Microbial Bioinformatics Group, SKMML, SJTU 
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 Book chapters:  
(1) H.Y. Ou*, Y. Wei, D. Bi (2013) Book chapter: “Type II Loci: Phylogeny”, Prokaryotic Toxin-Antitoxins, Editor Kenn Gerdes, Springer.  [Link to Springer]
(2) H.Y. Ou* and K. Rajakumar* (2011) Book chapter: “ArrayOme- & tRNAcc-facilitated mobilome discovery: comparative genomics approaches for identifying rich veins of bacterial novel DNA sequences”, Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, Editor F. J. de Bruijn, John Wiley & Sons, Inc. [Link to Wiley]
(3) 欧竑宇 (2012) 章节: “基于比较基因组学的细菌基因组岛识别与功能分析”, 中国微生物基因组研究, 喻子牛等主编, 科学出版社. [简介]
     H.Y. Ou* (2012) Book chapter: “Identification of bacterial genomic islands by comparative genomic analysis, Microbiology genomics in China, Editor Zi-Niu Yu, Science Press (in Chinese).


Papers (2007 - present):
(54) 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. DOI: 10.1093/nar/gkz563. [PubMed]

(53) 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. DOI: 10.1093/nar/gky1123. [Abstract]

(52) J. Liao, R.H. Orsi, L.M. Carroll, J. Kovac, H.Y. Ou, H. Zhang, M. Wiedmann*(2019) Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica. BMC Evolutionary Biology, 19:132.

(51) 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. DOI: 10.1093/nar/gky352. [Abstract]

(50) 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 pneumoniae. Molecular Microbiology, 108(4), 336–349. (Cover Story, and Comment in: Molecular Microbiology, 108(4), 331–335. [Abstract]

(49) 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. [Text]

(48) X. Wang#, Y. Xie#, G. Li, J. Liu, X. Li, L. Tian, J. Sun, H.Y. Ou*, H. Qu* (2018) Whole-Genome-Sequencing characterization of bloodstream infection-causing hypervirulent Klebsiella pneumoniae of capsular serotype K2 and ST374. Virulence, 9:1, 510-521. [Abstract]

(47) 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. [Abstract]

(46) 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. [Abstract]

(45) J. Zhang, X. Li, Z. Deng, H.Y. Ou* (2018) Comparative analysis of CRISPR loci found in Streptomyces genome sequences. Interdisciplinary Sciences: Computational Life Sciences, 10(4), 848-853.

(44) D. Bi, J. Zheng, J.J. Li, Z.K. Sheng, X. Zhu, H.Y. Ou, Q. Li, Q. Wei (2018) In Silico Typing and Comparative Genomic Analysis of IncFIIK Plasmids and Insights into the Evolution of Replicons, Plasmid Backbones, and Resistance Determinant Profiles. Antimicrob Agents Chemother, 24;62(10). pii: e00764-18.

(43) L. Liu, M. Ye, X. Li, J. Li, Z. Deng, Y. Yao, H.Y. Ou* (2017) Identification and characterization of an antibacterial type VI secretion system in the carbapenem-resistant strain Klebsiella pneumoniae HS11286. Frontiers in Cellular and Infection Microbiology, 7:442. doi: 10.3389/fcimb.2017.00442. [Abstract]

(42) Wan B, Zhang Q, Ni J, Li S, Wen D, Li J, Xiao H, He P, Ou HY, Tao J, Teng Q, Lu J, Wu W, Yao YF (2017) Type VI secretion system contributes to Enterohemorrhagic Escherichia coli virulence by secreting catalase against host reactive oxygen species (ROS). PLoS Pathog., 13(3):e1006246.

(41) Gao G, Liu X, Xu M, Wang Y, Zhang F, Xu L, Lv J, Long Q, Kang Q, Ou HY, Wang Y, Rohr J, Deng Z, Jiang M, Lin S Tao M (2017) Formation of an Angular Aromatic Polyketide from a Linear Anthrene Precursor via Oxidative Rearrangement. Cell Chem Biol.,24(7):881-891.e4

(40) Z. Xu, Y. Wang, K.F. Chater, H.Y. Ou, H.H. Xu, Z. Deng, M. Tao* (2017) Large-scale transposition mutagenesis of Streptomyces coelicolor identifies hundreds of genes influencing antibiotic biosynthesis. Appl Environ Microbiol., doi: 10.1128/AEM.02889-16.

