{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T20:40:32Z","timestamp":1791146432588,"version":"4.1.0"},"reference-count":97,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2010,10,21]],"date-time":"2010-10-21T00:00:00Z","timestamp":1287619200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2010,10,21]],"date-time":"2010-10-21T00:00:00Z","timestamp":1287619200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The <jats:italic>Enterobacteriaceae<\/jats:italic> comprise a large number of clinically relevant species with several individual subspecies. Overlapping virulence-associated gene pools and the high overall genome plasticity often interferes with correct enterobacterial strain typing and risk assessment. Array technology offers a fast, reproducible and standardisable means for bacterial typing and thus provides many advantages for bacterial diagnostics, risk assessment and surveillance. The development of highly discriminative broad-range microbial diagnostic microarrays remains a challenge, because of marked genome plasticity of many bacterial pathogens.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We developed a DNA microarray for strain typing and detection of major antimicrobial resistance genes of clinically relevant enterobacteria. For this purpose, we applied a global genome-wide probe selection strategy on 32 available complete enterobacterial genomes combined with a regression model for pathogen classification. The discriminative power of the probe set was further tested <jats:italic>in silico<\/jats:italic> on 15 additional complete enterobacterial genome sequences. DNA microarrays based on the selected probes were used to type 92 clinical enterobacterial isolates. Phenotypic tests confirmed the array-based typing results and corroborate that the selected probes allowed correct typing and prediction of major antibiotic resistances of clinically relevant <jats:italic>Enterobacteriaceae<\/jats:italic>, including the subspecies level, e.g. the reliable distinction of different <jats:italic>E. coli<\/jats:italic> pathotypes.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Our results demonstrate that the global probe selection approach based on longest common factor statistics as well as the design of a DNA microarray with a restricted set of discriminative probes enables robust discrimination of different enterobacterial variants and represents a proof of concept that can be adopted for diagnostics of a wide range of microbial pathogens. Our approach circumvents misclassifications arising from the application of virulence markers, which are highly affected by horizontal gene transfer. Moreover, a broad range of pathogens have been covered by an efficient probe set size enabling the design of high-throughput diagnostics.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2164-11-591","type":"journal-article","created":{"date-parts":[[2010,10,22]],"date-time":"2010-10-22T06:13:57Z","timestamp":1287728037000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis"],"prefix":"10.1186","volume":"11","author":[{"given":"Torben","family":"Friedrich","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sven","family":"Rahmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wilfried","family":"Weigel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wolfgang","family":"Rabsch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angelika","family":"Fruth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eliora","family":"Ron","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Gunzer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Dandekar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00f6rg","family":"Hacker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias","family":"M\u00fcller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulrich","family":"Dobrindt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2010,10,21]]},"reference":[{"key":"10011_CR1","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/nrmicro818","volume":"2","author":"JB Kaper","year":"2004","unstructured":"Kaper JB, Nataro JP, Mobley HL: Pathogenic Escherichia coli. Nat Rev Microbiol. 2004, 2: 123-140. 10.1038\/nrmicro818.","journal-title":"Nat Rev Microbiol"},{"key":"10011_CR2","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nrmicro1788","volume":"6","author":"A Haraga","year":"2008","unstructured":"Haraga A, Ohlson MB, Miller SI: Salmonellae interplay with host cells. Nat Rev Microbiol. 2008, 6: 53-66. 10.1038\/nrmicro1788.","journal-title":"Nat Rev Microbiol"},{"key":"10011_CR3","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nrmicro730","volume":"1","author":"BW Wren","year":"2003","unstructured":"Wren BW: The yersiniae--a model genus to study the rapid evolution of bacterial pathogens. Nat Rev Microbiol. 2003, 1: 55-64. 10.1038\/nrmicro730.","journal-title":"Nat Rev Microbiol"},{"key":"10011_CR4","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1128\/CMR.11.4.589","volume":"11","author":"R Podschun","year":"1998","unstructured":"Podschun R, Ullmann U: Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev. 1998, 11: 589-603.","journal-title":"Clin Microbiol Rev"},{"key":"10011_CR5","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1097\/MOG.0b013e3282f21388","volume":"24","author":"GA Grassl","year":"2008","unstructured":"Grassl GA, Finlay BB: Pathogenesis of enteric Salmonella infections. Curr Opin Gastroenterol. 