Shimada T, Ogasawara H, Kobayashi I, Ishihama A
Methods Mol Biol. 2024; 2819:77-102.
PMID: 39028503
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Deng S
Heliyon. 2023; 9(3):e14466.
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Camakaris H, Yang J, Fujii T, Pittard J
J Bacteriol. 2021; 203(19):e0025221.
PMID: 34309399
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Shimada T, Ogasawara H, Kobayashi I, Kobayashi N, Ishihama A
Front Microbiol. 2021; 12:697803.
PMID: 34220787
PMC: 8249747.
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Ali M, Provoost A, Mijnendonckx K, Van Houdt R, Charlier D
Front Microbiol. 2020; 11:1635.
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The GTPase BipA expressed at low temperature in assists ribosome assembly and has chaperone-like activity.
Choi E, Hwang J
J Biol Chem. 2018; 293(47):18404-18419.
PMID: 30305394
PMC: 6254333.
DOI: 10.1074/jbc.RA118.002295.
Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase.
Yoshida H, Shimada T, Ishihama A
mSystems. 2018; 3(5).
PMID: 30225374
PMC: 6134199.
DOI: 10.1128/mSystems.00057-18.
Single-target regulators form a minor group of transcription factors in Escherichia coli K-12.
Shimada T, Ogasawara H, Ishihama A
Nucleic Acids Res. 2018; 46(8):3921-3936.
PMID: 29529243
PMC: 5934670.
DOI: 10.1093/nar/gky138.
Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the K-12 Genome.
Yamamoto K, Yamanaka Y, Shimada T, Sarkar P, Yoshida M, Bhardwaj N
mSystems. 2018; 3(1).
PMID: 29468196
PMC: 5811629.
DOI: 10.1128/mSystems.00172-17.
cAMP receptor protein regulates mouse colonization, motility, fimbria-mediated adhesion, and stress tolerance in uropathogenic Proteus mirabilis.
Tsai Y, Chien H, Huang K, Lin W, Liaw S
Sci Rep. 2017; 7(1):7282.
PMID: 28779108
PMC: 5544767.
DOI: 10.1038/s41598-017-07304-7.
Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors.
Ishihama A, Shimada T, Yamazaki Y
Nucleic Acids Res. 2016; 44(5):2058-74.
PMID: 26843427
PMC: 4797297.
DOI: 10.1093/nar/gkw051.
The Role of α-CTD in the Genome-Wide Transcriptional Regulation of the Bacillus subtilis Cells.
Murayama S, Ishikawa S, Chumsakul O, Ogasawara N, Oshima T
PLoS One. 2015; 10(7):e0131588.
PMID: 26154296
PMC: 4495994.
DOI: 10.1371/journal.pone.0131588.
Different Modes of Transactivation of Bacteriophage Mu Late Promoters by Transcription Factor C.
Swapna G, Kumari V, Nagaraja V
PLoS One. 2015; 10(6):e0129504.
PMID: 26058069
PMC: 4461284.
DOI: 10.1371/journal.pone.0129504.
A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin.
Davlieva M, Shi Y, Leonard P, Johnson T, Zianni M, Arias C
Nucleic Acids Res. 2015; 43(9):4758-73.
PMID: 25897118
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Control of acid resistance pathways of enterohemorrhagic Escherichia coli strain EDL933 by PsrB, a prophage-encoded AraC-like regulator.
Yang J, Russell T, Hocking D, Bender J, Srikhanta Y, Tauschek M
Infect Immun. 2014; 83(1):346-53.
PMID: 25368119
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DOI: 10.1128/IAI.02758-14.
Mapping of protein-protein interactions of E. coli RNA polymerase with microfluidic mechanical trapping.
Bates S, Quake S
PLoS One. 2014; 9(3):e91542.
PMID: 24643045
PMC: 3958368.
DOI: 10.1371/journal.pone.0091542.
The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli.
Shimada T, Yamazaki Y, Tanaka K, Ishihama A
PLoS One. 2014; 9(3):e90447.
PMID: 24603758
PMC: 3946193.
DOI: 10.1371/journal.pone.0090447.
Transcriptional activation of the mrkA promoter of the Klebsiella pneumoniae type 3 fimbrial operon by the c-di-GMP-dependent MrkH protein.
Yang J, Wilksch J, Tan J, Hocking D, Webb C, Lithgow T
PLoS One. 2013; 8(11):e79038.
PMID: 24244411
PMC: 3828302.
DOI: 10.1371/journal.pone.0079038.
Control of bacterial virulence by the RalR regulator of the rabbit-specific enteropathogenic Escherichia coli strain E22.
Srikhanta Y, Hocking D, Wakefield M, Higginson E, Robins-Browne R, Yang J
Infect Immun. 2013; 81(11):4232-43.
PMID: 24002063
PMC: 3811808.
DOI: 10.1128/IAI.00710-13.
Prokaryotic genome regulation: a revolutionary paradigm.
Ishihama A
Proc Jpn Acad Ser B Phys Biol Sci. 2012; 88(9):485-508.
PMID: 23138451
PMC: 3511978.
DOI: 10.2183/pjab.88.485.