Microbial Bioinformatics Group at MML, SJTU


(90) Guan J, Chen Y, Goh YX, Wang M, Tai C, Deng Z, Song J, Ou HY* (2024) TADB 3.0: an updated database of bacterial toxin-antitoxin loci and associated mobile genetic elements. Nucleic Acids Research, 52(D1): D784–D790. doi: 10.1093/nar/gkad962.

(89) Wang M#, Liu G#, Liu M, Tai C, Deng Z, Song J, Ou HY* (2024) ICEberg 3.0: functional categorization and analysis of the integrative and conjugative elements in bacteria. Nucleic Acids Research, 52(D1): D732–D737. doi: 10.1093/nar/gkad935.

(88) Chen Y#, Goh YX#, Li P#, Guan J, Chao Y, Qu H*, Ou HY*, Wang X* (2024) RES-Xre toxin-antitoxin locus knaAT maintains the stability of the virulence plasmid in Klebsiella pneumoniae. Emerging Microbes & Infections, 13(1):2316814. doi: 10.1080/22221751.2024.2316814.

(87) Zhang J#, Xu Y#, Wang M#, Li X, Liu Z, Kuang D, Deng Z, Ou HY*, Qu J* (2023) Mobilizable plasmids drive the spread of antimicrobial resistance genes and virulence genes in Klebsiella pneumoniae. Genome Medicine, 15(1):106. doi: 10.1186/s13073-023-01260-w.

(86) Zhang Y, Guan J, Li C, Wang Z, Deng Z, Gasser RB, Song J*, Ou HY* (2023) DeepSecE: a deep learning-based framework for multi-class prediction of secreted proteins in Gram-negative bacteria. Research, 6:0258. doi: 10.34133/research.0258.

(85) Liu Z, Guan J, Chen Z, Tai C, Deng Z, Chao Y*, Ou HY* (2023) CpxR promotes the carbapenem antibiotic resistance of Klebsiella pneumoniae by directly regulating the expression and the dissemination of blaKPC on the IncFII conjugative plasmid. Emerging Microbes & Infections, 12(2):2256427. doi: 10.1080/22221751.2023.2256427.

(84) Li P, Goh YX, Wang M, Ilic B, Tai C, Deng Z, Djordjevic M, Ou HY* (2023) Antibiotic-induced degradation of antitoxin enhances the transcription of acetyltransferase-type toxin-antitoxin operon. Journal of Antimicrobial Chemotherapy, 78(4):1066-1075. doi: 10.1093/jac/dkad048.

(83) Zhang J#, Guan J#, Wang M, Li G, Djordjevic M, Tai C, Wang H, Deng Z, Chen Z*, Ou HY* (2023) SecReT6 update: a comprehensive resource of bacterial Type VI Secretion Systems. SCIENCE CHINA Life Sciences, 66(3):626-634. doi: 10.1007/s11427-022-2172-x. [Abstract]

(82) Goh YX, Wang M, Hou XP, He Y*, Ou HY* (2023) Analysis of CRISPR‑Cas loci and their targets in Levilactobacillus brevisz. Interdisciplinary Sciences: Computational Life Sciences, 15(3):349-359. doi: 10.1007/s12539-023-00555-1.

(81) Wang M, Goh YX, Tai C, Wang H, Deng Z, Ou HY* (2022) VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens. Nucleic Acids Research, 50(W1):W768-W773. doi: 10.1093/nar/gkac321.

(80) Goh YX#, Li P#, Wang M, Djordjevic M, Tai C, Wang H, Deng Z, Chen Z*, Ou HY* (2022) Comparative analysis of diverse acetyltransferase-type toxin-antitoxin loci in Klebsiella pneumoniae. Microbiology Spectrum, 10(4):e0032022. doi: 10.1128/spectrum.00320-22.

(79) Zhang Y#, Zhang YM#, Xiong Y, Wang H, Deng Z, Song J*, Ou HY* (2022) T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model. Briefings in Bioinformatics, 23(1):bbab420. doi: 10.1093/bib/bbab420.

(78) Wang X#, Tang Bin#, Liu G, Wang M, Sun J, Tan R, Pan T, Qu J, Liu J*, Ou HY*, Qu H* (2022) Transmission of nonconjugative virulence or resistance plasmids mediated by a self-transferable IncN3 plasmid from carbapenem-resistant Klebsiella pneumoniae. Microbiology Spectrum, 10(4):e0136422. doi: 10.1128/spectrum.01364-22.

(77) 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(1):11. doi: 10.1038/s41597-021-01112-5..

