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Concerns about "Stress-Induced MazF-Mediated Proteins in Escherichia coli".

Wade JT, Laub MT.

mBio. 2019 Jun 4;10(3). pii: e00825-19. doi: 10.1128/mBio.00825-19. No abstract available.


High-throughput determination of in vivo DNA sequence preferences for Cas protein binding using Library-ChIP.

Wade JT.

Methods Enzymol. 2019;616:117-132. doi: 10.1016/bs.mie.2018.10.019. Epub 2018 Dec 17.


Reply to Tobiasson et al.: Zinc depletion is a specific signal for induction of ribosome hibernation in mycobacteria.

Li Y, Sharma MR, Koripella RK, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK.

Proc Natl Acad Sci U S A. 2019 Feb 12;116(7):2398-2399. doi: 10.1073/pnas.1821103116. Epub 2019 Jan 25. No abstract available.


MrpJ Directly Regulates Proteus mirabilis Virulence Factors, Including Fimbriae and Type VI Secretion, during Urinary Tract Infection.

Debnath I, Stringer AM, Smith SN, Bae E, Mobley HLT, Wade JT, Pearson MM.

Infect Immun. 2018 Sep 21;86(10). pii: e00388-18. doi: 10.1128/IAI.00388-18. Print 2018 Oct.


Zinc depletion induces ribosome hibernation in mycobacteria.

Li Y, Sharma MR, Koripella RK, Yang Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK.

Proc Natl Acad Sci U S A. 2018 Aug 7;115(32):8191-8196. doi: 10.1073/pnas.1804555115. Epub 2018 Jul 23.


Maestro of regulation: Riboswitches orchestrate gene expression at the levels of translation, transcription and mRNA decay.

Bastet L, Turcotte P, Wade JT, Lafontaine DA.

RNA Biol. 2018;15(6):679-682. doi: 10.1080/15476286.2018.1451721. Epub 2018 Apr 3. Review.


The evolutionary impact of intragenic FliA promoters in proteobacteria.

Fitzgerald DM, Smith C, Lapierre P, Wade JT.

Mol Microbiol. 2018 May;108(4):361-378. doi: 10.1111/mmi.13941. Epub 2018 Mar 23.


Waking the neighbours: disruption of H-NS repression by overlapping transcription.

Wade JT, Grainger DC.

Mol Microbiol. 2018 May;108(3):221-225. doi: 10.1111/mmi.13939. Epub 2018 Mar 23.


Identification of regulatory targets for the bacterial Nus factor complex.

Baniulyte G, Singh N, Benoit C, Johnson R, Ferguson R, Paramo M, Stringer AM, Scott A, Lapierre P, Wade JT.

Nat Commun. 2017 Dec 11;8(1):2027. doi: 10.1038/s41467-017-02124-9.


The BvgAS Regulon of Bordetella pertussis.

Moon K, Bonocora RP, Kim DD, Chen Q, Wade JT, Stibitz S, Hinton DM.

mBio. 2017 Oct 10;8(5). pii: e01526-17. doi: 10.1128/mBio.01526-17.


Spurious transcription and its impact on cell function.

Wade JT, Grainger DC.

Transcription. 2018;9(3):182-189. doi: 10.1080/21541264.2017.1381794. Epub 2017 Nov 3.


Translational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation.

Bastet L, Chauvier A, Singh N, Lussier A, Lamontagne AM, Prévost K, Massé E, Wade JT, Lafontaine DA.

Nucleic Acids Res. 2017 Jul 7;45(12):7474-7486. doi: 10.1093/nar/gkx434.


Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12.

Wong GT, Bonocora RP, Schep AN, Beeler SM, Lee Fong AJ, Shull LM, Batachari LE, Dillon M, Evans C, Becker CJ, Bush EC, Hardin J, Wade JT, Stoebel DM.

J Bacteriol. 2017 Mar 14;199(7). pii: e00755-16. doi: 10.1128/JB.00755-16. Print 2017 Apr 1.


Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase.

Lamberte LE, Baniulyte G, Singh SS, Stringer AM, Bonocora RP, Stracy M, Kapanidis AN, Wade JT, Grainger DC.

Nat Microbiol. 2017 Jan 9;2:16249. doi: 10.1038/nmicrobiol.2016.249.


Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in E. coli.

Qian Z, Trostel A, Lewis DE, Lee SJ, He X, Stringer AM, Wade JT, Schneider TD, Durfee T, Adhya S.

Front Mol Biosci. 2016 Nov 16;3:74. eCollection 2016.


Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion.

Smith C, Stringer AM, Mao C, Palumbo MJ, Wade JT.

mBio. 2016 Sep 6;7(5). pii: e01024-16. doi: 10.1128/mBio.01024-16.


SuhB Associates with Nus Factors To Facilitate 30S Ribosome Biogenesis in Escherichia coli.

