Studying bacterial transcriptomes using RNA-seq von Croucher, Nicholas J, Thomson, Nicholas R

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Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China von Zhou, Kai, Xiao, Tingting, David, Sophia, Wang, Qin, Zhou, Yanzi, Guo, Lihua, Aanensen, David, Holt, Kathryn E, Thomson, Nicholas R, Grundmann, Hajo, Shen, Ping, Xiao, Yonghong

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'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution von McNally, Alan, Thomson, Nicholas R., Reuter, Sandra, Wren, Brendan W.

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The genomic signatures of Shigella evolution, adaptation and geographical spread von The, Hao Chung, Thanh, Duy Pham, Holt, Kathryn E., Thomson, Nicholas R., Baker, Stephen

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Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences von Blackwell, Grace A, Hunt, Martin, Malone, Kerri M, Lima, Leandro, Horesh, Gal, Alako, Blaise T F, Thomson, Nicholas R, Iqbal, Zamin

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Panakeia - a universal tool for bacterial pangenome analysis von Beier, Sina, Thomson, Nicholas R

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Evidence for several waves of global transmission in the seventh cholera pandemic von Mutreja, Ankur, Kim, Dong Wook, Thomson, Nicholas R., Connor, Thomas R., Lee, Je Hee, Kariuki, Samuel, Croucher, Nicholas J., Choi, Seon Young, Harris, Simon R., Lebens, Michael, Niyogi, Swapan Kumar, Kim, Eun Jin, Ramamurthy, T., Chun, Jongsik, Wood, James L. N., Clemens, John D., Czerkinsky, Cecil, Nair, G. Balakrish, Holmgren, Jan, Parkhill, Julian, Dougan, Gordon

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Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients von Gorrie, Claire L., Mirčeta, Mirjana, Wick, Ryan R., Edwards, David J., Thomson, Nicholas R., Strugnell, Richard A., Pratt, Nigel F., Garlick, Jill S., Watson, Kerri M., Pilcher, David V., McGloughlin, Steve A., Spelman, Denis W., Jenney, Adam W. J., Holt, Kathryn E.

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Patterns of genome evolution that have accompanied host adaptation in Salmonella von Langridge, Gemma C, Fookes, Maria, Connor, Thomas R, Feltwell, Theresa, Feasey, Nicholas, Parsons, Bryony N, Seth-Smith, Helena M B, Barquist, Lars, Stedman, Anna, Humphrey, Tom, Wigley, Paul, Peters, Sarah E, Maskell, Duncan J, Corander, Jukka, Chabalgoity, Jose A, Barrow, Paul, Parkhill, Julian, Dougan, Gordon, Thomson, Nicholas R

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A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi von Perkins, Timothy T, Kingsley, Robert A, Fookes, Maria C, Gardner, Paul P, James, Keith D, Yu, Lu, Assefa, Samuel A, He, Miao, Croucher, Nicholas J, Pickard, Derek J, Maskell, Duncan J, Parkhill, Julian, Choudhary, Jyoti, Thomson, Nicholas R, Dougan, Gordon

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Identification of Klebsiella capsule synthesis loci from whole genome data von Wyres, Kelly L, Wick, Ryan R, Gorrie, Claire, Jenney, Adam, Follador, Rainer, Thomson, Nicholas R, Holt, Kathryn E

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Genomic epidemiology of Vibrio cholerae during a mass vaccination campaign of displaced communities in Bangladesh von Taylor-Brown, Alyce, Afrad, Mokibul Hassan, Khan, Ashraful Islam, Lassalle, Florent, Islam, Md. Taufiqul, Tanvir, Nabid Anjum, Thomson, Nicholas R., Qadri, Firdausi

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Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages von Beale, Mathew A., Marks, Michael, Sahi, Sharon K., Tantalo, Lauren C., Nori, Achyuta V., French, Patrick, Lukehart, Sheila A., Marra, Christina M., Thomson, Nicholas R.

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Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis von Arnvig, Kristine B, Comas, Iñaki, Thomson, Nicholas R, Houghton, Joanna, Boshoff, Helena I, Croucher, Nicholas J, Rose, Graham, Perkins, Timothy T, Parkhill, Julian, Dougan, Gordon, Young, Douglas B

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Antagonistic coevolution accelerates molecular evolution von Brockhurst, Michael A, Paterson, Steve, Vogwill, Tom, Buckling, Angus, Benmayor, Rebecca, Spiers, Andrew J, Thomson, Nicholas R, Quail, Mike, Smith, Frances, Walker, Danielle, Libberton, Ben, Fenton, Andrew, Hall, Neil

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Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in Northeast Thailand von Seng, Rathanin, Chomkatekaew, Chalita, Tandhavanant, Sarunporn, Saiprom, Natnaree, Phunpang, Rungnapa, Thaipadungpanit, Janjira, Batty, Elizabeth M., Day, Nicholas P. J., Chantratita, Wasun, West, T. Eoin, Thomson, Nicholas R., Parkhill, Julian, Chewapreecha, Claire, Chantratita, Narisara

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Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia von Wyres, Kelly L, Nguyen, To N T, Lam, Margaret M C, Judd, Louise M, van Vinh Chau, Nguyen, Dance, David A B, Ip, Margaret, Karkey, Abhilasha, Ling, Clare L, Miliya, Thyl, Newton, Paul N, Lan, Nguyen Phu Huong, Sengduangphachanh, Amphone, Turner, Paul, Veeraraghavan, Balaji, Vinh, Phat Voong, Vongsouvath, Manivanh, Thomson, Nicholas R, Baker, Stephen, Holt, Kathryn E

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Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen von Gorrie, Claire L., Mirčeta, Mirjana, Wick, Ryan R., Judd, Louise M., Lam, Margaret M. C., Gomi, Ryota, Abbott, Iain J., Thomson, Nicholas R., Strugnell, Richard A., Pratt, Nigel F., Garlick, Jill S., Watson, Kerrie M., Hunter, Peter C., Pilcher, David V., McGloughlin, Steve A., Spelman, Denis W., Wyres, Kelly L., Jenney, Adam W. J., Holt, Kathryn E.

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Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae von Stecher, Bärbel, Denzler, Rémy, Maier, Lisa, Bernet, Florian, Sanders, Mandy J., Pickard, Derek J., Barthel, Manja, Westendorf, Astrid M., Krogfelt, Karen A., Walker, Alan W., Ackermann, Martin, Dobrindt, Ulrich, Thomson, Nicholas R., Hardt, Wolf-Dietrich

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Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital von Gorrie, Claire L, Mirceta, Mirjana, Wick, Ryan R, Judd, Louise M, Wyres, Kelly L, Thomson, Nicholas R, Strugnell, Richard A, Pratt, Nigel F, Garlick, Jill S, Watson, Kerrie M, Hunter, Peter C, McGloughlin, Steve A, Spelman, Denis W, Jenney, Adam W J, Holt, Kathryn E

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