(39) Q. Xu, Y. Xiong*, H. Dai, K.M. Kumari, Q. Xu, H.Y. Ou, D.Q. Wei (2017) PDC-SGB: Prediction of effective drug combinations using a stochastic gradient boosting algorithm. J Theor Biol., 417:1-7.

(38) P. Li, C. Tai, Z. Deng, J. Gan, M.R. Oggioni, H.Y. Ou* (2016) Identification and characterization of chromosomal relBE toxin-antitoxin locus in Streptomyces cattleya DSM46488. Scientific Reports, 6:32047.

(37) D. Bi#, Y. Xie#, C. Tai, X. Jiang, J. Zhang, E.M. Harrison, S. Jia, Z. Deng, K. Rajakumar, H.Y. Ou* (2016) A site-specific integrative plasmid found in Pseudomonas aeruginosa clinical isolate HS87 along with a plasmid carrying an aminoglycoside-resistant gene. PLoS ONE, 11:e0148367. (# These authors contributed equally to this work.)

(36) Y.Q. Wei, D.X. Bi, D.Q. Wei*, H.Y. Ou*. (2016) Prediction of Type II Toxin-Antitoxin Loci in Klebsiella pneumoniae Genome Sequences. Interdisciplinary Sciences: Computational Life Sciences, 8(2):143-9.

(35) L. Furi, R.H. Zaaima, J.H. Morrissey, H.Y. Ou, R. León-Sampedro, J.L. Martinez, T.M. Coque and M.R. Oggioni* (2016) Dissemination of novel antimicrobial resistance mechanisms through the insertion sequence mediated spread of metabolic genes. Front. Microbiol., 7:1008. doi: 10.3389/fmicb.2016.01008.

(34) M.J. Xu, J.H. Wang, X.L. Bu, H.L. Yu., P. Li, H.Y. Ou, Y. He, F.D. Xu, X.Y. Hu, X.M. Zhu, P. Ao, J. Xu * (2016) Deciphering the streamlined genome of Streptomyces xiamenensis 318 as the producer of the anti-fibrotic drug candidate xiamenmycin. Scientific Reports, 6:18977.

(33) D. Bi, X. Jiang, Z.K. Sheng, D. Ngmenterebo, C. Tai, M. Wang, Z. Deng, K. Rajakumar and H.Y. Ou* (2015) Mapping the resistance-associated mobilome of a carbapenem-resistant Klebsiella pneumoniae strain reveals insights into factors shaping these regions and facilitates generation of a 'resistance-disarmed' model organism. Journal of Antimicrobial Chemotherapy, 70:2770-2774.

(32) J. Li, Y. Yao, H. H. Xu, L. Hao, Z. Deng, K. Rajakumar and H.Y. Ou* (2015) SecReT6: a web-based resource for type VI secretion systems found in bacteria. Environmental Microbiology, 17:2196-202.

(31) H.Y. Ou, S. Kuang, X. He, B. Molgora, P. Ewing, Z. Deng, M. Osby, W. Chen and H. H. Xu* (2015) Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors. Scientific Reports, 5:8643.

(30) G. Li, Y. Zhang, D. Bi, P. Shen, F. Ai, H. Liu, Y. Tian, Y. Ma, B. Wang, K. Rajakumar, H.Y. Ou*, X. Jiang* (2015) First Report of a Clinical, Multidrug-Resistant Enterobacteriaceae Isolate Coharboring Fosfomycin Resistance Gene fosA3 and Carbapenemase Gene blaKPC-2 on the Same Transposon, Tn1721. Antimicrobial Agents and Chemotherapy, 59:338-343. DOI: 10.1128/AAC.03061-14

(29) W.S. Ho, H.Y. Ou, C.C. Yeo and K.L. Thong* (2015) The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands. BMC Genomics, 2015, 16:199.

(28) T. Han, M. Mabuchi, G. Zhao, L. Li., G. Liu, H.Y. Ou, Z. Deng, Y. Zheng, X. He (2015) Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins, Nucleic Acids Research, 43(2):1147-59.