2008, 24: 22-26. 10.1097\/MOG.0b013e3282f21388.","journal-title":"Curr Opin Gastroenterol"},{"key":"10011_CR6","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1128\/CMR.00032-07","volume":"21","author":"GN Schroeder","year":"2008","unstructured":"Schroeder GN, Hilbi H: Molecular pathogenesis of Shigella spp.: controlling host cell signaling, invasion, and death by type III secretion. Clin Microbiol Rev. 2008, 21: 134-156. 10.1128\/CMR.00032-07.","journal-title":"Clin Microbiol Rev"},{"key":"10011_CR7","doi-asserted-by":"crossref","first-page":"4555","DOI":"10.1128\/AEM.66.10.4555-4558.2000","volume":"66","author":"O Clermont","year":"2000","unstructured":"Clermont O, Bonacorsi S, Bingen E: Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol. 2000, 66: 4555-4558. 10.1128\/AEM.66.10.4555-4558.2000.","journal-title":"Appl Environ Microbiol"},{"key":"10011_CR8","doi-asserted-by":"crossref","first-page":"1356","DOI":"10.1046\/j.1537-2995.2001.41111356.x","volume":"41","author":"K Sen","year":"2001","unstructured":"Sen K, Asher DM: Multiplex PCR for detection of Enterobacteriaceae in blood. Transfusion. 2001, 41: 1356-1364. 10.1046\/j.1537-2995.2001.41111356.x.","journal-title":"Transfusion"},{"key":"10011_CR9","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nmeth757","volume":"2","author":"JE Larkin","year":"2005","unstructured":"Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J: Independence and reproducibility across microarray platforms. Nat Methods. 2005, 2: 337-344. 10.1038\/nmeth757.","journal-title":"Nat Methods"},{"key":"10011_CR10","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1128\/JCM.01361-06","volume":"45","author":"K Ballmer","year":"2007","unstructured":"Ballmer K, Korczak BM, Kuhnert P, Slickers P, Ehricht R, Hachler H: Fast DNA serotyping of Escherichia coli by use of an oligonucleotide microarray. J Clin Microbiol. 2007, 45: 370-379. 10.1128\/JCM.01361-06.","journal-title":"J Clin Microbiol"},{"key":"10011_CR11","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1016\/j.ab.2006.09.026","volume":"360","author":"T Kostic","year":"2007","unstructured":"Kostic T, Weilharter A, Rubino S, Delogu G, Uzzau S, Rudi K, Sessitsch A, Bodrossy L: A microbial diagnostic microarray technique for the sensitive detection and identification of pathogenic bacteria in a background of nonpathogens. Anal Biochem. 2007, 360: 244-254. 10.1016\/j.ab.2006.09.026.","journal-title":"Anal Biochem"},{"key":"10011_CR12","doi-asserted-by":"crossref","first-page":"4082","DOI":"10.1128\/AEM.01820-06","volume":"73","author":"W Han","year":"2007","unstructured":"Han W, Liu B, Cao B, Beutin L, Kruger U, Liu H, Li Y, Liu Y, Feng L, Wang L: DNA microarray-based identification of serogroups and virulence gene patterns of Escherichia coli isolates associated with porcine postweaning diarrhea and edema disease. Appl Environ Microbiol. 2007, 73: 4082-4088. 10.1128\/AEM.01820-06.","journal-title":"Appl Environ Microbiol"},{"key":"10011_CR13","doi-asserted-by":"crossref","first-page":"2113","DOI":"10.1128\/JCM.41.5.2113-2125.2003","volume":"41","author":"S Bekal","year":"2003","unstructured":"Bekal S, Brousseau R, Masson L, Prefontaine G, Fairbrother J, Harel J: Rapid identification of Escherichia coli pathotypes by virulence gene detection with DNA microarrays. J Clin Microbiol. 2003, 41: 2113-2125. 10.1128\/JCM.41.5.2113-2125.2003.","journal-title":"J Clin Microbiol"},{"key":"10011_CR14","doi-asserted-by":"crossref","first-page":"3780","DOI":"10.1128\/AEM.72.5.3780-3784.2006","volume":"72","author":"G Bruant","year":"2006","unstructured":"Bruant G, Maynard C, Bekal S, Gaucher I, Masson L, Brousseau R, Harel J: Development and validation of an oligonucleotide microarray for detection of multiple virulence and antimicrobial resistance genes in Escherichia coli. Appl Environ Microbiol. 2006, 72: 3780-3784. 10.1128\/AEM.72.5.3780-3784.2006.","journal-title":"Appl Environ Microbiol"},{"key":"10011_CR15","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1016\/j.ijantimicag.2008.04.020","volume":"32","author":"T Barl","year":"2008","unstructured":"Barl T, Dobrindt U, Yu X, Katcoff DJ, Sompolinsky D, Bonacorsi S, Hacker J, Bachmann TT: Genotyping DNA chip for the simultaneous assessment of antibiotic resistance and pathogenic potential of extraintestinal pathogenic Escherichia coli. Int J Antimicrob Agents. 2008, 32: 272-277. 10.1016\/j.ijantimicag.2008.04.020.","journal-title":"Int J Antimicrob Agents"},{"key":"10011_CR16","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/j.ijantimicag.2005.09.021","volume":"27","author":"JG Frye","year":"2006","unstructured":"Frye JG, Jesse T, Long F, Rondeau G, Porwollik S, McClelland M, Jackson CR, Englen M, Fedorka-Cray PJ: DNA microarray detection of antimicrobial resistance genes in diverse bacteria. Int J Antimicrob Agents. 2006, 27: 138-151. 10.1016\/j.ijantimicag.2005.09.021.","journal-title":"Int J Antimicrob Agents"},{"key":"10011_CR17","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1128\/JCM.01693-08","volume":"47","author":"SE McNamara","year":"2009","unstructured":"McNamara SE, Srinivasan U, Zhang L, Whittam TS, Marrs CF, Foxman B: Comparison of probe hybridization array typing to multilocus sequence typing for pathogenic Escherichia coli. J Clin Microbiol. 