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Improved analytical methods for microarray-based genome-composition analysis
Charles C Kim, Elizabeth A Joyce, Kaman Chan, Stanley Falkow
Genome Biol. 2002; 3(11): research0065.1–research0065.17. Published online 2002 October 29.
PMCID:
PMC133449
Abstract Full Text PDF–506K Supplementary Material

Is Cited by the Following 48 Articles in this Archive:

Salmonella Enteritidis Strains from Poultry Exhibit Differential Responses to Acid Stress, Oxidative Stress, and Survival in the Egg Albumen
Devendra H. Shah, Carol Casavant, Quincy Hawley, Tarek Addwebi, Douglas R. Call, Jean Guard
Foodborne Pathog Dis. 2012 March; 9(3): 258–264. doi: 10.1089/fpd.2011.1009
PMCID:
PMC3326446
Free in PMC on 2013/03/01
Analysis of Ultra Low Genome Conservation in Clostridium difficile
Joy Scaria, Lalit Ponnala, Tavan Janvilisri, Weiwei Yan, Lukas A. Mueller, Yung-Fu Chang
PLoS One. 2010; 5(12): e15147. Published online 2010 December 8. doi: 10.1371/journal.pone.0015147
PMCID:
PMC2999544
Abstract Full Text PDF–821K Supplementary Material
Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization
Richard A Lewis, Emma Laing, Nicholas Allenby, Giselda Bucca, Volker Brenner, Marcus Harrison, Andrzej M Kierzek, Colin P Smith
BMC Genomics. 2010; 11: 682. Published online 2010 December 1. doi: 10.1186/1471-2164-11-682
PMCID:
PMC3017869
Abstract Full Text PDF–1.8M Supplementary Material
Genetic diversity in Campylobacter jejuni is associated with differential colonization of broiler chickens and C57BL/6J IL10-deficient mice
David L. Wilson, Vijay A. K. Rathinam, Weihong Qi, Lukas M. Wick, Jeff Landgraf, Julia A. Bell, Anne Plovanich-Jones, Jodi Parrish, Russell L. Finley, Linda S. Mansfield, John E. Linz
Microbiology. 2010 July; 156(Pt 7): 2046–2057. doi: 10.1099/mic.0.035717-0
PMCID:
PMC3068676
Abstract Full Text PDF–654K
Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila
Suzy CP Renn, Heather E Machado, Albyn Jones, Kosha Soneji, Rob J Kulathinal, Hans A Hofmann
BMC Genomics. 2010; 11: 271. Published online 2010 April 29. doi: 10.1186/1471-2164-11-271
PMCID:
PMC2873954
Abstract Full Text PDF–1.5M Supplementary Material
Evaluating the Performance of Oligonucleotide Microarrays for Bacterial Strains with Increasing Genetic Divergence from the Reference Strain
Seungdae Oh, Deborah R. Yoder-Himes, James Tiedje, Joonhong Park, Konstantinos T. Konstantinidis
Appl Environ Microbiol. 2010 May; 76(9): 2980–2988. Published online 2010 March 12. doi: 10.1128/AEM.02826-09
PMCID:
PMC2863436
Abstract Full Text PDF–924K
Genome Sequence of Cronobacter sakazakii BAA-894 and Comparative Genomic Hybridization Analysis with Other Cronobacter Species
Eva Kucerova, Sandra W. Clifton, Xiao-Qin Xia, Fred Long, Steffen Porwollik, Lucinda Fulton, Catrina Fronick, Patrick Minx, Kim Kyung, Wesley Warren, Robert Fulton, Dongyan Feng, Aye Wollam, Neha Shah, Veena Bhonagiri, William E. Nash, Kymberlie Hallsworth-Pepin, Richard K. Wilson, Michael McClelland, Stephen J. Forsythe
PLoS One. 2010; 5(3): e9556. Published online 2010 March 8. doi: 10.1371/journal.pone.0009556
PMCID:
PMC2833190
Abstract Full Text PDF–560K Supplementary Material