(76) Li P, Zhang J, Deng Z, Gao F*, Ou HY* (2022) Identification and characterization of a central replication origin of the mega-plasmid pSCATT of Streptomyces cattleya. Microbiological Research, 257:126975. doi: 10.1016/j.micres.2022.126975.

(75) Goh YX, He Y*, Ou HY* (2022) Identification of type II toxin-antitoxin Loci in Levilactobacillus brevisz. Interdisciplinary Sciences: Computational Life Sciences, 14(1):80-88. doi: 10.1007/s12539-021-00486-9.

(74) 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 pneumoniae. Genome Medicine, 13(1):119.

(73) Tian D#, Wang M#, Zhou Y, Hu D, Ou HY*, Jiang X* (2021) Genetic diversity and evolution of the virulence plasmids encoding aerobactin and salmochelin in Klebsiella pneumoniae. Virulence, 12(1):1323-1333.

(72) Hu W, Wang Y, Yang B, Lin C, Yu H, Liu G, Deng Z, Ou HY, He X* (2021) Bacterial YedK represses plasmid DNA replication and transformation through its DNA single-strand binding activity. Microbiological Research, 252:126852.

(71) Qin J, Wu N, Bao J, Shi X, Ou HY, Ye S, Zhao W, Wei Z, Cai J, Li L, Guo M, Weng J, Lu H, Tan D, Zhang J, Huang Q, Zhu Z, Shi Y, Hu C, Guo* X, Zhu T* (2021) Heterogeneous Klebsiella pneumoniae co-infections complicate personalized bacteriophage therapy. Front. Cell. Infect. Microbiol., 10:608402. doi: 10.3389/fcimb.2020.608402.

(70) Bi D, Zheng J, Xie R, Zhu Y, Wei R, Ou HY, Wei Q*, Qin H* (2020) Comparative analysis of AbaR-type genomic islands reveals distinct patterns of genetic features in elements with different backbones. mSphere, 5(3):e00349-20. doi: 10.1128/mSphere.00349-20.

(69) Tang Y, Fu P, Zhou Y, Xie Y, Jin J, Wang B, Yu L, Huang Y, Li G, Li M, Liang W, Ou HY, Jiang X*. (2020) Absence of the type I-E CRISPR-Cas system in Klebsiella pneumoniae clonal complex 258 is associated with dissemination of IncF epidemic resistance plasmids in this clonal complex. J Antimicrob Chemother, 75(4):890-895. doi:10.1093/jac/dkz538.

(68) He Y, Zhou X, Chen Z, Deng X, Gehring A, Ou HY, Zhang L, Shi X* (2020) PRAP: Pan Resistome analysis pipeline. BMC Bioinformatics, 21(1):20. doi: 10.1186/s12859-019-3335-y.

(67) Qian H#, Yu H#, Li P, Zhu E, Yao Q, Tai C, Deng Z, Gerdes K, He X*, Gan J*, Ou HY* (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.

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

(65) Bi D, Xie R, Zheng J, Yang H, Zhu X, Ou HY, Wei Q* (2019) Large-Scale identification of AbaR-type genomic islands in Acinetobacter baumannii reveals diverse insertion sites and clonal lineage-specific antimicrobial resistance gene profiles. Antimicrob Agents Chemother., 63(4): pii: e02526-18.

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

(63) Li X, Xie Y, Liu M, Tai C, Sun J, Deng Z, Ou HY* (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.

(62) Qian H, Yao Q, Tai C, Deng Z, Gan J*, Ou HY* (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)

(61) Xie Y#, Tian L#, Li G#, Qu H, Sun J, Liang W, Li X, Wang X, Deng Z, Liu J*, Ou HY* (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.

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

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

(58) Li J, Tai C, Deng Z, Zhong W, He Y, Ou HY* (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.

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

(56) Bi D, Zheng J, Li JJ, Sheng ZK, Zhu X, Ou HY, Li Q, Wei Q (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.

(55) Wang Y, Jia B, Xu X, Zhang L, Wei C, Ou HY, Cui Y, Shi C, Shi X* (2018) Comparative genomic analysis and characterization of two Salmonella enterica serovar Enteritidis isolates from poultry with notably different survival abilities in egg whites. Front Microbiol., 9:2111. doi: 10.3389/fmicb.2018.02111.

(54) Liu L, Ye M, Li X, Li J, Deng Z, Yao YF, Ou HY* (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.

(53) 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.

(52) 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.