2009, 47: 596-602. 10.1128\/JCM.01693-08.","journal-title":"J Clin Microbiol"},{"key":"10011_CR18","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1016\/j.ijmm.2005.07.002","volume":"295","author":"Baum H von","year":"2005","unstructured":"von Baum H, Marre R: Antimicrobial resistance of Escherichia coli and therapeutic implications. Int J Med Microbiol. 2005, 295: 503-511. 10.1016\/j.ijmm.2005.07.002.","journal-title":"Int J Med Microbiol"},{"issue":"Suppl 2","key":"10011_CR19","doi-asserted-by":"crossref","first-page":"ii156","DOI":"10.1093\/bioinformatics\/btg1073","volume":"19","author":"S Rahmann","year":"2003","unstructured":"Rahmann S: The shortest common supersequence problem in a microarray production setting. Bioinformatics. 2003, 19 (Suppl 2): ii156-161.","journal-title":"Bioinformatics"},{"key":"10011_CR20","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.mimet.2004.02.002","volume":"57","author":"J Letowski","year":"2004","unstructured":"Letowski J, Brousseau R, Masson L: Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays. J Microbiol Methods. 2004, 57: 269-278. 10.1016\/j.mimet.2004.02.002.","journal-title":"J Microbiol Methods"},{"key":"10011_CR21","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1002\/bimj.200810425","volume":"50","author":"T Hothorn","year":"2008","unstructured":"Hothorn T, Bretz F, Westfall P: Simultaneous inference in general parametric models. Biom J. 2008, 50: 346-363. 10.1002\/bimj.200810425.","journal-title":"Biom J"},{"key":"10011_CR22","doi-asserted-by":"crossref","first-page":"5883","DOI":"10.1128\/JB.186.17.5883-5898.2004","volume":"186","author":"S Porwollik","year":"2004","unstructured":"Porwollik S, Boyd EF, Choy C, Cheng P, Florea L, Proctor E, McClelland M: Characterization of Salmonella enterica subspecies I genovars by use of microarrays. J Bacteriol. 2004, 186: 5883-5898. 10.1128\/JB.186.17.5883-5898.2004.","journal-title":"J Bacteriol"},{"key":"10011_CR23","doi-asserted-by":"crossref","first-page":"2018","DOI":"10.1101\/gr.1507303","volume":"13","author":"SJ Hinchliffe","year":"2003","unstructured":"Hinchliffe SJ, Isherwood KE, Stabler RA, Prentice MB, Rakin A, Nichols RA, Oyston PC, Hinds J, Titball RW, Wren BW: Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Res. 2003, 13: 2018-2029. 10.1101\/gr.1507303.","journal-title":"Genome Res"},{"key":"10011_CR24","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1111\/j.1755-0998.2009.02638.x","volume":"9","author":"W Chen","year":"2009","unstructured":"Chen W, Seifert KA, L\u00e9vesque CA: A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium. Molec Ecol Res. 2009, 9: 114-128. 10.1111\/j.1755-0998.2009.02638.x.","journal-title":"Molec Ecol Res"},{"key":"10011_CR25","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1111\/j.1755-0998.2008.02199.x","volume":"9","author":"JC Engelmann","year":"2009","unstructured":"Engelmann JC, Rahmann S, Wolf M, Schultz J, Fritzilas E, Kneitz S, Dandekar T, M\u00fcller T: Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molec Ecol Res. 2009, 9: 83-93. 10.1111\/j.1755-0998.2008.02199.x.","journal-title":"Molec Ecol Res"},{"key":"10011_CR26","doi-asserted-by":"crossref","first-page":"3554","DOI":"10.1128\/AAC.47.11.3554-3560.2003","volume":"47","author":"DL Paterson","year":"2003","unstructured":"Paterson DL, Hujer KM, Hujer AM, Yeiser B, Bonomo MD, Rice LB, Bonomo RA: Extended-spectrum beta-lactamases in Klebsiella pneumoniae bloodstream isolates from seven countries: dominance and widespread prevalence of SHV- and CTX-M-type beta-lactamases. Antimicrob Agents Chemother. 2003, 47: 3554-3560. 10.1128\/AAC.47.11.3554-3560.2003.","journal-title":"Antimicrob Agents Chemother"},{"key":"10011_CR27","doi-asserted-by":"crossref","first-page":"5639","DOI":"10.1128\/JB.183.19.5639-5644.2001","volume":"183","author":"N Kobayashi","year":"2001","unstructured":"Kobayashi N, Nishino K, Yamaguchi A: Novel macrolide-specific ABC-type efflux transporter in Escherichia coli. J Bacteriol. 2001, 183: 5639-5644. 10.1128\/JB.183.19.5639-5644.2001.","journal-title":"J Bacteriol"},{"key":"10011_CR28","doi-asserted-by":"crossref","first-page":"6855","DOI":"10.1128\/jb.179.21.6855-6857.1997","volume":"179","author":"L Sanchez","year":"1997","unstructured":"Sanchez L, Pan W, Vinas M, Nikaido H: The acrAB homolog of Haemophilus influenzae codes for a functional multidrug efflux pump. J Bacteriol. 1997, 179: 6855-6857.","journal-title":"J Bacteriol"},{"issue":"Suppl 4","key":"10011_CR29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1469-0691.2005.01160.x","volume":"11","author":"H Giamarellou","year":"2005","unstructured":"Giamarellou H: Multidrug resistance in Gram-negative bacteria that produce extended-spectrum beta-lactamases (ESBLs). Clin Microbiol Infect. 2005, 11 (Suppl 4): 1-16. 10.1111\/j.1469-0691.2005.01160.x.","journal-title":"Clin Microbiol Infect"},{"key":"10011_CR30","doi-asserted-by":"crossref","first-page":"6779","DOI":"10.1128\/JB.00661-08","volume":"190","author":"WF Fricke","year":"2008","unstructured":"Fricke WF, Wright MS, Lindell AH, Harkins DM, Baker-Austin C, Ravel J, Stepanauskas R: Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5. J Bacteriol. 