Singh N, Bubunenko M, Smith C, Abbott DM, Stringer AM, Shi R, Court DL, Wade JT.

mBio. 2016 Mar 15;7(2):e00114. doi: 10.1128/mBio.00114-16.


Chemical Inhibition of Kynureninase Reduces Pseudomonas aeruginosa Quorum Sensing and Virulence Factor Expression.

Kasper SH, Bonocora RP, Wade JT, Musah RA, Cady NC.

ACS Chem Biol. 2016 Apr 15;11(4):1106-17. doi: 10.1021/acschembio.5b01082. Epub 2016 Feb 10.


Mapping Transcription Regulatory Networks with ChIP-seq and RNA-seq.

Wade JT.

Adv Exp Med Biol. 2015;883:119-34. doi: 10.1007/978-3-319-23603-2_7. Review.


Identification of bacterial sRNA regulatory targets using ribosome profiling.

Wang J, Rennie W, Liu C, Carmack CS, Prévost K, Caron MP, Massé E, Ding Y, Wade JT.

Nucleic Acids Res. 2015 Dec 2;43(21):10308-20. doi: 10.1093/nar/gkv1158. Epub 2015 Nov 5.


Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape.

Shell SS, Wang J, Lapierre P, Mir M, Chase MR, Pyle MM, Gawande R, Ahmad R, Sarracino DA, Ioerger TR, Fortune SM, Derbyshire KM, Wade JT, Gray TA.

PLoS Genet. 2015 Nov 4;11(11):e1005641. doi: 10.1371/journal.pgen.1005641. eCollection 2015 Nov.


Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding.

Bonocora RP, Smith C, Lapierre P, Wade JT.

PLoS Genet. 2015 Oct 1;11(10):e1005552. doi: 10.1371/journal.pgen.1005552. eCollection 2015 Oct.


Correction: Comprehensive Mapping of the Escherichia coli Flagellar Regulatory Network.

Fitzgerald DM, Bonocora RP, Wade JT.

PLoS Genet. 2015 Sep 17;11(9):e1005456. doi: 10.1371/journal.pgen.1005456. eCollection 2015 Sep. No abstract available.


A 3' external transcribed spacer in a tRNA transcript acts as a sponge for small RNAs to prevent transcriptional noise.

Lalaouna D, Carrier MC, Semsey S, Brouard JS, Wang J, Wade JT, Massé E.

Mol Cell. 2015 May 7;58(3):393-405. doi: 10.1016/j.molcel.2015.03.013. Epub 2015 Apr 16.


ChIP-seq for genome-scale analysis of bacterial DNA-binding proteins.

Bonocora RP, Wade JT.

Methods Mol Biol. 2015;1276:327-40. doi: 10.1007/978-1-4939-2392-2_20.


H-NS and RNA polymerase: a love-hate relationship?

Landick R, Wade JT, Grainger DC.

Curr Opin Microbiol. 2015 Apr;24:53-9. doi: 10.1016/j.mib.2015.01.009. Epub 2015 Jan 30. Review.


The molecular basis for control of ETEC enterotoxin expression in response to environment and host.

Haycocks JR, Sharma P, Stringer AM, Wade JT, Grainger DC.

PLoS Pathog. 2015 Jan 8;11(1):e1004605. doi: 10.1371/journal.ppat.1004605. eCollection 2015 Jan.


Where to begin? Mapping transcription start sites genome-wide in Escherichia coli.

Wade JT.

J Bacteriol. 2015 Jan 1;197(1):4-6. doi: 10.1128/JB.02410-14. Epub 2014 Oct 20.


Comprehensive mapping of the Escherichia coli flagellar regulatory network.

Fitzgerald DM, Bonocora RP, Wade JT.

PLoS Genet. 2014 Oct 2;10(10):e1004649. doi: 10.1371/journal.pgen.1004649. eCollection 2014 Oct. Erratum in: PLoS Genet. 2014 Oct;10(10):e1004807. PLoS Genet. 2015 Sep;11(9):e1005456.


Pervasive transcription: illuminating the dark matter of bacterial transcriptomes.

Wade JT, Grainger DC.

Nat Rev Microbiol. 2014 Sep;12(9):647-53. doi: 10.1038/nrmicro3316. Epub 2014 Jul 28. Review.


Interplay of transcriptional and small RNA-dependent control mechanisms regulates chitosugar uptake in Escherichia coli and Salmonella.

Plumbridge J, Bossi L, Oberto J, Wade JT, Figueroa-Bossi N.

Mol Microbiol. 2014 May;92(4):648-58. doi: 10.1111/mmi.12573. Epub 2014 Mar 28.


Widespread suppression of intragenic transcription initiation by H-NS.

Singh SS, Singh N, Bonocora RP, Fitzgerald DM, Wade JT, Grainger DC.