(51) Xu Z, Wang Y, Chater KF, Ou HY, Xu HH, Deng Z, Tao M* (2017) Large-scale transposition mutagenesis of Streptomyces coelicolor identifies hundreds of genes influencing antibiotic biosynthesis. Appl Environ Microbiol., 83(6): e02889-16.

(50) Xu Q, Xiong Y*, Dai H, Kumari KM, Xu Q, Ou HY, Wei DQ (2017) PDC-SGB: Prediction of effective drug combinations using a stochastic gradient boosting algorithm. J Theor Biol., 417:1-7. doi: 10.1016/j.jtbi.2017.01.019.

(49) Li P, Tai C, Deng Z, Gan J, Oggioni MR, Ou HY* (2016) Identification and characterization of chromosomal relBE toxin-antitoxin locus in Streptomyces cattleya DSM46488. Scientific Reports, 6:32047. doi: 10.1038/srep32047.

(48) Bi D#, Xie Y#, Tai C, Jiang X, Zhang J, Harrison EM, Jia S, Deng Z, Rajakumar K, Ou HY* (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.)

(47) Wei YQ, Bi DX, Wei DQ*, Ou HY* (2016) Prediction of type II toxin-antitoxin loci in Klebsiella pneumoniae genome sequences. Interdisciplinary Sciences: Computational Life Sciences, 8(2):143-9.

(46) Furi L, Haigh R, Al Jabri ZJ, Morrissey I, Ou HY, León-Sampedro R, Martinez JL, Coque TM, Oggioni MR* (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.

(45) Xu MJ, Wang JH, Bu XL, Yu HL, Li P, Ou HY, He Y, Xu FD, Hu XY, Zhu XM, Ao P, Xu J * (2016) Deciphering the streamlined genome of Streptomyces xiamenensis 318 as the producer of the anti-fibrotic drug candidate xiamenmycin. Scientific Reports, 6:18977.

(44) Bi D, Jiang X, Sheng ZK, Ngmenterebo D, Tai C, Wang M, Deng Z, Rajakumar K, Ou HY* (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. doi: 10.1093/jac/dkv204.

(43) Li J, Yao Y, Xu HH, Hao L, Deng Z, Rajakumar K, Ou HY* (2015) SecReT6: a web-based resource for type VI secretion systems found in bacteria. Environmental Microbiology, 17:2196-202. doi: 10.1111/1462-2920.12794.

(42) Ou HY, Kuang SN, He X, Molgora BM, Ewing PJ, Deng Z, Osby M, Chen W, Xu HH* (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.

(41) Li G, Zhang Y, Bi D, Shen P, Ai F, Liu H, Tian Y, Ma Y, Wang B, Rajakumar K, Ou HY*, Jiang X* (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

(40) Ho WS, Ou HY, Yeo CC, Thong KL* (2015) The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands. BMC Genomics, 2015, 16:199.

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

(38) Zhang R*, Ou HY, Gao F, Luo H (2014). Identification of horizontally-transferred genomic islands and genome segmentation points by using the GC profile method. Current Genomics, 15(2), 113-121.

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

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

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

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

(33) Liu P, Li P, Jiang X, Bi D, Xie Y, Tai C, Deng Z, Rajakumar K, Ou HY* (2012) Complete Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. Journal of Bacteriology, 194, 1841-1842.

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

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

(30) Kochar M, Crosatti M, Harrison EM, Rieck B, Chan J, Constantinidou C, Pallen M, Ou HY, Rajakumar K* (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.

(29) van Aartsen JJ, Stahlhut SG, Harrison EM, Crosatti M, Ou HY, Krogfelt KA, Struve C, Rajakumar K* (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.

(28) Rieck B, Tourigny DS, Crosatti M, Schmid R, Kochar M, Harrison EM, Ou HY, Turton JF, Rajakumar K* (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.

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

(26) Zhang J, van Aartsen JJ, Jiang X, Shao Y, Tai C, He X, Tan Z, Deng Z, Jia S* Rajakumar K, Ou HY* (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.

(25) Su F, Yu B, Sun J, Ou HY, Zhao B, Wang L, Qin J, Tang H, Tao F, Jarek M, Scharfe M, Ma C, Ma Y, Xu P. (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.

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

(23) Liu G, Ou HY, Wang T, Li L, Tan H, Zhou X, Rajakumar K, Deng Z*, He X* (2010) Cleavage of phosphothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA. PLoS Genetics, 6, e1001253.

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

(21) Chen N#, Ou HY#, van Aartsen JJ, Jiang X, Li M, Yang Z, Wei Q, Chen X, He X, Deng Z, Rajakumar K, Lu Y* (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.)