2008, 190: 6779-6794. 10.1128\/JB.00661-08.","journal-title":"J Bacteriol"},{"key":"10011_CR31","doi-asserted-by":"crossref","first-page":"e1000141","DOI":"10.1371\/journal.pgen.1000141","volume":"4","author":"DE Fouts","year":"2008","unstructured":"Fouts DE, Tyler HL, DeBoy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S: Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genet. 2008, 4: e1000141-10.1371\/journal.pgen.1000141.","journal-title":"PLoS Genet"},{"key":"10011_CR32","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/nrmicro1889","volume":"6","author":"N Ahmed","year":"2008","unstructured":"Ahmed N, Dobrindt U, Hacker J, Hasnain SE: Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention. Nat Rev Microbiol. 2008, 6: 387-394. 10.1038\/nrmicro1889.","journal-title":"Nat Rev Microbiol"},{"key":"10011_CR33","doi-asserted-by":"crossref","first-page":"13826","DOI":"10.1073\/pnas.0404012101","volume":"101","author":"PS Chain","year":"2004","unstructured":"Chain PS, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, Regala WM, Georgescu AM, Vergez LM, Land ML, Motin VL: Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci USA. 2004, 101: 13826-13831. 10.1073\/pnas.0404012101.","journal-title":"Proc Natl Acad Sci USA"},{"key":"10011_CR34","doi-asserted-by":"crossref","first-page":"5432","DOI":"10.1128\/JB.186.16.5432-5441.2004","volume":"186","author":"L Grozdanov","year":"2004","unstructured":"Grozdanov L, Raasch C, Schulze J, Sonnenborn U, Gottschalk G, Hacker J, Dobrindt U: Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917. J Bacteriol. 2004, 186: 5432-5441. 10.1128\/JB.186.16.5432-5441.2004.","journal-title":"J Bacteriol"},{"key":"10011_CR35","doi-asserted-by":"crossref","first-page":"6881","DOI":"10.1128\/JB.00619-08","volume":"190","author":"DA Rasko","year":"2008","unstructured":"Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R: The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol. 2008, 190: 6881-6893. 10.1128\/JB.00619-08.","journal-title":"J Bacteriol"},{"key":"10011_CR36","doi-asserted-by":"crossref","first-page":"1156","DOI":"10.1093\/molbev\/msj125","volume":"23","author":"LA Wilson","year":"2006","unstructured":"Wilson LA, Sharp PM: Enterobacterial repetitive intergenic consensus (ERIC) sequences in Escherichia coli: Evolution and implications for ERIC-PCR. Mol Biol Evol. 2006, 23: 1156-1168. 10.1093\/molbev\/msj125.","journal-title":"Mol Biol Evol"},{"key":"10011_CR37","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1101\/gr.1739204","volume":"14","author":"M Pritsker","year":"2004","unstructured":"Pritsker M, Liu YC, Beer MA, Tavazoie S: Whole-genome discovery of transcription factor binding sites by network-level conservation. Genome Res. 2004, 14: 99-108. 10.1101\/gr.1739204.","journal-title":"Genome Res"},{"key":"10011_CR38","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1007\/s00248-006-9072-6","volume":"52","author":"TJ Gentry","year":"2006","unstructured":"Gentry TJ, Wickham GS, Schadt CW, He Z, Zhou J: Microarray applications in microbial ecology research. Microb Ecol. 2006, 52: 159-175. 10.1007\/s00248-006-9072-6.","journal-title":"Microb Ecol"},{"key":"10011_CR39","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1007\/s00248-006-9197-7","volume":"53","author":"M Wagner","year":"2007","unstructured":"Wagner M, Smidt H, Loy A, Zhou J: Unravelling microbial communities with DNA-microarrays: challenges and future directions. Microb Ecol. 2007, 53: 498-506. 10.1007\/s00248-006-9197-7.","journal-title":"Microb Ecol"},{"key":"10011_CR40","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1016\/j.mib.2005.08.012","volume":"8","author":"N Dorrell","year":"2005","unstructured":"Dorrell N, Hinchliffe SJ, Wren BW: Comparative phylogenomics of pathogenic bacteria by microarray analysis. Curr Opin Microbiol. 2005, 8: 620-626. 10.1016\/j.mib.2005.08.012.","journal-title":"Curr Opin Microbiol"},{"key":"10011_CR41","doi-asserted-by":"crossref","first-page":"R267","DOI":"10.1186\/gb-2007-8-12-r267","volume":"8","author":"H Willenbrock","year":"2007","unstructured":"Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW: Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol. 2007, 8: R267-10.1186\/gb-2007-8-12-r267.","journal-title":"Genome Biol"},{"key":"10011_CR42","doi-asserted-by":"crossref","first-page":"7713","DOI":"10.1128\/JB.01043-06","volume":"188","author":"H Willenbrock","year":"2006","unstructured":"Willenbrock H, Petersen A, Sekse C, Kiil K, Wasteson Y, Ussery DW: Design of a seven-genome Escherichia coli microarray for comparative genomic profiling. J Bacteriol. 2006, 188: 7713-7721. 10.1128\/JB.01043-06.","journal-title":"J Bacteriol"},{"key":"10011_CR43","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.cccn.2005.05.041","volume":"363","author":"A Loy","year":"2006","unstructured":"Loy A, Bodrossy L: Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin Chim Acta. 2006, 363: 106-119. 10.1016\/j.cccn.2005.05.041.","journal-title":"Clin Chim Acta"},{"key":"10011_CR44","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.femsle.2005.04.002","volume":"246","author":"A Lehner","year":"2005","unstructured":"Lehner A, Loy A, Behr T, Gaenge H, Ludwig W, Wagner M, Schleifer KH: Oligonucleotide microarray for identification of Enterococcus species. FEMS Microbiol Lett. 2005, 246: 133-142. 