Hongyu Ou

Professor

Selected Publications

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    Liu M#, Liu J#, Liu G, Wang H, Wang X, Deng Z, He Y*, Ou HY* (2022) ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements. Scientific Data, 9:11

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    Zhang Y#, Zhang Y#, Xiong Y, Wang H, Deng Z, Song J*, Ou HY* (2021) T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model. Briefings in Bioinformatics, DOI: 10.1093/bib/bbab420.

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    Xu Y#, Zhang J#, Wang M, Liu M, Liu G, Qu H, Liu J, Deng Z, Sun J*, Ou HY*, Qu J* (2021) Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniaeGenome Medicine, 13(1):119.

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    H. Qian#, H. Yu#, P. Li, E Zhu, Q. Yao, C. Tai, Z. Deng, K. Gerdes, X. He*, J. Gan*, H.Y. Ou* (2019) Toxin-antitoxin operon kacAT of Klebsiella pneumoniae is regulated by conditional cooperativity via a W-shaped KacA-KacT complex. Nucleic Acids Research, 47(14):7690-7702

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    H. Qian#, H. Yu#, P. Li, E Zhu, Q. Yao, C. Tai, Z. Deng, K. Gerdes, X. He*, J. Gan*, H.Y. Ou* (2019) Toxin-antitoxin operon kacAT of Klebsiella pneumoniae is regulated by conditional cooperativity via a W-shaped KacA-KacT complex. Nucleic Acids Research, 47(14):7690-7702

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    M. Liu, X. Li, Y. Xie, D. Bi, J. Sun, J. Li, C. Tai, Z. Deng, H.Y. Ou* (2019) ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Research, 47(D1):D660-D665

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    M. Liu, X. Li, Y. Xie, D. Bi, J. Sun, J. Li, C. Tai, Z. Deng, H.Y. Ou* (2019) ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Research, 47(D1):D660-D665

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    H. Qian, Q. Yao, C. Tai, Z. Deng, J. Gan*, H.Y. Ou*(2018) Identification and characterization of acetyltransferase-type toxin-antitoxin loci in Klebsiella pneumoniaeMolecular Microbiology, 108(4), 336–349. (Cover Story, and Comment in: Molecular Microbiology, 108(4), 331–335)

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    H. Qian, Q. Yao, C. Tai, Z. Deng, J. Gan*, H.Y. Ou*(2018) Identification and characterization of acetyltransferase-type toxin-antitoxin loci in Klebsiella pneumoniaeMolecular Microbiology, 108(4), 336–349. (Cover Story, and Comment in: Molecular Microbiology, 108(4), 331–335)

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    X. Li, Y. Xie, M. Liu, C. Tai, J. Sun, Z. Deng, H.Y. Ou* (2018) oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements. Nucleic Acids Research, 46(W1):W229–W234. 

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    X. Li, Y. Xie, M. Liu, C. Tai, J. Sun, Z. Deng, H.Y. Ou* (2018) oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements. Nucleic Acids Research, 46(W1):W229–W234. 

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     Y. Xie#, L. Tian#, G. Li#, H. Qu, J. Sun, W. Liang, X. Li, X. Wang, Z. Deng, J. Liu*, H.Y. Ou* (2018) Emergence of the third-generation cephalosporin-resistant hypervirulent Klebsiella pneumoniae due to the acquisition of a self-transferable blaDHA-1-carrying plasmid by an ST23 strain. Virulence, 9(1):838-844

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     Y. Xie#, L. Tian#, G. Li#, H. Qu, J. Sun, W. Liang, X. Li, X. Wang, Z. Deng, J. Liu*, H.Y. Ou* (2018) Emergence of the third-generation cephalosporin-resistant hypervirulent Klebsiella pneumoniae due to the acquisition of a self-transferable blaDHA-1-carrying plasmid by an ST23 strain. Virulence, 9(1):838-844

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    Y. Xie#, Y. Wei#, Y. Shen#, X. Li, H. Zhou, C. Tai, Z. Deng, H.Y. Ou* (2018) TADB 2.0: an updated database of bacterial type II toxin-antitoxin loci. Nucleic Acids Research, 46:D749-D753.

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    Y. Xie#, Y. Wei#, Y. Shen#, X. Li, H. Zhou, C. Tai, Z. Deng, H.Y. Ou* (2018) TADB 2.0: an updated database of bacterial type II toxin-antitoxin loci. Nucleic Acids Research, 46:D749-D753.

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    Y. Xie#, Y. Wei#, Y. Shen#, X. Li, H. Zhou, C. Tai, Z. Deng, H.Y. Ou* (2018) TADB 2.0: an updated database of bacterial type II toxin-antitoxin loci. Nucleic Acids Research, 46:D749-D753.

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    J. Li, C. Tai, Z. Deng, W. Zhong, Y. He, H.Y. Ou* (2018) VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria. Briefings in Bioinformatics, 19(4):566-574.

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    J. Li, C. Tai, Z. Deng, W. Zhong, Y. He, H.Y. Ou* (2018) VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria. Briefings in Bioinformatics, 19(4):566-574.