New methods to analyse microarray data that partially lack a reference signal
Neeltje Carpaij, Ad C Fluit, Jodi A Lindsay, Marc JM Bonten, Rob JL Willems
BMC Genomics. 2009; 10: 522. Published online 2009 November 13. doi: 10.1186/1471-2164-10-522
PMCID:
PMC2779823
Abstract Full Text PDF–303K
Highly Penicillin-Resistant Multidrug-Resistant Pneumococcus-Like Strains Colonizing Children in Oeiras, Portugal: Genomic Characteristics and Implications for Surveillance
Alexandra S. Simões, Raquel Sá-Leão, Marc J. Eleveld, Débora A. Tavares, João A. Carriço, Hester J. Bootsma, Peter W. M. Hermans
J Clin Microbiol. 2010 January; 48(1): 238–246. Published online 2009 November 11. doi: 10.1128/JCM.01313-09
PMCID:
PMC2812262
Abstract Full Text PDF–734K Supplementary Material
Two distinct groups of porcine enteropathogenic Escherichia coli strains of serogroup O45 are revealed by comparative genomic hybridization and virulence gene microarray
Guillaume Bruant, Yongxiang Zhang, Philippe Garneau, Justin Wong, Chad Laing, John M Fairbrother, Victor PJ Gannon, Josée Harel
BMC Genomics. 2009; 10: 402. Published online 2009 August 26. doi: 10.1186/1471-2164-10-402
PMCID:
PMC2749873
Abstract Full Text PDF–342K Supplementary Material
Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens
Leighton Pritchard, Hui Liu, Clare Booth, Emma Douglas, Patrice François, Jacques Schrenzel, Peter E. Hedley, Paul R. J. Birch, Ian K. Toth
PLoS Comput Biol. 2009 August; 5(8): e1000473. Published online 2009 August 21. doi: 10.1371/journal.pcbi.1000473
PMCID:
PMC2718846
Abstract Full Text PDF–874K Supplementary Material
Identification of a Modular Pathogenicity Island That Is Widespread among Urease-Producing Uropathogens and Shares Features with a Diverse Group of Mobile Elements
Erika L. Flannery, Lona Mody, Harry L. T. Mobley
Infect Immun. 2009 November; 77(11): 4887–4894. Published online 2009 August 17. doi: 10.1128/IAI.00705-09
PMCID:
PMC2772549
Abstract Full Text PDF–3.0M
Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex
Galeb S Abu-Ali, David W Lacher, Lukas M Wick, Weihong Qi, Thomas S Whittam
BMC Genomics. 2009; 10: 296. Published online 2009 July 3. doi: 10.1186/1471-2164-10-296
PMCID:
PMC2713265
Abstract Full Text PDF–813K Supplementary Material
Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)
Roy R Chaudhuri, Andrew G Allen, Paul J Owen, Gil Shalom, Karl Stone, Marcus Harrison, Timothy A Burgis, Michael Lockyer, Jorge Garcia-Lara, Simon J Foster, Stephen J Pleasance, Sarah E Peters, Duncan J Maskell, Ian G Charles
BMC Genomics. 2009; 10: 291. Published online 2009 July 1. doi: 10.1186/1471-2164-10-291
PMCID:
PMC2721850
Abstract Full Text PDF–484K Supplementary Material
Microarray Identification of Clostridium difficile Core Components and Divergent Regions Associated with Host Origin
Tavan Janvilisri, Joy Scaria, Angela D. Thompson, Ainsley Nicholson, Brandi M. Limbago, Luis G. Arroyo, J. Glenn Songer, Yrjö T. Gröhn, Yung-Fu Chang
J Bacteriol. 2009 June; 191(12): 3881–3891. Published online 2009 April 17. doi: 10.1128/JB.00222-09
PMCID:
PMC2698405
Abstract Full Text PDF–1.9M Supplementary Material
