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Bryce E. Nickels, PhD

Publications since 2011

Winkelman, J. T. Vvedenskaya, I. O. Zhang, Y. Zhang, Y. Bird, J. G. Taylor, D. M. Gourse, R. L. Ebright, R. H. Nickels, B. E. Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Science, 351:1090-1093, . (PMID: 26941320)

Schifano, J. M. Cruz, J. W. Vvedenskaya, I. O. Edifor, R. Ouyang, M. Husson, R. N. Nickels, B. E. Woychik, N. A. tRNA is a new target for cleavage by a MazF toxin. Nucleic Acids Res, In process, . (PMID: 26740583)

Vvedenskaya, I. O. Zhang, Y. Goldman, S. R. Valenti, A. Visone, V. Taylor, D. M. Ebright, R. H. Nickels, B. E. Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields. Mol Cell, In process, . (PMID: 26626484)

Goldman, S. R. Nair, N. U. Wells, C. D. Nickels, B. E. Hochschild, A. The primary sigma factor in can access the transcription elongation complex from solution . Elife, In process, . (PMID: 26371553)

Druzhinin, S. Y. Tran, N. T. Skalenko, K. S. Goldman, S. R. Knoblauch, J. G. Dove, S. L. Nickels, B. E. A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq. PLoS Genet, 11:e1005348, . (PMID: 26131907)

Ramsey, K. M. Osborne, M. L. Vvedenskaya, I. O. Su, C. Nickels, B. E. Dove, S. L. Ubiquitous Promoter-Localization of Essential Virulence Regulators in Francisella tularensis. PLoS Pathog, 11:e1004793, . (PMID: 25830507)

Vvedenskaya, I. O. Goldman, S. R. Nickels, B. E. Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5' ends. Methods Mol Biol, 1276:211-228, . (PMID: 25665566)

Cruz, J. W. Sharp, J. D. Hoffer, E. D. Maehigashi, T. Vvedenskaya, I. O. Konkimalla, A. Husson, R. N. Nickels, B. E. Dunham, C. M. Woychik, N. A. Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase. Nat Commun, 6:7480, . (PMID: 26158745)

Vvedenskaya, I. O. Vahedian-Movahed, H. Bird, J. G. Knoblauch, J. G. Goldman, S. R. Zhang, Y. Ebright, R. H. Nickels, B. E. Transcription. Interactions between RNA polymerase and the "core recognition element" counteract pausing. Science, 344:1285-1289, . (PMID: 24926020)

Vorobiev, S. M. Gensler, Y. Vahedian-Movahed, H. Seetharaman, J. Su, M. Huang, J. Y. Xiao, R. Kornhaber, G. Montelione, G. T. Tong, L. Ebright, R. H. Nickels, B. E. Structure of the DNA-Binding and RNA-Polymerase-Binding Region of Transcription Antitermination Factor lambdaQ. Structure, 22:488-495, . (PMID: 24440517, PMCID: PMC3951671)

Schifano, J. M. Vvedenskaya, I. O. Knoblauch, J. G. Ouyang, M. Nickels, B. E. Woychik, N. A. An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3. Nat Commun, 5:3538, . (PMID: 24709835, PMCID: PMC4090939)

Nickels, B. E. A new way to start: nanoRNA-mediated priming of transcription initiation. Transcription, 3:300-304, . (PMID: 23117822, PMCID: PMC3630185)

Bao, X. Nickels, B. E. Fan, H. Chlamydia trachomatis protein GrgA activates transcription by contacting the nonconserved region of sigma66. Proc Natl Acad Sci U S A, 109:16870-16875, . (PMID: 23027952, PMCID: PMC3479454)

Weiss, L. A. Harrison, P. G. Nickels, B. E. Glickman, M. S. Campbell, E. A. Darst, S. A. Stallings, C. L. Interaction of CarD with RNA Polymerase Mediates Mycobacterium tuberculosis Viability, Rifampin Resistance, and Pathogenesis. J Bacteriol, 194:5621-5631, . (PMID: 22904282, PMCID: PMC3458692)

Vvedenskaya, I. O. Sharp, J. S. Goldman, S. R. Kanabar, P. N. Livny, J. Dove, S. L. Nickels, B. E. Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs. Genes Dev, 26:1498-1507, . (PMID: 22751503, PMCID: PMC3403017)

Berdygulova, Z. Esyunina, D. Miropolskaya, N. Mukhamedyarov, D. Kuznedelov, K. Nickels, B. E. Severinov, K. Kulbachinskiy, A. Minakhin, L. A novel phage-encoded transcription antiterminator acts by suppressing bacterial RNA polymerase pausing. Nucleic Acids Res, 40:4052-4063, . (PMID: 22238378, PMCID: PMC3351154)

Nickels, B. E. Dove, S. L. NanoRNAs: a class of small RNAs that can prime transcription initiation in bacteria. J Mol Biol, 412:772-781, . (PMID: 21704045, PMCID: PMC3184357)

Bao, X. Pachikara, N. D. Oey, C. B. Balakrishnan, A. Westblade, L. F. Tan, M. Chase, T. Jr Nickels, B. E. Fan, H. Non-coding nucleotides and amino acids near the active site regulate peptide deformylase expression and inhibitor susceptibility in Chlamydia trachomatis. Microbiology, 157:2569-2581, . (PMID: 21719536, PMCID: PMC3352175)

Goldman, S. R. Sharp, J. S. Vvedenskaya, I. O. Livny, J. Dove, S. L. Nickels, B. E. NanoRNAs prime transcription initiation in vivo. Mol Cell, 42:817-825, . (PMID: 21700226, PMCID: PMC3130991)

Twist, K. A. Husnain, S. I. Franke, J. D. Jain, D. Campbell, E. A. Nickels, B. E. Thomas, M. S. Darst, S. A. Westblade, L. F. A novel method for the production of in vivo-assembled, recombinant Escherichia coli RNA polymerase lacking the alpha C-terminal domain. Protein Sci, 20:986-995, . (PMID: 21416542, PMCID: PMC3104228)

Deighan, P. Pukhrambam, C. Nickels, B. E. Hochschild, A. Initial transcribed region sequences influence the composition and functional properties of the bacterial elongation complex. Genes Dev, 25:77-88, . (PMID: 21205867, PMCID: PMC3012938)