(27) R. Zhang*, H.Y. Ou, F. Gao and H. Luo (2014). Identification of Horizontally-transferred Genomic Islands and Genome Segmentation Points by Using the GC Profile Method. Current Genomics, 15(2), 113-121.

(26) T. Bai, D. Zhang, S. Lin, Q. Long, Y. WANG, H.Y. Ou, Q. Kang, Z. Deng, W. Liu and M. Tao* (2014).Operon for biosynthesis of lipstatin, the beta-lactone inhibitor of human pancreatic lipase Applied and Environmental Microbiology, 80(24):7473-83.

(25) D. Bi, L. Liu, C. Tai, Z. Deng, K. Rajakumar* and H.Y. Ou* (2013) SecReT4: a web-based bacterial type IV secretion system resource. Nucleic Acids Research, 41, D660-D665.

(24) F. Su, H.Y. Ou, F. Tao, H. Tang and P. Xu* (2013) PSP: rapid identification of orthologous coding genes under positive selection across multiple closely related prokaryotic genomes. BMC Genomics, 14, 924.

(23) D. Bi, Z. Xu, E. Harrison, C. Tai, Y. Wei, X. He, S. Jia, Z. Deng, K. Rajakumar* and H.Y. Ou* (2012) ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Research, 40, D621-D626.

(22) P. Liu, P. Li, X. Jiang, D. Bi, Y. Xie, C. Tai, Z. Deng, K. Rajakumar and H.Y. Ou* (2012) Complete Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a Multidrug-Resistant Strain Isolated from Human Sputum. Journal of Bacteriology, 194, 1841-1842.

(21) C. Zhao, P. Li, Z. Deng, H.Y. Ou *, R.P. McGlinchey, D. O'Hagan * (2012) Insights into fluorometabolite biosynthesis in Streptomyces cattleya DSM46488 through knockout mutants. Bioorganic Chemistry, 44, 1-7.

(20) J. Li, X. Qu, X. He, L. Duan, G. Wu, D. Bi, Z. Deng, W. Liu*, H.Y. Ou* (2012) ThioFinder: a web-based tool for the identification of thiopeptide gene clusters in DNA sequences. PloS ONE, 7, e45878.

(19) M. Kochar, M. Crosatti, E.M. Harrison, B. Rieck, J. Chan, C. Constantinidou, M. Pallen, H.Y. Ou and K. Rajakumar (2012) Deletion of TnAbaR23 results in both expected and unexpected antibiogram changes in a multi-drug resistant Acinetobacter baumannii strain. Antimicrob Agents Chemother, 56, 1845-1853.

(18) J.J. van Aartsen, S.G. Stahlhut, E.M. Harrison, M. Crosatti, H.Y. Ou, K.A. Krogfelt, C. Struve and K. Rajakumar (2012) Characterization of a novel chaperone/usher fimbrial operon present on KpGI-5, a methionine tRNA gene-associated genomic island in Klebsiella pneumoniae. BMC Microbiology, 12, 59.

(17) B. Rieck, D. Tourigny, M. Crosatti, R. Schmid, M. Kochar, E. Harrison, H.Y. Ou, J. Turton and K. Rajakumar (2012) Acinetobacter insertion sequence ISAba11 belongs to a novel family that encodes transposases with a signature HHEK motif. Applied and Environmental Microbiology, 78, 471-480.

(16) Y. Shao, E.M. Harrison, D. Bi, C. Tai, X. He, H.Y. Ou*, K. Rajakumar and Z. Deng (2011) TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea. Nucleic Acids Research, 39, D606-D611.

(15) J. Zhang, J. Jurriaan van Aartsen, X. Jiang, Y. Shao, C. Tai, X. He, Z. Tan, Z. Deng, S. Jia*, K. Rajakumar and H.Y. Ou* (2011) Expansion of the known Klebsiella pneumoniae species gene pool by characterization of novel alien DNA islands integrated into tmRNA gene sites. Journal of Microbiological Methods, 84, 283-289.

(14) F. Su, B. Yu, J. Sun, H.Y. Ou, B. Zhao, L. Wang, J. Qin, H. Tang, F. Tao, M. Jarek, M. Scharfe, C. Ma, Y. Ma, P. Xu (2011) Genome sequence of thermophilic strain Bacillus coagulans 2-6, an efficient producer of high optical purity L-lactic acid. Journal of Bacteriology, 193, 4563-4.