10.1016\/j.femsle.2005.04.002.","journal-title":"FEMS Microbiol Lett"},{"key":"10011_CR45","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1128\/AEM.01177-06","volume":"73","author":"RJ Case","year":"2007","unstructured":"Case RJ, Boucher Y, Dahllof I, Holmstrom C, Doolittle WF, Kjelleberg S: Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol. 2007, 73: 278-288. 10.1128\/AEM.01177-06.","journal-title":"Appl Environ Microbiol"},{"key":"10011_CR46","doi-asserted-by":"crossref","first-page":"1831","DOI":"10.1128\/JB.185.6.1831-1840.2003","volume":"185","author":"U Dobrindt","year":"2003","unstructured":"Dobrindt U, Agerer F, Michaelis K, Janka A, Buchrieser C, Samuelson M, Svanborg C, Gottschalk G, Karch H, Hacker J: Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J Bacteriol. 2003, 185: 1831-1840. 10.1128\/JB.185.6.1831-1840.2003.","journal-title":"J Bacteriol"},{"key":"10011_CR47","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1128\/JCM.43.3.1024-1031.2005","volume":"43","author":"B Korczak","year":"2005","unstructured":"Korczak B, Frey J, Schrenzel J, Pluschke G, Pfister R, Ehricht R, Kuhnert P: Use of diagnostic microarrays for determination of virulence gene patterns of Escherichia coli K1, a major cause of neonatal meningitis. J Clin Microbiol. 2005, 43: 1024-1031. 10.1128\/JCM.43.3.1024-1031.2005.","journal-title":"J Clin Microbiol"},{"key":"10011_CR48","doi-asserted-by":"crossref","first-page":"4092","DOI":"10.1128\/JCM.43.8.4092-4106.2005","volume":"43","author":"C Pelludat","year":"2005","unstructured":"Pelludat C, Prager R, Tschape H, Rabsch W, Schuchhardt J, Hardt WD: Pilot study to evaluate microarray hybridization as a tool for Salmonella enterica serovar Typhimurium strain differentiation. J Clin Microbiol. 2005, 43: 4092-4106. 10.1128\/JCM.43.8.4092-4106.2005.","journal-title":"J Clin Microbiol"},{"key":"10011_CR49","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1111\/j.1365-2958.2006.05172.x","volume":"60","author":"T Wirth","year":"2006","unstructured":"Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, Karch H, Reeves PR, Maiden MC, Ochman H, Achtman M: Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol. 2006, 60: 1136-1151. 10.1111\/j.1365-2958.2006.05172.x.","journal-title":"Mol Microbiol"},{"key":"10011_CR50","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/nrmicro884","volume":"2","author":"U Dobrindt","year":"2004","unstructured":"Dobrindt U, Hochhut B, Hentschel U, Hacker J: Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol. 2004, 2: 414-424. 10.1038\/nrmicro884.","journal-title":"Nat Rev Microbiol"},{"key":"10011_CR51","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1099\/mic.0.27469-0","volume":"151","author":"J Hejnova","year":"2005","unstructured":"Hejnova J, Dobrindt U, Nemcova R, Rusniok C, Bomba A, Frangeul L, Hacker J, Glaser P, Sebo P, Buchrieser C: Characterization of the flexible genome complement of the commensal Escherichia coli strain A0 34\/86 (O83:K24:H31). Microbiology. 2005, 151: 385-398. 10.1099\/mic.0.27469-0.","journal-title":"Microbiology"},{"key":"10011_CR52","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/1471-2180-7-81","volume":"7","author":"S Kariyawasam","year":"2007","unstructured":"Kariyawasam S, Scaccianoce JA, Nolan LK: Common and specific genomic sequences of avian and human extraintestinal pathogenic Escherichia coli as determined by genomic subtractive hybridization. BMC Microbiol. 2007, 7: 81-10.1186\/1471-2180-7-81.","journal-title":"BMC Microbiol"},{"key":"10011_CR53","doi-asserted-by":"crossref","first-page":"2097","DOI":"10.1099\/mic.0.27499-0","volume":"151","author":"KE Rodriguez-Siek","year":"2005","unstructured":"Rodriguez-Siek KE, Giddings CW, Doetkott C, Johnson TJ, Fakhr MK, Nolan LK: Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis. Microbiology. 2005, 151: 2097-2110. 10.1099\/mic.0.27499-0.","journal-title":"Microbiology"},{"key":"10011_CR54","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1128\/IAI.01215-07","volume":"76","author":"J Zdziarski","year":"2008","unstructured":"Zdziarski J, Svanborg C, Wullt B, Hacker J, Dobrindt U: Molecular basis of commensalism in the urinary tract: low virulence or virulence attenuation?. Infect Immun. 2008, 76: 695-703. 10.1128\/IAI.01215-07.","journal-title":"Infect Immun"},{"key":"10011_CR55","first-page":"145","volume":"3","author":"IT Paulsen","year":"2001","unstructured":"Paulsen IT, Chen J, Nelson KE, Saier MH: Comparative genomics of microbial drug efflux systems. J Mol Microbiol Biotechnol. 2001, 3: 145-150.","journal-title":"J Mol Microbiol Biotechnol"},{"key":"10011_CR56","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.diagmicrobio.2005.10.019","volume":"55","author":"C Jenkins","year":"2006","unstructured":"Jenkins C, Chart H, Willshaw GA, Cheasty T, Smith HR: Genotyping of enteroaggregative Escherichia coli and identification of target genes for the detection of both typical and atypical strains. Diagn Microbiol Infect Dis. 2006, 55: 13-19. 10.1016\/j.diagmicrobio.2005.10.019.","journal-title":"Diagn Microbiol Infect Dis"},{"key":"10011_CR57","doi-asserted-by":"crossref","first-page":"2687","DOI":"10.1128\/jcm.27.12.2687-2691.1989","volume":"27","author":"MM Venkatesan","year":"1989","unstructured":"Venkatesan MM, Buysse JM, Kopecko DJ: Use of Shigella flexneri ipaC and ipaH gene sequences for the general identification of Shigella spp. and enteroinvasive Escherichia coli. J Clin Microbiol. 