2024:

Zhang P, Zhang B, Ji YY, Jiao J, Zhang Z, Tian CF. Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome. mLife. 2024 Jun 28;3(2):277-290. doi: 10.1002/mlf2.12132.

Yang X, Wuchty S, Liang Z, Ji L, Wang B, Zhu J, Zhang Z, Dong Y. Multi-modal features-based human-herpesvirus protein-protein interaction prediction by using LightGBM.Brief Bioinform. 2024, 25(2):bbae005. doi: 10.1093/bib/bbae005.

Zhao M, Lei C, Zhou K, Huang Y, Fu C, Yang S, and Zhang Z. (2024) POOE: predicting oomycete effectors based on a pre-trained large protein language model. mSystems. 9(1):e0100423. doi: 10.1128/msystems.01004-23.

Lei C, Zhou K, Zheng J, Zhao M, Huang Y, He H, Yang S, and Zhang Z. (2024) AraPathogen2.0: An Improved Prediction of Plant-Pathogen Protein-Protein Interactions Empowered by the Natural Language Processing Technique. J Proteome Res. 23(1), 494-499. doi: 10.1021/acs.jproteome.3c00364.

2023:

Zhou, K., Lei, C., Zheng, J., Huang, Y., and Zhang, Z. (2023) Pre-trained protein language model sheds new light on the prediction of Arabidopsis protein-protein interactions. Plant Methods. 19(1), 141. doi: 10.1186/s13007-023-01119-6.

Guo, X., Wang, T., Jiang, L., Qi, H., and Zhang, Z. (2023). PlaASDB: a comprehensive database of plant alternative splicing events in response to stress. BMC Plant Biol. 23, 225. 10.1186/s12870-023-04234-7.

Zheng, J., Yang, X., Huang, Y., Yang, S., Wuchty, S., and Zhang, Z. (2023). Deep learning‐assisted prediction of protein–protein interactions in Arabidopsis thaliana. The Plant Journal 114, 984–994. 10.1111/tpj.16188

Huang, Y., Wuchty, S., Zhou, Y., and Zhang, Z. (2023). SGPPI: structure-aware prediction of protein–protein interactions in rigorous conditions with graph convolutional network. Briefings in Bioinformatics 24, bbad020. 10.1093/bib/bbad020.

2022:

Huang, Y., Zhang, Z., and Zhou, Y. (2022). AbAgIntPre: A deep learning method for predicting antibody-antigen interactions based on sequence information. Front. Immunol. 13, 1053617. 10.3389/fimmu.2022.1053617.

Wang, T., Guo, Y., Roellig, D.M., Li, N., Santín, M., Lombard, J., Kváč, M., Naguib, D., Zhang, Z., Feng, Y., et al. Preference. Mol. Biol. Evol. 39, msac150. 10.1093/molbev/msac150.

Yang, X., Yang, S., Ren, P., Wuchty, S., and Zhang, Z. (2022). Deep Learning-Powered Prediction of Human-Virus Protein-Protein Interactions. Front. Microbiol. 13, 842976. 10.3389/fmicb.2022.842976.

Qi, H., Guo, X., Wang, T., and Zhang, Z. (2022). ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data. International Journal of Molecular Sciences 23, 4079. 10.3390/ijms23084079.

Li, Y., Han, L., and Zhang, Z. (2022). Understanding the influence of AMG 510 on the structure of KRASG12C empowered by molecular dynamics simulation. Comput. Struct. Biotechnol. J. 20, 1056–1067. 10.1016/j.csbj.2022.02.018.

2021:

Yang, X., Yang, S., Lian, X., Wuchty, S., and Zhang, Z. (2021). Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction. Bioinformatics 37, 4771–4778. 10.1093/bioinformatics/btab533.

Lian, X., Yang, X., Yang, S., & Zhang, Z. (2021). Current status and future perspectives of computational studies on human–virus protein–protein interactions. Briefings in Bioinformatics, 22(5), 1-16.

Yang, X., Lian, X., Fu, C., Wuchty, S., Yang, S., and Zhang, Z. (2021). HVIDB: a comprehensive database for human–virus protein–protein interactions. Briefings in Bioinformatics 22, 832–844. 10.1093/bib/bbaa

2020 and before:

Lian, X., Yang, X., Shao, J., Hou, F., Yang, S., Pan, D., and Zhang, Z. (2020). Prediction and analysis of human-herpes simplex virus type 1 protein-protein interactions by integrating multiple methods. Quant Biol 8, 312–324. 10.1007/s40484-020-0222-5.

Fu, C., Yang, S., Yang, X., Lian, X., Huang, Y., Dong, X., & Zhang, Z. (2020). Human Gene Functional Network-Informed Prediction of HIV-1 Host Dependency Factors. mSystems, 5: e00960-20.

