-incorporated Evolutionary Conservation Scheme, Current Topics in Medicinal Chemistry, 2020, 20(21), 1888-1897. link
(4) Jian Zhang#*, Haiting Chai. Recent Advances in Drug Discovery and Cancer Diagnoses, Current Topics in Medicinal Chemistry, 2020, 20(21), 1855-1857. link
2019
(1) Jian Zhang#, Lukasz Kurgan*. SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences, Bioinformatics, 2019, 35(14): i343-i353. link
(2) Jian Zhang#*, Haiting Chai. Recent In Silico Research in High-Throughput Drug Discovery and Molecular Biochemistry, Current Topics in Medicinal Chemistry, 2019, 19(2), 103-104. link
(3) Jian Zhang#†*, Yu Zhang†, Zhiqiang Ma. In silico Prediction of Human Secretory Proteins in Plasma Based on Discrete Firefly Optimization and Application to Cancer Biomarkers Identification, Frontiers in Genetics, 2019, 10, 542. link
2018
(1) Haiting Chai, Jian Zhang*. Identification of Mammalian Enzymatic Proteins Based on Sequence-derived Features and Species-specific Scheme, IEEE Access, 2018, 6, 8452-8458. link
(2) Jian Zhang#, Zhiqiang Ma, Lukasz Kurgan. Comprehensive Review and Empirical Analysis of Hallmarks of DNA, RNA, and Protein Binding Residues in Protein Chains, Briefings in Bioinformatics, 2019, 20(4), 1250-1268. link
(3) Shomeek Chowdhury#†, Jian Zhang#†, Lukasz Kurgan. In-silico Prediction and Validation of Novel RNA Binding Proteins and Residues in the Human Proteome, Protemics, 2018, 18, 1800064. link
(4) Jian Zhang#†*, Haiting Chai#†, Song Guo, Huaping Guo, Yanling Li. High-Throughput Identification of Mammalian Secreted Proteins Using Species-Specific Scheme and Application to Human Proteome, Molecules, 2018, 23(6), 1448. link
2017
(1) Jian Zhang#, Lukasz Kurgan. Review and Comparative Assessment of Sequence-based Predictors of Protein-binding Residues, Briefings in Bioinformatics, 2018, 19(5), 821-837. link
(2) Jian Zhang#, Haiting Chai, Guifu Yang, Zhiqiang Ma, Prediction of bioluminescent proteins by using sequence-derived features and lineage-specific scheme, BMC bioinformatics, 2016, 18(1), 294. link
2016
(1) Jian Zhang#, Haiting Chai, Bo Gao, Guifu Yang, Zhiqiang Ma. HEMEsPred: Structure-based Ligand-specific Heme Binding Residues Prediction by Using Fast-adaptive Ensemble Learning Scheme, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 2018, 15(1), 147-156. link
(2) Jian Zhang#, Bo Gao, Haiting Chai, Zhiqiang Ma, Guifu Yang. Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm, BMC bioinformatics, 2016, 17(1), 323. link
(3) Haiting Chai, Jian Zhang, Guifu Yang, Zhiqiang Ma. An evolution-based DNA- binding residues predictor by using dynamic query-driven learning scheme, Molecular BioSystems, 2016, 12(12), 3643-3650. link
2015
(1) Jian Zhang#, Wenhan Chen, Pingping Sun, Zhiqiang Ma. Prediction of protein solvent accessibility using PSO-SVR with multiple sequence-derived features and weighted sliding window scheme, BioData mining, 2015, 8(1), 3. link
2014
(1) Jian Zhang#, Xiaowei Zhao, Pingping Sun, Zhiqiang Ma. PSNO: Predicting Cysteine S-Nitrosylation Sites by Incorporating Various Sequence-Derived Features into the General Form of Chou's PseAAC, International Journal of Molecular Sciences, 2014, 15(7), 11204-11219. link
(2) Jian Zhang#, Pingping Sun, Xiaowei Zhao, Zhiqiang Ma. PECM: Prediction of extracellular matrix proteins using the concept of Chou's pseudo amino acid composition, Journal of Theoretical Biology, 2014, 363, 412-418. link
(3) Jian Zhang#, Xiaowei Zhao, Pingping Sun, Bo Gao, Zhiqiang Ma. Conformational B-Cell Epitopes Prediction from Sequences Using Cost-Sensitive Ensemble Classifiers and Spatial Clustering, BioMed Research International, 2014, 689219: 1-13. link
2013
(1) Pingping Sun, Haixu Ju, Zhenbang Liu, Qiao Ning, Jian Zhang, Xiaowei Zhao, Yanxin Huang, Zhiqiang Ma, Yuxin Li. Bioinformatics resources and tools for conformational B-cell epitope prediction, Computational and mathematical methods in medicine, 2013, 943636: 1-12. link
(2) Xiaowei Zhao, Jian Zhang, Qiao Ning, Pingping Sun, Zhiqiang Ma, Minghao Yin. Identification of Protein Pupylation Sites Using Bi-Profile Bayes Feature Extraction and Ensemble Learning, Mathematical Problems in Engineering, 2013, 283129: 1-8. link