1989, 27: 2687-2691.","journal-title":"J Clin Microbiol"},{"key":"10011_CR58","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1016\/j.ces.2005.05.054","volume":"61","author":"HG Park","year":"2006","unstructured":"Park HG, Song JY, K.H P, Kim MH: Fluorescence-based assay formats and signal amplification strategies for DNA microarray analysis. Chem Engin Sci. 2006, 61: 954-965. 10.1016\/j.ces.2005.05.054.","journal-title":"Chem Engin Sci"},{"key":"10011_CR59","doi-asserted-by":"crossref","first-page":"163901","DOI":"10.1063\/1.2364459","volume":"89","author":"X Wang","year":"2006","unstructured":"Wang X, Cooper KL, Wang A, Xu J, Wang Z, Zhang Y, Tu Z: Label-free DNA sequence detection using oligonucleotide functionalized optical fiber. Appl Phys Lett. 2006, 89: 163901-10.1063\/1.2364459.","journal-title":"Appl Phys Lett"},{"key":"10011_CR60","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1142\/S0219720003000125","volume":"1","author":"S Rahmann","year":"2003","unstructured":"Rahmann S: Fast large scale oligonucleotide selection using the longest common factor approach. J Bioinform Comput Biol. 2003, 1: 343-361. 10.1142\/S0219720003000125.","journal-title":"J Bioinform Comput Biol"},{"key":"10011_CR61","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1109\/CSB.2002.1039329","volume":"1","author":"S Rahmann","year":"2002","unstructured":"Rahmann S: Rapid large-scale oligonucleotide selection for microarrays. Proc IEEE Comput Soc Bioinform Conf. 2002, 1: 54-63. full_text.","journal-title":"Proc IEEE Comput Soc Bioinform Conf"},{"key":"10011_CR62","doi-asserted-by":"crossref","first-page":"W535","DOI":"10.1093\/nar\/gki423","volume":"33","author":"PE Saebo","year":"2005","unstructured":"Saebo PE, Andersen SM, Myrseth J, Laerdahl JK, Rognes T: PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology. Nucleic Acids Res. 2005, 33: W535-539. 10.1093\/nar\/gki423.","journal-title":"Nucleic Acids Res"},{"key":"10011_CR63","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1093\/bioinformatics\/btg086","volume":"19","author":"X Wang","year":"2003","unstructured":"Wang X, Seed B: Selection of oligonucleotide probes for protein coding sequences. Bioinformatics. 2003, 19: 796-802. 10.1093\/bioinformatics\/btg086.","journal-title":"Bioinformatics"},{"key":"10011_CR64","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.","journal-title":"J Mol Biol"},{"key":"10011_CR65","volume-title":"Molecular cloning: a laboratory manual","author":"J Sambrook","year":"1989","unstructured":"Sambrook J, Fritsch EF, Maniatis T: Molecular cloning: a laboratory manual. 1989, Cold Spring Harbor, N. Y.: Cold Spring Harbor Laboratory, second","edition":"second"},{"key":"10011_CR66","volume-title":"R: A language and environment for statistical computing","author":"RDC Team","year":"2004","unstructured":"Team RDC: R: A language and environment for statistical computing. 2004, Vienna, Austria"},{"issue":"Suppl 1","key":"10011_CR67","doi-asserted-by":"crossref","first-page":"S96","DOI":"10.1093\/bioinformatics\/18.suppl_1.S96","volume":"18","author":"W Huber","year":"2002","unstructured":"Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M: Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002, 18 (Suppl 1): S96-104.","journal-title":"Bioinformatics"},{"key":"10011_CR68","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1198\/016214502760047131","volume":"97","author":"C Fraley","year":"2002","unstructured":"Fraley C, Raftery AE: Model-Based Clustering, Discriminant Analysis and Density Estimation. J Am Stat Assoc. 2002, 97: 611-631. 10.1198\/016214502760047131.","journal-title":"J Am Stat Assoc"},{"key":"10011_CR69","volume-title":"R package version 0993-1","author":"T Hothorn","year":"2009","unstructured":"Hothorn T, Bretz F, Westfall P, Heiberger RM: multcomp: Simultaneous Inference for General Linear Hypotheses. R package version 0993-1. 2009"},{"key":"10011_CR70","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1126\/science.277.5331.1453","volume":"277","author":"FR Blattner","year":"1997","unstructured":"Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF: The complete genome sequence of Escherichia coli K-12. Science. 1997, 277: 1453-1462. 10.1126\/science.277.5331.1453.","journal-title":"Science"},{"key":"10011_CR71","doi-asserted-by":"crossref","first-page":"2006","DOI":"10.1038\/msb4100049","volume":"2","author":"K Hayashi","year":"2006","unstructured":"Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T: Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2006, 2: 2006-0007. 10.1038\/msb4100049.","journal-title":"Mol Syst Biol"},{"key":"10011_CR72","doi-asserted-by":"crossref","first-page":"12879","DOI":"10.1073\/pnas.0603038103","volume":"103","author":"E Brzuszkiewicz","year":"2006","unstructured":"Brzuszkiewicz E, Bruggemann H, Liesegang H, Emmerth M, Olschlager T, Nagy G, Albermann K, Wagner C, Buchrieser C, Emody L: How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc Natl Acad Sci USA. 2006, 103: 12879-12884. 