Li, Y., Zhang, Z., Yang, L., Lian, X., Xie, Y., Li, S., Xin, S., Cao, P., and Lu, J. (2020). The MERS-CoV Receptor DPP4 as a Candidate Binding Target of the SARS-CoV-2 Spike. iScience 23: 101160.

Li, H., Jiang, S., Li, C., Liu, L., Lin, Z., He, H., Deng, X.W., Zhang, Z., and Wang, X. (2020). The hybrid protein interactome contributes to rice heterosis as epistatic effects. Plant J, 102: 116-128.

Yang X, Yang S, Li Q, Wuchty S & Zhang Z (2020) Prediction of human-virus protein-protein interactions through a sequence embedding-based machine learning method. Comput Struct Biotechnol J. 18:153-161.

Yang X, Yang S, Qi H, Wang T, Li H & Zhang Z (2020) PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. BMC Plant Biol. 20(1):61.

Li, Q., Yan, Y., Liu, X., Zhang, Z., Tian, J., and Wu, N. (2020). Enhancing thermostability of a psychrophilic alpha-amylase by the structural energy optimization in the trajectories of molecular dynamics simulations. Int J Biol Macromol 142, 624-633.

Lian X, Yang S, Li H, Fu C & Zhang Z (2019) Machine-Learning-Based Predictor of Human-Bacteria Protein-Protein Interactions by Incorporating Comprehensive Host-Network Properties. J. Proteome Res., 18: 2195-2205

Yang S, Fu C, Lian X, Dong X, Zhang Z. (2019). Understanding human-virus protein-protein interactions using a human protein complex-based analysis framework. mSystems 4: e00303-18.

Qi H, Jiang Z, Zhang K, Yang S, Zhang Z (2018) PlaD: a transcriptomics database for plant defense responses to pathogens, providing new insights into plant immune system. Genomics Proteomics Bioinformatics, 16: 283-293.

Lyu Z, Li Z-G, He F & Zhang Z (2017) An important role for purifying selection in archaeal genome evolution. mSystems, 2: e00112-17.

Li H, Zhou Y & Zhang Z (2017) Network analysis reveals a common host-pathogen interaction pattern in arabidopsis immune responses. Front. Plant Sci. 8:893.

Jiang Z, He F & Zhang Z (2017) Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens.Plant Mol. Biol., 94:453-467.

Yang S, Li H, He H, Zhou Y & Zhang Z. (2017) Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methods. Brief Bioinform, doi:10.1093/bib/bbx123.

Jiang Z, Dong X, Li ZG, He F & Zhang Z (2016) Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection. Sci Rep, 6: 35064.

Li H, Yang S, Wang C, Zhou Y & Zhang Z (2016) AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana. Plant Mol Biol, 92: 105-116.

Li H & Zhang Z (2016) Systems understanding of plant-pathogen interactions through genome-wide protein-protein interaction networks. Front Agr Sci Eng, 3: 102-112.

Liu X, Yang S, Li C, Zhang Z & Song J (2016) SPAR: a random forest-based predictor for self-interacting proteins with fine-grained domain information. Amino Acids, 48: 1655-1665.

Wang C, Dong X, Han L, Su XD, Zhang Z, Li J & Song J (2016) Identification of WD40 repeats by secondary structure-aided profile-profile alignment. J Theor Biol, 398: 122-129.

Jiang Z, Dong X & Zhang Z (2016) Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections. Sci. Rep, 6: 19149.

Zhou Y, Yang S, Mao T & Zhang Z (2015) MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins. Database, doi:10.1093/database/ bav108.

Chen Z, Zhou Y, Zhang Z & Song J (2015) Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features. Brief Bioinform, 16: 640-657.

Dong X, Lu X & Zhang Z (2015) BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors. Database, doi:10.1093/database/bav064.

Li H, Zhou Y & Zhang Z (2015) Competition-cooperation relationship networks characterize the competition and cooperation between proteins. Sci. Rep, 5: 11619.

Hasan MM, Zhou Y, Lu X, Li J, Song J & Zhang Z (2015) Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs. PLoS ONE, 6: e0129635.

Dong X, Jiang Z, Peng Y-L & Zhang Z (2015) Revealing Shared and Distinct Gene Network Organization in Arabidopsis Immune Responses by Integrative Analysis. Plant Physiology, 167: 1186-1203.

Li C, Wang X-F, Chen Z, Zhang Z & Song J (2015) Computational characterization of parallel dimeric and trimeric coiled-coils using effective amino acid indices. Mol Biosyst, 11: 354-360.

Han L, Zhang YJ, Zhang L, Cui X, Yu J, Zhang Z & Liu MS (2014) Operating Mechanism and Molecular Dynamics of Pheromone-Binding Protein ASP1 as Influenced by pH. PLoS One, 9: e110565.

