Publication List

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. [pdf]

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. [pdf]

Jiao, J., Ni, M., Zhang, B., Zhang, Z., Young, J. P. W., Chan, T. F., ... & Tian, C. F. (2018). Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii. PLoS genetics, 14(5), e1007428. [pdf]

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

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.  [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

Jiao J, Wu L, Zhang B, Hu Y, Li Y, Zhang X, Guo H, Liu L, Chen W, Zhang Z & Tian C (2016) MucR is required for transcriptional activation of conserved ion transporters to support nitrogen fixation of Sinorhizobium fredii in soybean nodules. Molecular Plant-Microbe Interactions, 29(5), 352-361. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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

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. [pdf]

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. [pdf]

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. [pdf]

Han LZhang 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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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

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, : 2213-2222. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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

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. [pdf]

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. [pdf]

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

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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. [pdf]

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