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Select item 25662211.

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

David A. Rasko, M. J. Rosovitz, Garry S. A. Myers, Emmanuel F. Mongodin, W. Florian Fricke, Pawel Gajer, Jonathan Crabtree, Mohammed Sebaihia, Nicholas R. Thomson, Roy Chaudhuri, Ian R. Henderson, Vanessa Sperandio, Jacques Ravel

J Bacteriol. 2008 Oct; 190(20): 6881–6893. Published online 2008 Aug 1. doi: 10.1128/JB.00619-08

PMCID:: PMC2566221

Abstract Article PDF–1.5M

Select item 68929152.

The Escherichia coli transcriptome mostly consists of independently regulated modules

Anand V. Sastry, Ye Gao, Richard Szubin, Ying Hefner, Sibei Xu, Donghyuk Kim, Kumari Sonal Choudhary, Laurence Yang, Zachary A. King, Bernhard O. Palsson

Nat Commun. 2019; 10: 5536. Published online 2019 Dec 4. doi: 10.1038/s41467-019-13483-w

PMCID:: PMC6892915

Abstract Article PDF–1.8M

Select item 68373863.

Comparative distribution of extended-spectrum beta-lactamase–producing Escherichia coli from urine infections and environmental waters

Anna Fagerström, Paula Mölling, Faisal Ahmad Khan, Martin Sundqvist, Jana Jass, Bo Söderquist

PLoS One. 2019; 14(11): e0224861. Published online 2019 Nov 7. doi: 10.1371/journal.pone.0224861

PMCID:: PMC6837386

Abstract Article PDF–2.0M

Select item 67137064.

Interrogation of a live-attenuated enterotoxigenic Escherichia coli vaccine highlights features unique to wild-type infection

Subhra Chakraborty, Arlo Randall, Tim J. Vickers, Doug Molina, Clayton D. Harro, Barbara DeNearing, Jessica Brubaker, David A. Sack, A. Louis Bourgeois, Philip L. Felgner, Xiaowu Liang, Sachin Mani, Heather Wenzel, R. Reid Townsend, Petra E. Gilmore, Michael J. Darsley, David A. Rasko, James M. Fleckenstein

NPJ Vaccines. 2019; 4: 37. Published online 2019 Aug 28. doi: 10.1038/s41541-019-0131-7

PMCID:: PMC6713706

Abstract Article PDF–2.0M

Select item 65621415.

Virulence behavior of uropathogenic Escherichia coli strains in the host model Caenorhabditis elegans

Emily Schifano, Massimiliano Marazzato, Maria Grazia Ammendolia, Elena Zanni, Marta Ricci, Antonella Comanducci, Paola Goldoni, Maria Pia Conte, Daniela Uccelletti, Catia Longhi

Microbiologyopen. 2019 Jun; 8(6): e00756. Published online 2018 Oct 31. doi: 10.1002/mbo3.756

PMCID:: PMC6562141

Abstract Article PDF–841K

Select item 63267886.

BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site

Julia Gordeeva, Natalya Morozova, Nicolas Sierro, Artem Isaev, Tomas Sinkunas, Ksenia Tsvetkova, Mikhail Matlashov, Lidija Truncaitė, Richard D Morgan, Nikolai V Ivanov, Virgis Siksnys, Lanying Zeng, Konstantin Severinov

Nucleic Acids Res. 2019 Jan 10; 47(1): 253–265. Published online 2018 Nov 12. doi: 10.1093/nar/gky1125

PMCID:: PMC6326788

Abstract Article PDF–3.7M

Select item 62195847.

Abundant production of exopolysaccharide by EAEC strains enhances the formation of bacterial biofilms in contaminated sprouts

Quintin Borgersen, David T. Bolick, Glynis L. Kolling, Matthew Aijuka, Fernando Ruiz-Perez, Richard L. Guerrant, James P. Nataro, Araceli E. Santiago

Gut Microbes. 2018; 9(3): 264–278. Published online 2018 Apr 19. doi: 10.1080/19490976.2018.1429877

PMCID:: PMC6219584

Abstract Article PDF–1.9M

Select item 58884118.

Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code

Claude Kwe Yinda, Stephen Mbigha Ghogomu, Nádia Conceição-Neto, Leen Beller, Ward Deboutte, Emiel Vanhulle, Piet Maes, Marc Van Ranst, Jelle Matthijnssens

Virus Evol. 2018 Jan; 4(1): vey008. Published online 2018 Mar 30. doi: 10.1093/ve/vey008

PMCID:: PMC5888411

Abstract Article PDF–3.1M

Select item 58866879.

The CSR-1 endogenous RNAi pathway ensures accurate transcriptional reprogramming during the oocyte-to-embryo transition in Caenorhabditis elegans

Christina Fassnacht, Cristina Tocchini, Pooja Kumari, Dimos Gaidatzis, Michael B. Stadler, Rafal Ciosk

PLoS Genet. 2018 Mar; 14(3): e1007252. Published online 2018 Mar 26. doi: 10.1371/journal.pgen.1007252

PMCID:: PMC5886687

Abstract Article PDF–8.0M

Select item 563517110.

Alterations of c‐di‐GMP turnover proteins modulate semi‐constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli

Annika Cimdins, Roger Simm, Fengyang Li, Petra Lüthje, Kaisa Thorell, Åsa Sjöling, Annelie Brauner, Ute Römling

Microbiologyopen. 2017 Oct; 6(5): e00508. Published online 2017 Sep 15. doi: 10.1002/mbo3.508

PMCID:: PMC5635171

Abstract Article PDF–1.2M

Select item 522830711.