(20) Sridhar J, Sambaturu N, Sabarinathan R, Ou HY, Deng Z, Sekar K, Rafi ZA, Rajakumar K* (2010) sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes. PLoS ONE, 5, e11970.

(19) Harrison EM, Carter ME, Luck S, Ou HY, He X, Deng Z, O'Callaghan C, Kadioglu A, Rajakumar K (2010) Pathogenicity islands PAPI-1 and PAPI-2 contribute individually and synergistically to the virulence of Pseudomonas aeruginosa strain PA14. Infection and Immunity, 78, 1437-1446.

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

(17) Wang F, Xiao X, Ou HY, Gai Y, Wang F* (2009) Role and regulation of fatty acid biosynthesis in the response of Shewanella piezotolerans WP3 to different temperatures and pressures. Journal Bacteriology, 191, 2574-84.

(16) Shaikh F, Spence RP, Levi K, Ou HY, Deng Z, Towner KJ, Rajakumar K (2009) ATPase genes of diverse multi-drug resistant Acinetobacter baumannii isolates frequently harbour integrated DNA. Journal of Antimicrobial Chemotherapy, 63, 260-4.

(15) Malkin J, Kimmitt PT, Ou HY, Bhasker PS, Khare M, Deng Z, Stephenson I, Sosnowski AW, Perera N, Rajakumar K (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.

(14) Ou HY#, Ju CT#, Thong KL, Ahmad N, Deng Z, Barer MR, Rajakumar K* (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.)

(13) Ou HY, He X, Harrison EM, Kulasekara BR, Thani AB, Kadioglu A, Lory S, Hinton JC, Barer MR, Deng Z*, Rajakumar K* (2007). MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Research, 35, W97-W104.

(12) He X, Ou HY, Yu Q, Zhou X, Wu J, Liang J, Zhang W, Rajakumar K, Deng Z* (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.

(11) Ou HY, Chen LL, Lonnen J, Chaudhuri RR, Thani AB, Smith R, Garton NJ, Hinton J, Pallen M, Barer MR, Rajakumar K* (2006) A novel strategy for identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res., 34, e3.

(10) Ou HY, Smith R, Lucchini S, Hinton J, Chaudhuri RR, Pallen M, Barer MR, Rajakumar K* (2005) ArrayOme: a program for estimating the sizes of the microarray-visualised genomes. Nucleic Acids Res., 33, e3.

(9) Zheng WX, Chen LL, Ou HY, Gao F, Zhang CT* (2005) Coronavirus phylogeny based on a geometric approach. Mol. Phyl. Evol., 36, 224-232.

(8) Ou HY, Guo FB, Zhang CT* (2004). GS-Finder: a program to find bacterial gene start sites with a self-training method. Int. J. Biochem. Cell Biol., 36, 535-544.

(7) Zhang R, Ou HY, Zhang CT* (2004) DEG, a Database of Essential Genes. Nucleic Acids Res., 32, D271-D272.

(6) Ou HY, Guo FB, Zhang CT* (2003) Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3(2) using the Z curve method. FEBS Letters, 540, 188-194.

(5) Guo FB, Ou HY, Zhang CT* (2003) ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res., 31, 1780-1789.

(4) Zhang CT*, Zhang R, Ou HY (2003) The Z curve database: a graphic representation of genome sequences. Bioinformatics, 19, 593-599.

(3) Wang Y*, Ou HY, Guo F (2003) Recognition of translation initiation sites of eukaryotic genes based on EM algorithm. J. Comput. Biol., 10, 699-708.

(2) Chen LL#, Ou HY#, Zhang R, Zhang CT* (2003) ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes. Biochem. Biophys. Res. Commun., 307, 382-388. (#These authors contributed equally to this work.)

(1) Gao F, Ou HY, Chen LL, Zheng WX, Zhang CT* (2003) Prediction of proteinase cleavage sites in polyproteins of coronaviruses and its applications in analyzing SARS-CoV genomes. FEBS Letters, 553, 451-456.

Book chapters:
(i) Ou HY, Wei Y, Bi D (2013) Book chapter: “Type II Loci: Phylogeny”, Prokaryotic Toxin-Antitoxins, Editor Kenn Gerdes, Springer.

(ii) Ou HY and Rajakumar K (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.

(iii) Ou HY (2012) Book chapter: “Identification of bacterial genomic islands by comparative genomic analysis”, Microbiology Genomics in China, Editor Z.N. Yu, Science Press (in Chinese).
    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.