Multiple factors interact to produce responses resembling spectrum of human disease in Campylobacter jejuni infected C57BL/6 IL-10-/- mice
Julia A Bell, Jessica L St Charles, Alice J Murphy, Vijay AK Rathinam, Anne E Plovanich-Jones, Erin L Stanley, John E Wolf, Jenna R Gettings, Thomas S Whittam, Linda S Mansfield
BMC Microbiol. 2009; 9: 57. Published online 2009 March 18. doi: 10.1186/1471-2180-9-57
PMCID:
PMC2669091
Abstract Full Text PDF–969K Supplementary Material
Comparative Genomic Hybridization Analysis of Two Predominant Nordic Group I (Proteolytic) Clostridium botulinum Type B Clusters
Miia Lindström, Katja Hinderink, Panu Somervuo, Katri Kiviniemi, Mari Nevas, Ying Chen, Petri Auvinen, Andrew T. Carter, David R. Mason, Michael W. Peck, Hannu Korkeala
Appl Environ Microbiol. 2009 May; 75(9): 2643–2651. Published online 2009 March 6. doi: 10.1128/AEM.02557-08
PMCID:
PMC2681723
Abstract Full Text PDF–399K Supplementary Material
Genomic analysis of an emerging multiresistant Staphylococcus aureus strain rapidly spreading in cystic fibrosis patients revealed the presence of an antibiotic inducible bacteriophage
Jean-Marc Rolain, Patrice François, David Hernandez, Fadi Bittar, Hervé Richet, Ghislain Fournous, Yves Mattenberger, Emmanuelle Bosdure, Nathalie Stremler, Jean-Christophe Dubus, Jacques Sarles, Martine Reynaud-Gaubert, Stephanie Boniface, Jacques Schrenzel, Didier Raoult
Biol Direct. 2009; 4: 1. Published online 2009 January 13. doi: 10.1186/1745-6150-4-1
PMCID:
PMC2629466
Abstract Full Text PDF–1.3M Supplementary Material
Characterization of the Genomes of a Diverse Collection of Salmonella enterica Serovar Typhimurium Definitive Phage Type 104
Fiona J. Cooke, Derek J. Brown, Maria Fookes, Derek Pickard, Alasdair Ivens, John Wain, Mark Roberts, Robert A. Kingsley, Nicholas R. Thomson, Gordon Dougan
J Bacteriol. 2008 December; 190(24): 8155–8162. Published online 2008 October 10. doi: 10.1128/JB.00636-08
PMCID:
PMC2593209
Abstract Full Text PDF–696K
Genomic Diversity within the Enterobacter cloacae Complex
Armand Paauw, Martien P. M. Caspers, Frank H. J. Schuren, Maurine A. Leverstein-van Hall, Alexis Delétoile, Roy C. Montijn, Jan Verhoef, Ad C. Fluit
PLoS ONE. 2008; 3(8): e3018. Published online 2008 August 21. doi: 10.1371/journal.pone.0003018
PMCID:
PMC2515634
Abstract Full Text PDF–333K Supplementary Material
Optimal control and analysis of two-color genomotyping experiments using bacterial multistrain arrays
Francisco R Pinto, Sandra I Aguiar, J Melo-Cristino, Mário Ramirez
BMC Genomics. 2008; 9: 230. Published online 2008 May 19. doi: 10.1186/1471-2164-9-230
PMCID:
PMC2410139
Abstract Full Text PDF–267K Supplementary Material
A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes
Ben Carter, Guanghui Wu, Martin J Woodward, Muna F Anjum
BMC Genomics. 2008; 9: 53. Published online 2008 January 29. doi: 10.1186/1471-2164-9-53
PMCID:
PMC2262894
Abstract Full Text PDF–1.1M
Comparative Genomic Analysis Using Microarray Demonstrates a Strong Correlation between the Presence of the 80-Kilobase Pathogenicity Island and Pathogenicity in Kanagawa Phenomenon-Positive Vibrio parahaemolyticus Strains
