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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.
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. Plant J.
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.
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, 7919.
Wang, T., Guo, Y., Roellig, D.M., Li, N., Santin, M., Lombard, J., Kvac, M., Naguib, D., Zhang, Z., Feng, Y., et al. (2022). Sympatric Recombination in Zoonotic Cryptosporidium Leads to Emergence of Populations with Modified Host Preference. Mol Biol Evol 39.
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.
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.
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.
Yang, X., Yang, S., Lian, X., Wuchty, S., & Zhang, Z. (2021). Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction. Bioinformatics, 37(24), 4771-4778.
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., & Zhang, Z. (2021). HVIDB: a comprehensive database for human–virus protein–protein interactions. Briefings in Bioinformatics, 22(2), 832-844.
Lian, X., Yang, X., Shao, J., Hou, F., Yang, S., Pan, D., & 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.
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.
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