Browsing by Author "Livny, Jonathan"
Now showing items 1-11 of 11
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Comparative RNA-Seq based dissection of the regulatory networks and environmental stimuli underlying Vibrio parahaemolyticus gene expression during infection
Livny, Jonathan; Zhou, Xiaohui; Mandlik, Anjali; Hubbard, Troy; Davis, Brigid M.; Waldor, Matthew K. (Oxford University Press, 2014)Vibrio parahaemolyticus is the leading worldwide cause of seafood-associated gastroenteritis, yet little is known regarding its intraintestinal gene expression or physiology. To date, in vivo analyses have focused on ... -
Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing
Liu, Jane M.; Livny, Jonathan; Lawrence, Michael; Kimball, Marc D.; Waldor, Matthew K; Camilli, Andrew (Oxford University Press, 2009)Direct cloning and parallel sequencing, an extremely powerful method for microRNA (miRNA) discovery, has not yet been applied to bacterial transcriptomes. Here we present sRNA-Seq, an unbiased method that allows for ... -
High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data
Chao, Michael C.; Pritchard, Justin R.; Zhang, Yanjia J.; Rubin, Eric J.; Livny, Jonathan; Davis, Brigid M.; Waldor, Matthew K. (Oxford University Press, 2013)The coupling of high-density transposon mutagenesis to high-throughput DNA sequencing (transposon-insertion sequencing) enables simultaneous and genome-wide assessment of the contributions of individual loci to bacterial ... -
High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs
Teonadi, Hidayat; Livny, Miron; Livny, Jonathan; Waldor, Matthew K (Public Library of Science, 2008)Background: Diverse bacterial genomes encode numerous small non-coding RNAs (sRNAs) that regulate myriad biological processes. While bioinformatic algorithms have proven effective in identifying sRNA-encoding loci, the ... -
A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes
Avraham, Roi; Haseley, Nathan; Fan, Amy; Bloom-Ackermann, Zohar; Livny, Jonathan; Hung, Deborah Tan (Springer Nature, 2016)The ability to simultaneously characterize the bacterial and host expression programs during infection would facilitate a comprehensive understanding of pathogen-host interactions. While RNA-Seq has greatly advanced our ... -
How Deep Is Deep enough for RNA-Seq Profiling of Bacterial Transcriptomes?
Haas, Brian J; Chin, Melissa; Nusbaum, Chad; Birren, Bruce W; Livny, Jonathan (BioMed Central, 2012)Background: High-throughput sequencing of cDNA libraries (RNA-Seq) has proven to be a highly effective approach for studying bacterial transcriptomes. A central challenge in designing RNA-Seq-based experiments is estimating ... -
Identification of Novel sRNAs in Mycobacterial Species
Tsai, Chen-Hsun; Baranowski, Catherine; Livny, Jonathan; McDonough, Kathleen A.; Wade, Joseph T.; Contreras, Lydia M. (Public Library of Science, 2013)Bacterial small RNAs (sRNAs) are short transcripts that typically do not encode proteins and often act as regulators of gene expression through a variety of mechanisms. Regulatory sRNAs have been identified in many species, ... -
Identification of Small RNAs in Francisella tularensis
Postic, Guillaume; Frapy, Eric; Dupuis, Marion; Dubail, Iharilalao; Livny, Jonathan; Charbit, Alain; Meibom, Karin L (BioMed Central, 2010)Background: Regulation of bacterial gene expression by small RNAs (sRNAs) have proved to be important for many biological processes. Francisella tularensis is a highly pathogenic Gram-negative bacterium that causes the ... -
Mining Regulatory 5′UTRs from cDNA Deep Sequencing Datasets
Livny, Jonathan; Waldor, Matthew K (Oxford University Press, 2010)Regulatory 5′ untranslated regions (r5′UTRs) of mRNAs such as riboswitches modulate the expression of genes involved in varied biological processes in both bacteria and eukaryotes. New high-throughput sequencing technologies ... -
Multiple Small RNAs Identified in Mycobacterium bovis BCG are Also Expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis
DiChiara, Jeanne M.; Contreras-Martinez, Lydia M.; Livny, Jonathan; Smith, Dorie; McDonough, Kathleen A.; Belfort, Marlene (Oxford University Press, 2010)Tuberculosis (TB) is a major global health problem, infecting millions of people each year. The causative agent of TB, Mycobacterium tuberculosis, is one of the world’s most ancient and successful pathogens. However, until ... -
Prediction of Sinorhizobium Meliloti sRNA Genes and Experimental Detection in Strain 2011
Valverde, Claudio; Livny, Jonathan; Schlüter, Jan-Philip; Reinkensmeier, Jan; Becker, Anke; Parisi, Gustavo (BioMed Central, 2008)Background: Small non-coding RNAs (sRNAs) have emerged as ubiquitous regulatory elements in bacteria and other life domains. However, few sRNAs have been identified outside several well-studied species of gamma-proteobacteria ...