Overcoming Enterotoxigenic Escherichia coli Pathogen Diversity: Translational Molecular Approaches to Inform Vaccine Design

James M. Fleckenstein, David A. Rasko

Methods Mol Biol. Author manuscript; available in PMC 2017 Jan 12.

Published in final edited form as: Methods Mol Biol. 2016; 1403: 363–383. doi: 10.1007/978-1-4939-3387-7_19

PMCID:: PMC5228307

Abstract Article PDF–530K

Select item 506715512.

Genomic diversity of EPEC associated with clinical presentations of differing severity

Tracy H. Hazen, Michael S. Donnenberg, Sandra Panchalingam, Martin Antonio, Anowar Hossain, Inacio Mandomando, John Benjamin Ochieng, Thandavarayan Ramamurthy, Boubou Tamboura, Shahida Qureshi, Farheen Quadri, Anita Zaidi, Karen L. Kotloff, Myron M. Levine, Eileen M. Barry, James B. Kaper, David A. Rasko, James P. Nataro

Nat Microbiol. Author manuscript; available in PMC 2016 Oct 17.

Published in final edited form as: Nat Microbiol. 2016 Jan 18; 1: 15014. Published online 2016 Jan 18. doi: 10.1038/nmicrobiol.2015.14

PMCID:: PMC5067155

Abstract Article PDF–1.2M

Select item 502504513.

XRN2 Autoregulation and Control of Polycistronic Gene Expresssion in Caenorhabditis elegans

Takashi S. Miki, Sarah H. Carl, Michael B. Stadler, Helge Großhans

PLoS Genet. 2016 Sep; 12(9): e1006313. Published online 2016 Sep 15. doi: 10.1371/journal.pgen.1006313

PMCID:: PMC5025045

Abstract Article PDF–10M

Select item 484671714.

Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction

Payam Behzadi, Ali Najafi, Elham Behzadi, Reza Ranjbar

Cent European J Urol. 2016; 69(1): 105–111. Published online 2016 Jan 18. doi: 10.5173/ceju.2016.654

PMCID:: PMC4846717

Abstract Article PDF–573K

Select item 471204415.

Simultaneous generation of many RNA-seq libraries in a single reaction

Alexander A Shishkin, Georgia Giannoukos, Alper Kucukural, Dawn Ciulla, Michele Busby, Christine Surka, Jenny Chen, Roby P Bhattacharyya, Robert F Rudy, Milesh M Patel, Nathaniel Novod, Deborah T Hung, Andreas Gnirke, Manuel Garber, Mitchell Guttman, Jonathan Livny

Nat Methods. Author manuscript; available in PMC 2016 Jan 13.

Published in final edited form as: Nat Methods. 2015 Apr; 12(4): 323–325. Published online 2015 Mar 2. doi: 10.1038/nmeth.3313

PMCID:: PMC4712044

Abstract Article PDF–404K

Select item 464770916.

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads

Xiao Zhu, Henry C. M. Leung, Rongjie Wang, Francis Y. L. Chin, Siu Ming Yiu, Guangri Quan, Yajie Li, Rui Zhang, Qinghua Jiang, Bo Liu, Yucui Dong, Guohui Zhou, Yadong Wang

BMC Bioinformatics. 2015; 16: 386. Published online 2015 Nov 16. doi: 10.1186/s12859-015-0818-3

PMCID:: PMC4647709

Abstract Article PDF–1.6M

Select item 457878117.

Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033

Canying Liu, Huajun Zheng, Minjun Yang, Zhuofei Xu, Xiangru Wang, Liuya Wei, Biao Tang, Feng Liu, Yanyan Zhang, Yi Ding, Xibiao Tang, Bin Wu, Timothy J. Johnson, Huanchun Chen, Chen Tan

BMC Genomics. 2015; 16(1): 717. Published online 2015 Sep 21. doi: 10.1186/s12864-015-1890-9

PMCID:: PMC4578781

Abstract Article PDF–2.2M

Select item 450957418.

Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis

Yuanhao Zhang, Leahana Rowehl, Julia M. Krumsiek, Erika P. Orner, Nurmohammad Shaikh, Phillip I. Tarr, Erica Sodergren, George M. Weinstock, Edgar C. Boedeker, Xuejian Xiong, John Parkinson, Daniel N. Frank, Ellen Li, Grace Gathungu

PLoS One. 2015; 10(6): e0130902. Published online 2015 Jun 30. doi: 10.1371/journal.pone.0130902

Correction in:: PLoS One. 2015; 10(7): e0134759.

PMCID:: PMC4509574

Abstract Article PDF–813K

Select item 415075619.

Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli

Adam N. Nilsson, Gustav Emilsson, Lena K. Nyberg, Charleston Noble, Liselott Svensson Stadler, Joachim Fritzsche, Edward R. B. Moore, Jonas O. Tegenfeldt, Tobias Ambjörnsson, Fredrik Westerlund

Nucleic Acids Res. 2014 Sep 2; 42(15): e118. Published online 2014 Jul 10. doi: 10.1093/nar/gku556

PMCID:: PMC4150756

Abstract Article PDF–2.1M

Select item 414819120.

The TRIM-NHL Protein LIN-41 Controls the Onset of Developmental Plasticity in Caenorhabditis elegans

Cristina Tocchini, Jeremy J. Keusch, Sarah B. Miller, Susanne Finger, Heinz Gut, Michael B. Stadler, Rafal Ciosk

PLoS Genet. 2014 Aug; 10(8): e1004533. Published online 2014 Aug 28. doi: 10.1371/journal.pgen.1004533

PMCID:: PMC4148191

Abstract Article PDF–3.5M

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