Li Y, Wang M-J, Wang H-L, Tan H, Zhang Z, Webb G & Song J (2014) Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features. Sci. Rep, 4: 5765.

Yan R, Wang X, Huang L, Lin J, Cai W & Zhang Z (2014) GPCRserver: an accurate and novel G protein-coupled receptor predictor. Mol Biosyst, 10: 2495-2504.

Yan R, Lin J, Chen Z, Wang X, Huang L, Cai W & Zhang Z (2014) Prediction of outer membrane proteins by combining the position- and composition-based features of sequence profiles. Mol Biosyst, 10: 1004-1013.

Zhou Y, Liu S, Song J & Zhang Z (2013) Structural propensities of human ubiquitination sites: accessibility, centrality and local conformation. PLoS ONE, 8: e83167.

Chen Z, Wang Y, Zhai Y F, Song J & Zhang Z (2013) ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences. Mol BioSyst, 9 : 2213-2222.

Chen Z, Zhou Y, Song J & Zhang Z (2013) hCKSAAP_UbSite: Improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties. BBA - Proteins and Proteomics, 1834: 1461-1467.

Dong X, Zhang Y-J & Zhang Z, (2013) Using Weakly Conserved Motifs Hidden in Secretion Signals to Identify Type-III Effectors from Bacterial Pathogen Genomes. PLoS ONE, 8(2): e56632.

Zhou Y, Zhou Y-S, He F, Song J & Zhang Z (2012) Can simple codon pair usage predict protein-protein interaction? Mol BioSyst, 8 : 1396-1404.

Han L, Zhang Y-J, Song J, Liu MS & Zhang Z (2012) Identification of catalytic residues using a novel feature that Integrates the microenvironment and geometrical location properties of residues. PLoS ONE, 7: e41370.

Wang X-F, Chen Z, Wang C, Yan R-X, Zhang Z & Song J. (2011) Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach. PLoS ONE, 6: e26767.

Li Z-G, He F, Zhang Z & Peng Y-L (2012) Prediction of protein-protein interactions between Ralstonia solanacearum and Arabidopsis thaliana. Amino Acids, 42: 2363-2371.

Wang C, Yan R-X, Wang X-F, Si J-N & Zhang Z. (2011) Comparison of linear gap penalties and profile-based variable gap penalties in profile-profile alignments. Comput Biol Chem, 35 : 308-318.

Chen Z, Chen Y-Z, Wang X-F, Wang C, Yan R-X & Zhang Z (2011) Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs. PLoS ONE, 6 : e22930.

Wang T-Y, He F,Hu Q-W & Zhang Z(2011) A predicted protein-protein interaction network of the filamentous fungus Neurospora crassa. Molecular BioSystems,7 (7), 2278 - 2285.

Yan R-X, Chen Z & Zhang Z (2011) Outer membrane proteins can be simply identified using secondary structure element alignment. BMC Bioinformatics 12: 76.

Zhou Y, Liu J, Han L, Li Z-G & Zhang Z. (2011) Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes. BMC Genomics, 12: 632.

He F, Zhou Y & Zhang Z (2010) Deciphering the Arabidopsis floral transition process by integrating a protein-protein interaction network and gene expression data. Plant Physiology, 153:1492-1505.

Yan R-X , Si J-N , Wang C & Zhang Z . (2009) DescFold: A web server for protein fold recognition. BMC Bioinformatics, 10:416.

Si J-N , Yan R-Y , Wang C , Zhang Z & Xiao-Dong Su (2009) TIM-Finder: A novel method to recognize TIM-barrel proteins. BMC Structural Biology, 9:73.

Zhang Z, Tang Y-R, Sheng Z-Y, Zhao D. (2009) An Overview of the De Novo Prediction of Enzyme Catalytic Residues. Current Bioinformatics, 4(3): 197-206.

He F, Zhang Y, Chen H, Zhang Z & Peng Y-L (2008) The prediction of protein-protein interaction networks in rice blast fungus. BMC Genomics, 9: 519.

Chen Y-Z, Tang Y-R, Sheng Z-Y & Zhang Z (2008) Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs. BMC Bioinformatics, 9: 101.

Tang Y-R, Sheng Z-Y, Chen Y-Z & Zhang Z (2008) An improved prediction of catalytic residues in enzyme structures. Protein Engineering Design & Selection (PEDS), 21: 295-302.

Tang Y-R, Chen Y-Z, Canchaya CA & Zhang Z (2007) GANNPhos: a new phosphorylation site predictor based on a genetic algorithm integrated neural network. Protein Engineering Design & Selection (PEDS), 20: 405-412.

Zhang Z & Tang Y-R (2007) Genome-wide analysis of enzyme structure-function combination across three domains of life. Protein Pept Lett, 14: 291-297.

Zhang Z & Grigorov M (2006) Similarity networks of protein binding sites. Proteins, 62: 470-478.