10.1073\/pnas.0603038103.","journal-title":"Proc Natl Acad Sci USA"},{"key":"10011_CR73","doi-asserted-by":"crossref","first-page":"5977","DOI":"10.1073\/pnas.0600938103","volume":"103","author":"SL Chen","year":"2006","unstructured":"Chen SL, Hung CS, Xu J, Reigstad CS, Magrini V, Sabo A, Blasiar D, Bieri T, Meyer RR, Ozersky P: Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci USA. 2006, 103: 5977-5982. 10.1073\/pnas.0600938103.","journal-title":"Proc Natl Acad Sci USA"},{"key":"10011_CR74","doi-asserted-by":"crossref","first-page":"17020","DOI":"10.1073\/pnas.252529799","volume":"99","author":"RA Welch","year":"2002","unstructured":"Welch RA, Burland V, Plunkett G, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J: Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA. 2002, 99: 17020-17024. 10.1073\/pnas.252529799.","journal-title":"Proc Natl Acad Sci USA"},{"key":"10011_CR75","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/35054089","volume":"409","author":"NT Perna","year":"2001","unstructured":"Perna NT, Plunkett G, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA: Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature. 2001, 409: 529-533. 10.1038\/35054089.","journal-title":"Nature"},{"key":"10011_CR76","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/dnares\/8.1.11","volume":"8","author":"T Hayashi","year":"2001","unstructured":"Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T: Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 2001, 8: 11-22. 10.1093\/dnares\/8.1.11.","journal-title":"DNA Res"},{"issue":"1","key":"10011_CR77","doi-asserted-by":"crossref","first-page":"e8801","DOI":"10.1371\/journal.pone.0008801","volume":"5","author":"Roy R. Chaudhuri","year":"2010","unstructured":"Chaudhuri RR, Sebaihia M, Hobman JL, Webber MA, Leyton DL, Goldberg MD, Cunningham AF, Scott-Tucker A, Ferguson PR, Thomas CM: Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042. PLoS One. 5: e8801-10.1371\/journal.pone.0008801.","journal-title":"PLoS ONE"},{"key":"10011_CR78","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1128\/JB.01238-08","volume":"191","author":"A Iguchi","year":"2009","unstructured":"Iguchi A, Thomson NR, Ogura Y, Saunders D, Ooka T, Henderson IR, Harris D, Asadulghani M, Kurokawa K, Dean P: Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348\/69. J Bacteriol. 2009, 191: 347-354. 10.1128\/JB.01238-08.","journal-title":"J Bacteriol"},{"key":"10011_CR79","doi-asserted-by":"crossref","first-page":"3228","DOI":"10.1128\/JB.01726-06","volume":"189","author":"TJ Johnson","year":"2007","unstructured":"Johnson TJ, Kariyawasam S, Wannemuehler Y, Mangiamele P, Johnson SJ, Doetkott C, Skyberg JA, Lynne AM, Johnson JR, Nolan LK: The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes. J Bacteriol. 2007, 189: 3228-3236. 10.1128\/JB.01726-06.","journal-title":"J Bacteriol"},{"key":"10011_CR80","doi-asserted-by":"crossref","first-page":"4432","DOI":"10.1093\/nar\/gkf566","volume":"30","author":"Q Jin","year":"2002","unstructured":"Jin Q, Yuan Z, Xu J, Wang Y, Shen Y, Lu W, Wang J, Liu H, Yang J, Yang F: Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 2002, 30: 4432-4441. 10.1093\/nar\/gkf566.","journal-title":"Nucleic Acids Res"},{"key":"10011_CR81","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1186\/1471-2164-7-173","volume":"7","author":"H Nie","year":"2006","unstructured":"Nie H, Yang F, Zhang X, Yang J, Chen L, Wang J, Xiong Z, Peng J, Sun L, Dong J: Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a. BMC Genomics. 2006, 7: 173-10.1186\/1471-2164-7-173.","journal-title":"BMC Genomics"},{"key":"10011_CR82","doi-asserted-by":"crossref","first-page":"2775","DOI":"10.1128\/IAI.71.5.2775-2786.2003","volume":"71","author":"J Wei","year":"2003","unstructured":"Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, Mayhew GF, Plunkett G, Rose DJ, Darling A: Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun. 2003, 71: 2775-2786. 10.1128\/IAI.71.5.2775-2786.2003.","journal-title":"Infect Immun"},{"key":"10011_CR83","doi-asserted-by":"crossref","first-page":"6445","DOI":"10.1093\/nar\/gki954","volume":"33","author":"F Yang","year":"2005","unstructured":"Yang F, Yang J, Zhang X, Chen L, Jiang Y, Yan Y, Tang X, Wang J, Xiong Z, Dong J: Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 2005, 33: 6445-6458. 10.1093\/nar\/gki954.","journal-title":"Nucleic Acids Res"},{"key":"10011_CR84","doi-asserted-by":"crossref","first-page":"4974","DOI":"10.1093\/nar\/28.24.4974","volume":"28","author":"M McClelland","year":"2000","unstructured":"McClelland M, Florea L, Sanderson K, Clifton SW, Parkhill J, Churcher C, Dougan G, Wilson RK, Miller W: Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. Nucleic Acids Res. 2000, 28: 4974-4986. 10.1093\/nar\/28.24.4974.","journal-title":"Nucleic Acids Res"},{"key":"10011_CR85","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1038\/ng1470","volume":"36","author":"M McClelland","year":"2004","unstructured":"McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P, McLellan M: Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat Genet. 2004, 36: 1268-1274. 10.1038\/ng1470.","journal-title":"Nat Genet"},{"key":"10011_CR86","doi-asserted-by":"crossref","first-page":"1690","DOI":"10.1093\/nar\/gki297","volume":"33","author":"CH Chiu","year":"2005","unstructured":"Chiu CH, Tang P, Chu C, Hu S, Bao Q, Yu J, Chou YY, Wang HS, Lee YS: The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Res. 2005, 33: 1690-1698. 