Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death von Botella, Laure, Vaubourgeix, Julien, Livny, Jonathan, Schnappinger, Dirk

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How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? von Haas, Brian J, Chin, Melissa, Nusbaum, Chad, Birren, Bruce W, Livny, Jonathan

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High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs von Livny, Jonathan, Teonadi, Hidayat, Livny, Miron, Waldor, Matthew K

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Best practices on the differential expression analysis of multi-species RNA-seq von Chung, Matthew, Bruno, Vincent M, Rasko, David A, Cuomo, Christina A, Muñoz, José F, Livny, Jonathan, Shetty, Amol C, Mahurkar, Anup, Dunning Hotopp, Julie C

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Distribution of Centromere-Like parS Sites in Bacteria: Insights from Comparative Genomics von LIVNY, Jonathan, YAMAICHI, Yoshiharu, WALDOR, Matthew K

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RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression von Mandlik, Anjali, Livny, Jonathan, Robins, William P, Ritchie, Jennifer M, Mekalanos, John J, Waldor, Matthew K

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Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY von Brinsmade, Shaun R., Alexander, Elizabeth L., Livny, Jonathan, Stettner, Arion I., Segrè, Daniel, Rhee, Kyu Y., Sonenshein, Abraham L.

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Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes von Giannoukos, Georgia, Ciulla, Dawn M, Huang, Katherine, Haas, Brian J, Izard, Jacques, Levin, Joshua Z, Livny, Jonathan, Earl, Ashlee M, Gevers, Dirk, Ward, Doyle V, Nusbaum, Chad, Birren, Bruce W, Gnirke, Andreas

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RNA-Seq of Borrelia burgdorferi in Multiple Phases of Growth Reveals Insights into the Dynamics of Gene Expression, Transcriptome Architecture, and Noncoding RNAs von Arnold, William K, Savage, Christina R, Brissette, Catherine A, Seshu, Janakiram, Livny, Jonathan, Stevenson, Brian

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A putative Vibrio cholerae two-component system controls a conserved periplasmic protein in response to the antimicrobial peptide polymyxin B von Matson, Jyl S, Livny, Jonathan, DiRita, Victor J

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TargetRNA2: identifying targets of small regulatory RNAs in bacteria von Kery, Mary Beth, Feldman, Monica, Livny, Jonathan, Tjaden, Brian

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Hybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis von Betin, Viktoria, Penaranda, Cristina, Bandyopadhyay, Nirmalya, Yang, Rui, Abitua, Angela, Bhattacharyya, Roby P., Fan, Amy, Avraham, Roi, Livny, Jonathan, Shoresh, Noam, Hung, Deborah T.

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Comparative RNA-Seq based dissection of the regulatory networks and environmental stimuli underlying Vibrio parahaemolyticus gene expression during infection von Livny, Jonathan, Zhou, Xiaohui, Mandlik, Anjali, Hubbard, Troy, Davis, Brigid M, Waldor, Matthew K

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Impact of CodY protein on metabolism, sporulation and virulence in Clostridioides difficile ribotype 027 von Daou, Nadine, Wang, Yuanguo, Levdikov, Vladimir M, Nandakumar, Madhumitha, Livny, Jonathan, Bouillaut, Laurent, Blagova, Elena, Zhang, Keshan, Belitsky, Boris R, Rhee, Kyu, Wilkinson, Anthony J, Sun, Xingmin, Sonenshein, Abraham L

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The complete Campylobacter jejuni transcriptome during colonization of a natural host determined by RNAseq von Taveirne, Michael E, Theriot, Casey M, Livny, Jonathan, DiRita, Victor J

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Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing von Liu, Jane M., Livny, Jonathan, Lawrence, Michael S., Kimball, Marc D., Waldor, Matthew K., Camilli, Andrew

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Wisdom of the crowds: A suggested polygenic plan for small-RNA-mediated regulation in bacteria von Goldberger, Omer, Livny, Jonathan, Bhattacharyya, Roby, Amster-Choder, Orna

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Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics von Ma, Peijun, He, Lorrie L, Pironti, Alejandro, Laibinis, Hannah H, Ernst, Christoph M, Manson, Abigail L, Bhattacharyya, Roby P, Earl, Ashlee M, Livny, Jonathan, Hung, Deborah T

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Legionella pneumophila 6S RNA optimizes intracellular multiplication von Faucher, Sébastien P, Friedlander, Gilgi, Livny, Jonathan, Margalit, Hanah, Shuman, Howard A

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Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment von Gomez, James E, Kaufmann-Malaga, Benjamin B, Wivagg, Carl N, Kim, Peter B, Silvis, Melanie R, Renedo, Nikolai, Ioerger, Thomas R, Ahmad, Rushdy, Livny, Jonathan, Fishbein, Skye, Sacchettini, James C, Carr, Steven A, Hung, Deborah T

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