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Items: 1 to 50 of 103

1.

Asymmetric polar localization dynamics of the serine chemoreceptor protein Tsr in Escherichia coli.

Oh D, Yu Y, Lee H, Jeon JH, Wanner BL, Ritchie K.

PLoS One. 2018 May 17;13(5):e0195887. doi: 10.1371/journal.pone.0195887. eCollection 2018.

2.

Design, synthesis, and testing toward a 57-codon genome.

Ostrov N, Landon M, Guell M, Kuznetsov G, Teramoto J, Cervantes N, Zhou M, Singh K, Napolitano MG, Moosburner M, Shrock E, Pruitt BW, Conway N, Goodman DB, Gardner CL, Tyree G, Gonzales A, Wanner BL, Norville JE, Lajoie MJ, Church GM.

Science. 2016 Aug 19;353(6301):819-22. doi: 10.1126/science.aaf3639.

3.

Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling.

Nakahigashi K, Takai Y, Kimura M, Abe N, Nakayashiki T, Shiwa Y, Yoshikawa H, Wanner BL, Ishihama Y, Mori H.

DNA Res. 2016 Jun;23(3):193-201. doi: 10.1093/dnares/dsw008. Epub 2016 Mar 23.

4.

Toward Network Biology in E. coli Cell.

Mori H, Takeuchi R, Otsuka Y, Bowden S, Yokoyama K, Muto A, Libourel I, Wanner BL.

Adv Exp Med Biol. 2015;883:155-68. doi: 10.1007/978-3-319-23603-2_9. Review.

PMID:
26621467
5.

Identification of essential genes and synthetic lethal gene combinations in Escherichia coli K-12.

Mori H, Baba T, Yokoyama K, Takeuchi R, Nomura W, Makishi K, Otsuka Y, Dose H, Wanner BL.

Methods Mol Biol. 2015;1279:45-65. doi: 10.1007/978-1-4939-2398-4_4.

PMID:
25636612
6.

GenoBase: comprehensive resource database of Escherichia coli K-12.

Otsuka Y, Muto A, Takeuchi R, Okada C, Ishikawa M, Nakamura K, Yamamoto N, Dose H, Nakahigashi K, Tanishima S, Suharnan S, Nomura W, Nakayashiki T, Aref WG, Bochner BR, Conway T, Gribskov M, Kihara D, Rudd KE, Tohsato Y, Wanner BL, Mori H.

Nucleic Acids Res. 2015 Jan;43(Database issue):D606-17. doi: 10.1093/nar/gku1164. Epub 2014 Nov 15.

7.

Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing.

Conway T, Creecy JP, Maddox SM, Grissom JE, Conkle TL, Shadid TM, Teramoto J, San Miguel P, Shimada T, Ishihama A, Mori H, Wanner BL.

MBio. 2014 Jul 8;5(4):e01442-14. doi: 10.1128/mBio.01442-14.

8.

Colony-live--a high-throughput method for measuring microbial colony growth kinetics--reveals diverse growth effects of gene knockouts in Escherichia coli.

Takeuchi R, Tamura T, Nakayashiki T, Tanaka Y, Muto A, Wanner BL, Mori H.

BMC Microbiol. 2014 Jun 26;14:171. doi: 10.1186/1471-2180-14-171.

9.

Development of a system for discovery of genetic interactions for essential genes in Escherichia coli K-12.

Yong HT, Yamamoto N, Takeuchi R, Hsieh YJ, Conrad TM, Datsenko KA, Nakayashiki T, Wanner BL, Mori H.

Genes Genet Syst. 2013;88(4):233-40.

10.

Dynamics of the serine chemoreceptor in the Escherichia coli inner membrane: a high-speed single-molecule tracking study.

Oh D, Yu Y, Lee H, Wanner BL, Ritchie K.

Biophys J. 2014 Jan 7;106(1):145-53. doi: 10.1016/j.bpj.2013.09.059.

11.
12.

The tRNA thiolation pathway modulates the intracellular redox state in Escherichia coli.

Nakayashiki T, Saito N, Takeuchi R, Kadokura H, Nakahigashi K, Wanner BL, Mori H.

J Bacteriol. 2013 May;195(9):2039-49. doi: 10.1128/JB.02180-12. Epub 2013 Mar 1.

13.

Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system.

Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E.

Nat Commun. 2012 Jul 10;3:945. doi: 10.1038/ncomms1937.

PMID:
22781758
14.

Characterization of peptide chain length and constituency requirements for YejABEF-mediated uptake of microcin C analogues.