Genes Dev. 2014 Feb 1;28(3):214-9. doi: 10.1101/gad.234336.113. Epub 2014 Jan 21. Erratum in: Genes Dev. 2014 Aug 1;28(15):1733.


Identification of HilD-regulated genes in Salmonella enterica serovar Typhimurium.

Petrone BL, Stringer AM, Wade JT.

J Bacteriol. 2014 Mar;196(5):1094-101. doi: 10.1128/JB.01449-13. Epub 2013 Dec 27.


Identification of regulatory RNA in bacterial genomes by genome-scale mapping of transcription start sites.

Singh N, Wade JT.

Methods Mol Biol. 2014;1103:1-10. doi: 10.1007/978-1-62703-730-3_1.


Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon.

Stringer AM, Currenti S, Bonocora RP, Baranowski C, Petrone BL, Palumbo MJ, Reilly AA, Zhang Z, Erill I, Wade JT.

J Bacteriol. 2014 Feb;196(3):660-71. doi: 10.1128/JB.01007-13. Epub 2013 Nov 22.


Identification of novel sRNAs in mycobacterial species.

Tsai CH, Baranowski C, Livny J, McDonough KA, Wade JT, Contreras LM.

PLoS One. 2013 Nov 14;8(11):e79411. doi: 10.1371/journal.pone.0079411. eCollection 2013.


An enhanced protocol for constraint-induced aphasia therapy II: a case series.

Johnson ML, Taub E, Harper LH, Wade JT, Bowman MH, Bishop-McKay S, Haddad MM, Mark VW, Uswatte G.

Am J Speech Lang Pathol. 2014 Feb;23(1):60-72.


Non-canonical protein-DNA interactions identified by ChIP are not artifacts.

Bonocora RP, Fitzgerald DM, Stringer AM, Wade JT.

BMC Genomics. 2013 Apr 15;14:254. doi: 10.1186/1471-2164-14-254.


Role of Ess1 in growth, morphogenetic switching, and RNA polymerase II transcription in Candida albicans.

Samaranayake D, Atencio D, Morse R, Wade JT, Chaturvedi V, Hanes SD.

PLoS One. 2013;8(3):e59094. doi: 10.1371/journal.pone.0059094. Epub 2013 Mar 14.


Identification and characterization of small RNAs in Yersinia pestis.

Beauregard A, Smith EA, Petrone BL, Singh N, Karch C, McDonough KA, Wade JT.

RNA Biol. 2013 Mar;10(3):397-405. doi: 10.4161/rna.23590. Epub 2013 Jan 16.


FRUIT, a scar-free system for targeted chromosomal mutagenesis, epitope tagging, and promoter replacement in Escherichia coli and Salmonella enterica.

Stringer AM, Singh N, Yermakova A, Petrone BL, Amarasinghe JJ, Reyes-Diaz L, Mantis NJ, Wade JT.

PLoS One. 2012;7(9):e44841. doi: 10.1371/journal.pone.0044841. Epub 2012 Sep 27.


Distinct role of Mediator tail module in regulation of SAGA-dependent, TATA-containing genes in yeast.

Ansari SA, Ganapathi M, Benschop JJ, Holstege FC, Wade JT, Morse RH.

EMBO J. 2012 Jan 4;31(1):44-57. doi: 10.1038/emboj.2011.362. Epub 2011 Oct 4.


Reply to "Concerns about Recently Identified Widespread Antisense Transcription in Escherichia coli".

Wade JT, Dornenburg JE, Devita AM, Palumbo MJ.

mBio. 2010 May 18;1(2). pii: e00119-10. doi: 10.1128/mBio.00119-10. No abstract available.


Widespread antisense transcription in Escherichia coli.

Dornenburg JE, Devita AM, Palumbo MJ, Wade JT.

mBio. 2010 May 18;1(1). pii: e00024-10. doi: 10.1128/mBio.00024-10.


Technical considerations in using DNA microarrays to define regulons.

Rhodius VA, Wade JT.

Methods. 2009 Jan;47(1):63-72. doi: 10.1016/j.ymeth.2008.10.017. Epub 2008 Oct 26.


The transition from transcriptional initiation to elongation.

Wade JT, Struhl K.

Curr Opin Genet Dev. 2008 Apr;18(2):130-6. doi: 10.1016/j.gde.2007.12.008. Epub 2008 Feb 20. Review.


Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization.

Wade JT, Struhl K, Busby SJ, Grainger DC.

Mol Microbiol. 2007 Jul;65(1):21-6. Review.


The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting.

Reppas NB, Wade JT, Church GM, Struhl K.

Mol Cell. 2006 Dec 8;24(5):747-757. doi: 10.1016/j.molcel.2006.10.030.


Extensive functional overlap between sigma factors in Escherichia coli.

Wade JT, Castro Roa D, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E.

Nat Struct Mol Biol. 2006 Sep;13(9):806-14. Epub 2006 Aug 6.


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