(13) D.Q. Wu, J. Ye, H.Y. Ou, X. Wei, X. Huang , Y.W. He and Y. Xu (2011) Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18. BMC Genomics, 2011, 12:438.

(12) G. Liu, H.Y. Ou, T. Wang, L. Li, H. Tan, X. Zhou, K. Rajakumar, Z. Deng* and X. He* (2010) Cleavage of Phosphothioated DNA and Methylated DNA by the Type IV Restriction Endonuclease ScoMcrA. PLoS Genetics, 6, e1001253.

(11) Y. Shao, X. He, C. Tai, H.Y. Ou*, K. Rajakumar and Z. Deng (2010) mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes. Nucleic Acids Research, 38, W194-W200.

(10) N. Chen#, H.Y. Ou#, J.J. van Aartsen, X. Jiang, M. Li, Z. Yang, Q.Wei, X. Chen, X. He, Z.Deng, K. Rajakumar,Y. Lu (2010) The pheV phenylalanine tRNA gene in Klebsiella pneumoniae clinical isolates is an integration hotspot for possible niche-adaptation genomic islands. Current Microbiology, 60, 210-6. ( #These authors contributed equally to this work.)

(9) J. Sridhar, S.R. Narmada, R. Sabarinathan, H.Y. Ou, Z. Deng, K. Sekar, Z.A. Rafi, K. Rajakumar (2010) sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes. PLoS ONE, 5, e11970.

(8) E.M. Harrison, M.E.K. Carter, S. Luck, H.Y. Ou, X. He, Z. Deng, C. Oallaghan, A. Kadioglu and K. Rajakumar (2010) The pathogenicity islands PAPI-1 and 2 PAPI-2 contribute individually and synergistically to virulence of Pseudomonas aeruginosa strain PA14. Infection and Immunity, 78, 1437-1446.

(7) H.Y. Ou, X. He, Y. Shao, C. Tai, K. Rajakumar and Z. Deng* (2009) dndDB: a database focused on phosphorothioation of the DNA backbone. PLoS ONE, 4, e5132.

(6) F. Wang, X. Xiao, H.Y. Ou, Y. Gai, F. Wang (2009) The role and regulation of fatty acid biosynthesis in Shewanella piezotolerans WP3 response to different temperatures and pressures. Journal Bacteriology, 191, 2574-84.
(5) F. Shaikh, R.P. Spence, K. Levi, H.Y. Ou, Z. Deng, K.J. Towner and K. Rajakumar (2009) ATPase genes of diverse multi-drug resistant Acinetobacter baumannii isolates frequently harbour integrated DNA. Journal of Antimicrobial Chemotherapy, 63, 260-4.

(4) J. Malkin, P.T. Kimmitt, H.Y. Ou, P.S. Bhasker, M. Khare, Z. Deng, I. Stephenson, A.W. Sosnowski, N. Perera and K. Rajakumar (2008) Identification of Streptococcus gallolyticus subsp. macedonicus as the etiological agent in a case of culture-negative multivalve infective endocarditis by 16S rDNA PCR analysis of resected valvular tissue. Journal of Heart Valve Disease, 17, 589-92.

(3) H.Y. Ou #, C.T.S. Ju #, K.L. Thong, N. Ahmad, Z. Deng, M.R. Barer and K. Rajakumar* (2007). Translational Genomics to Develop a Salmonella enterica Serovar Paratyphi A Multiplex PCR Assay. Journal of Molecular Diagnostics, 2007, 9, 624-630. (# These authors contributed equally to this work.) (Cover Story and Comment in: J Mol Diagn. 2007, 9, 572-573.)

(2) H.Y. Ou, X. He, E.M. Harrison, B.R. Kulasekara, A.B. Thani, A. Kadioglu, S. Lory, J.C. Hinton, M.R. Barer, Z. Deng* and K. Rajakumar* (2007). MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Research, 35, W97-W104.

(1) X. He, H.Y. Ou, Q. Yu, X. Zhou, J. Wu, J. Liang, W. Zhang, K. Rajakumar and Z. Deng* (2007). Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria. Molecular Microbiology, 65, 1034-48.


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