Vondenhoff GH, Blanchaert B, Geboers S, Kazakov T, Datsenko KA, Wanner BL, Rozenski J, Severinov K, Van Aerschot A.

J Bacteriol. 2011 Jul;193(14):3618-23. doi: 10.1128/JB.00172-11. Epub 2011 May 20.

15.

Welcome to microbial informatics and experimentation.

Wise MJ, Wanner BL.

Microb Inform Exp. 2011 Jun 14;1(1):1. doi: 10.1186/2042-5783-1-1. No abstract available.

16.

Environmental dependency of gene knockouts on phenotype microarray analysis in Escherichia coli.

Tohsato Y, Baba T, Mazaki Y, Ito M, Wanner BL, Mori H.

J Bioinform Comput Biol. 2010 Dec;8 Suppl 1:83-99.

PMID:
21155021
17.

The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology.

Rajagopala SV, Yamamoto N, Zweifel AE, Nakamichi T, Huang HK, Mendez-Rios JD, Franca-Koh J, Boorgula MP, Fujita K, Suzuki K, Hu JC, Wanner BL, Mori H, Uetz P.

BMC Genomics. 2010 Aug 11;11:470. doi: 10.1186/1471-2164-11-470.

18.

Transcription, processing and function of CRISPR cassettes in Escherichia coli.

Pougach K, Semenova E, Bogdanova E, Datsenko KA, Djordjevic M, Wanner BL, Severinov K.

Mol Microbiol. 2010 Sep;77(6):1367-79. doi: 10.1111/j.1365-2958.2010.07265.x.

19.

Stochastic kinetic model of two component system signalling reveals all-or-none, graded and mixed mode stochastic switching responses.

Kierzek AM, Zhou L, Wanner BL.

Mol Biosyst. 2010 Mar;6(3):531-42. doi: 10.1039/b906951h. Epub 2009 Dec 2.

PMID:
20174681
20.

Global regulation by the seven-component Pi signaling system.

Hsieh YJ, Wanner BL.

Curr Opin Microbiol. 2010 Apr;13(2):198-203. doi: 10.1016/j.mib.2010.01.014. Epub 2010 Feb 18. Review.

21.

Update on the Keio collection of Escherichia coli single-gene deletion mutants.

Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H.

Mol Syst Biol. 2009;5:335. doi: 10.1038/msb.2009.92. Epub 2009 Dec 22. No abstract available.

22.

Evidence against the physiological role of acetyl phosphate in the phosphorylation of the ArcA response regulator in Escherichia coli.

Liu X, Peña Sandoval GR, Wanner BL, Jung WS, Georgellis D, Kwon O.

J Microbiol. 2009 Oct;47(5):657-62. doi: 10.1007/s12275-009-0087-9. Epub 2009 Oct 24.

PMID:
19851741
23.

Genome-wide screens: novel mechanisms in colicin import and cytotoxicity.

Sharma O, Datsenko KA, Ess SC, Zhalnina MV, Wanner BL, Cramer WA.

Mol Microbiol. 2009 Aug;73(4):571-85. doi: 10.1111/j.1365-2958.2009.06788.x. Epub 2009 Jul 22.

24.

In vivo recognition of Bacillus subtilis by desorption electrospray ionization mass spectrometry (DESI-MS).

Song Y, Talaty N, Datsenko K, Wanner BL, Cooks RG.

Analyst. 2009 May;134(5):838-41. doi: 10.1039/b900069k. Epub 2009 Mar 16.

PMID:
19381372
25.

High-throughput, quantitative analyses of genetic interactions in E. coli.

Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL, Mori H, Weissman JS, Krogan NJ, Gross CA.

Nat Methods. 2008 Sep;5(9):781-7.

26.

eSGA: E. coli synthetic genetic array analysis.

Butland G, Babu M, Díaz-Mejía JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H, Sheikh B, Moreno-Hagelseib G, Greenblatt JF, Emili A.

Nat Methods. 2008 Sep;5(9):789-95. doi: 10.1038/nmeth.1239.

PMID:
18677321
27.

The emerging world of wikis.

Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Kihara D, Knight TF Jr, Pico AR, Siegele DA, Wanner BL, Welch RD.

Science. 2008 Jun 6;320(5881):1289-90. doi: 10.1126/science.320.5881.1289b. No abstract available.

PMID:
18535227
28.

The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12.

Baba T, Huan HC, Datsenko K, Wanner BL, Mori H.

Methods Mol Biol. 2008;416:183-94. doi: 10.1007/978-1-59745-321-9_12.