10.1093\/nar\/gki297.","journal-title":"Nucleic Acids Res"},{"key":"10011_CR87","doi-asserted-by":"crossref","first-page":"2330","DOI":"10.1128\/JB.185.7.2330-2337.2003","volume":"185","author":"W Deng","year":"2003","unstructured":"Deng W, Liou SR, Plunkett G, Mayhew GF, Rose DJ, Burland V, Kodoyianni V, Schwartz DC, Blattner FR: Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol. 2003, 185: 2330-2337. 10.1128\/JB.185.7.2330-2337.2003.","journal-title":"J Bacteriol"},{"key":"10011_CR88","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1038\/35101607","volume":"413","author":"J Parkhill","year":"2001","unstructured":"Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT: Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature. 2001, 413: 848-852. 10.1038\/35101607.","journal-title":"Nature"},{"key":"10011_CR89","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/35101614","volume":"413","author":"M McClelland","year":"2001","unstructured":"McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F: Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature. 2001, 413: 852-856. 10.1038\/35101614.","journal-title":"Nature"},{"key":"10011_CR90","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/35097083","volume":"413","author":"J Parkhill","year":"2001","unstructured":"Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL: Genome sequence of Yersinia pestis, the causative agent of plague. Nature. 2001, 413: 523-527. 10.1038\/35097083.","journal-title":"Nature"},{"key":"10011_CR91","doi-asserted-by":"crossref","first-page":"4601","DOI":"10.1128\/JB.184.16.4601-4611.2002","volume":"184","author":"W Deng","year":"2002","unstructured":"Deng W, Burland V, Plunkett G, Boutin A, Mayhew GF, Liss P, Perna NT, Rose DJ, Mau B, Zhou S: Genome sequence of Yersinia pestis KIM. J Bacteriol. 2002, 184: 4601-4611. 10.1128\/JB.184.16.4601-4611.2002.","journal-title":"J Bacteriol"},{"key":"10011_CR92","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1093\/dnares\/11.3.179","volume":"11","author":"Y Song","year":"2004","unstructured":"Song Y, Tong Z, Wang J, Wang L, Guo Z, Han Y, Zhang J, Pei D, Zhou D, Qin H: Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. DNA Res. 2004, 11: 179-197. 10.1093\/dnares\/11.3.179.","journal-title":"DNA Res"},{"key":"10011_CR93","doi-asserted-by":"crossref","first-page":"4453","DOI":"10.1128\/JB.00124-06","volume":"188","author":"PS Chain","year":"2006","unstructured":"Chain PS, Hu P, Malfatti SA, Radnedge L, Larimer F, Vergez LM, Worsham P, Chu MC, Andersen GL: Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J Bacteriol. 2006, 188: 4453-4463. 10.1128\/JB.00124-06.","journal-title":"J Bacteriol"},{"key":"10011_CR94","doi-asserted-by":"crossref","first-page":"e206","DOI":"10.1371\/journal.pgen.0020206","volume":"2","author":"NR Thomson","year":"2006","unstructured":"Thomson NR, Howard S, Wren BW, Holden MT, Crossman L, Challis GL, Churcher C, Mungall K, Brooks K, Chillingworth T: The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS Genet. 2006, 2: e206-10.1371\/journal.pgen.0020206.","journal-title":"PLoS Genet"},{"key":"10011_CR95","doi-asserted-by":"crossref","first-page":"2597","DOI":"10.1128\/JB.01695-07","volume":"190","author":"T Durfee","year":"2008","unstructured":"Durfee T, Nelson R, Baldwin S, Plunkett G, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M: The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol. 2008, 190: 2597-2606. 10.1128\/JB.01695-07.","journal-title":"J Bacteriol"},{"key":"10011_CR96","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1093\/dnares\/dsn026","volume":"15","author":"K Oshima","year":"2008","unstructured":"Oshima K, Toh H, Ogura Y, Sasamoto H, Morita H, Park SH, Ooka T, Iyoda S, Taylor TD, Hayashi T: Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Res. 2008, 15: 375-386. 10.1093\/dnares\/dsn026.","journal-title":"DNA Res"},{"key":"10011_CR97","doi-asserted-by":"crossref","first-page":"1624","DOI":"10.1101\/gr.077404.108","volume":"18","author":"NR Thomson","year":"2008","unstructured":"Thomson NR, Clayton DJ, Windhorst D, Vernikos G, Davidson S, Churcher C, Quail MA, Stevens M, Jones MA, Watson M: Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287\/91 provides insights into evolutionary and host adaptation pathways. Genome Res. 2008, 18: 1624-1637. 10.1101\/gr.077404.108.","journal-title":"Genome Res"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-11-591.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2164-11-591\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-11-591.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T12:58:20Z","timestamp":1630501100000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-11-591"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,10,21]]},"references-count":97,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["10011"],"URL":"https:\/\/doi.org\/10.1186\/1471-2164-11-591","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,10,21]]},"assertion":[{"value":"25 February 2010","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 October 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 October 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"591"}}