Kaori Izutsu, Ken Kurokawa, Kosuke Tashiro, Satoru Kuhara, Tetsuya Hayashi, Takeshi Honda, Tetsuya Iida
Infect Immun. 2008 March; 76(3): 1016–1023. Published online 2008 January 14. doi: 10.1128/IAI.01535-07
PMCID:
PMC2258825
Abstract Full Text PDF–1.0M Supplementary Material
Comparative genomic analysis of Tropheryma whipplei strains reveals that diversity among clinical isolates is mainly related to the WiSP proteins
My-Van La, Nicolas Crapoulet, Pascal Barbry, Didier Raoult, Patricia Renesto
BMC Genomics. 2007; 8: 349. Published online 2007 October 2. doi: 10.1186/1471-2164-8-349
PMCID:
PMC2078596
Abstract Full Text PDF–440K Supplementary Material
Microarray Analysis of Escherichia coli Strains from Interstitial Beach Waters of Lake Huron (Canada)
T. Kon, S. C. Weir, J. T. Trevors, H. Lee, J. Champagne, L. Meunier, R. Brousseau, L. Masson
Appl Environ Microbiol. 2007 December; 73(23): 7757–7758. Published online 2007 September 21. doi: 10.1128/AEM.01333-07
PMCID:
PMC2168082
Abstract Full Text PDF–145K
Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes
Yoshitoshi Ogura, Tadasuke Ooka, Asadulghani, Jun Terajima, Jean-Philippe Nougayrède, Ken Kurokawa, Kousuke Tashiro, Toru Tobe, Keisuke Nakayama, Satoru Kuhara, Eric Oswald, Haruo Watanabe, Tetsuya Hayashi
Genome Biol. 2007; 8(7): R138. Published online 2007 July 10. doi: 10.1186/gb-2007-8-7-r138
PMCID:
PMC2323221
Abstract Full Text PDF–1.5M Supplementary Material
Genome evolution in major Escherichia coli O157:H7 lineages
Yongxiang Zhang, Chad Laing, Marina Steele, Kim Ziebell, Roger Johnson, Andrew K Benson, Eduardo Taboada, Victor PJ Gannon
BMC Genomics. 2007; 8: 121. Published online 2007 May 16. doi: 10.1186/1471-2164-8-121
PMCID:
PMC1890555
Abstract Full Text PDF–674K Supplementary Material
Genetic Analysis of Helicobacter pylori Strain Populations Colonizing the Stomach at Different Times Postinfection
Nina R. Salama, Gerardo Gonzalez-Valencia, Brooke Deatherage, Francisco Aviles-Jimenez, John C. Atherton, David Y. Graham, Javier Torres
J Bacteriol. 2007 May; 189(10): 3834–3845. Published online 2007 March 2. doi: 10.1128/JB.01696-06
PMCID:
PMC1913316
Abstract Full Text PDF–390K Supplementary Material
Comparative Transcriptional Analysis of Human Macrophages Exposed to Animal and Human Isolates of Mycobacterium avium Subspecies paratuberculosis with Diverse Genotypes
Alifiya S. Motiwala, Harish K. Janagama, Michael L. Paustian, Xiaochun Zhu, John P. Bannantine, Vivek Kapur, Srinand Sreevatsan
Infect Immun. 2006 November; 74(11): 6046–6056. doi: 10.1128/IAI.00326-06
PMCID:
PMC1695517
Abstract Full Text PDF–842K Supplementary Material
Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial
Daniel G Lee, Jonathan M Urbach, Gang Wu, Nicole T Liberati, Rhonda L Feinbaum, Sachiko Miyata, Lenard T Diggins, Jianxin He, Maude Saucier, Eric Déziel, Lisa Friedman, Li Li, George Grills, Kate Montgomery, Raju Kucherlapati, Laurence G Rahme, Frederick M Ausubel
Genome Biol. 2006; 7(10): R90. Published online 2006 October 12. doi: 10.1186/gb-2006-7-10-r90
PMCID:
PMC1794565
Abstract Full Text PDF–769K Supplementary Material
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