PMID:
18392968
29.

The phosphate regulon and bacterial virulence: a regulatory network connecting phosphate homeostasis and pathogenesis.

Lamarche MG, Wanner BL, Crépin S, Harel J.

FEMS Microbiol Rev. 2008 May;32(3):461-73. doi: 10.1111/j.1574-6976.2008.00101.x. Epub 2008 Jan 29. Review.

30.

Escherichia coli peptidase A, B, or N can process translation inhibitor microcin C.

Kazakov T, Vondenhoff GH, Datsenko KA, Novikova M, Metlitskaya A, Wanner BL, Severinov K.

J Bacteriol. 2008 Apr;190(7):2607-10. doi: 10.1128/JB.01956-07. Epub 2008 Jan 25.

31.

Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro.

Stepanova E, Lee J, Ozerova M, Semenova E, Datsenko K, Wanner BL, Severinov K, Borukhov S.

J Bacteriol. 2007 Dec;189(24):8772-85. Epub 2007 Aug 31.

32.

Structure of the complex of the colicin E2 R-domain and its BtuB receptor. The outer membrane colicin translocon.

Sharma O, Yamashita E, Zhalnina MV, Zakharov SD, Datsenko KA, Wanner BL, Cramer WA.

J Biol Chem. 2007 Aug 10;282(32):23163-70. Epub 2007 Jun 4.

33.

The X-ray crystal structures of two constitutively active mutants of the Escherichia coli PhoB receiver domain give insights into activation.

Arribas-Bosacoma R, Kim SK, Ferrer-Orta C, Blanco AG, Pereira PJ, Gomis-Rüth FX, Wanner BL, Coll M, Solà M.

J Mol Biol. 2007 Feb 16;366(2):626-41. Epub 2006 Nov 14.

34.

The pathogen-associated iroA gene cluster mediates bacterial evasion of lipocalin 2.

Fischbach MA, Lin H, Zhou L, Yu Y, Abergel RJ, Liu DR, Raymond KN, Wanner BL, Strong RK, Walsh CT, Aderem A, Smith KD.

Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16502-7. Epub 2006 Oct 23.

35.

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.

Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H.

Mol Syst Biol. 2006;2:2006.0008. Epub 2006 Feb 21.

36.

Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.

Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T.

Mol Syst Biol. 2006;2:2006.0007. Epub 2006 Feb 21.

37.

Escherichia coli K-12: a cooperatively developed annotation snapshot--2005.

Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL.

Nucleic Acids Res. 2006 Jan 5;34(1):1-9. Print 2006.

38.

Minimum information requested in the annotation of biochemical models (MIRIAM).

Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL.

Nat Biotechnol. 2005 Dec;23(12):1509-15.

PMID:
16333295
39.

Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays.

Tong X, Campbell JW, Balázsi G, Kay KA, Wanner BL, Gerdes SY, Oltvai ZN.

Biochem Biophys Res Commun. 2004 Sep 10;322(1):347-54.

PMID:
15313213
40.

Chromosomal expression of foreign and native genes from regulatable promoters in Escherichia coli.

Zhou L, Zhang K, Wanner BL.

Methods Mol Biol. 2004;267:123-34.

PMID:
15269420
41.
42.

Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli.

Ismail W, El-Said Mohamed M, Wanner BL, Datsenko KA, Eisenreich W, Rohdich F, Bacher A, Fuchs G.

Eur J Biochem. 2003 Jul;270(14):3047-54.

44.

Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12.

Oshima T, Aiba H, Masuda Y, Kanaya S, Sugiura M, Wanner BL, Mori H, Mizuno T.

Mol Microbiol. 2002 Oct;46(1):281-91.

45.

The 2-aminoethylphosphonate-specific transaminase of the 2-aminoethylphosphonate degradation pathway.

Kim AD, Baker AS, Dunaway-Mariano D, Metcalf WW, Wanner BL, Martin BM.

J Bacteriol. 2002 Aug;184(15):4134-40.

46.

Homogeneous expression of the P(BAD) promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter.

Khlebnikov A, Datsenko KA, Skaug T, Wanner BL, Keasling JD.

Microbiology. 2001 Dec;147(Pt 12):3241-7.

PMID:
11739756
49.

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

Datsenko KA, Wanner BL.

Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6640-5.

50.

Multiple factors independently regulate hilA and invasion gene expression in Salmonella enterica serovar typhimurium.

Lucas RL, Lostroh CP, DiRusso CC, Spector MP, Wanner BL, Lee CA.

J Bacteriol. 2000 Apr;182(7):1872-82.

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