ArticlePLoS genetics2009
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.
Article in PLoS genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 papers.
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Who cites it
129 citing papers in PubMed.
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- Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance.Applied microbiology and biotechnology · 2024Review
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- Differentially Expressed Genes ofInfection and drug resistance · 2022Article
- Explainability in transformer models for functional genomics.Briefings in bioinformatics · 2021Article
- Cross-species RNA-seq for deciphering host-microbe interactions.Nature reviews. Genetics · 2021Review
- Bias in RNA-seq Library Preparation: Current Challenges and Solutions.BioMed research international · 2021Review
- RNA-Seq analysis of differentially expressed genes of Staphylococcus epidermidis isolated from postoperative endophthalmitis and the healthy conjunctiva.Scientific reports · 2020Article
- New Roles for Two-Component System Response Regulators ofMicroorganisms · 2020Article
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- TREM2-activating antibodies abrogate the negative pleiotropic effects of the Alzheimer's disease variantThe Journal of biological chemistry · 2018Article
- High-throughput detection of RNA processing in bacteria.BMC genomics · 2018Article
- Article
- Transcriptomic response to GABA-producing Lactobacillus plantarum CGMCC 1.2437T induced by L-MSG.PloS one · 2018Article
- Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology.BMC genomics · 2017Article
- Transcriptomic study of Salmonella enterica subspecies enterica serovar Typhi biofilm.BMC genomics · 2017Article
- Long-Range Interactions in Riboswitch Control of Gene Expression.Annual review of biophysics · 2017Review
- An improved method for identification of small non-coding RNAs in bacteria using support vector machine.Scientific reports · 2017Article
- Global Gene-expression Analysis of the Response ofFrontiers in microbiology · 2017Article
69 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
High-density, strand-specific cDNA sequencing (ssRNA-seq) was used to analyze the transcriptome of Salmonella enterica serovar Typhi (S. Typhi). By mapping sequence data to the entire S. Typhi genome, we analyzed the transcriptome in a strand-specific manner and further defined transcribed regions encoded within prophages, pseudogenes, previously un-annotated, and 3'- or 5'-untranslated regions (UTR). An additional 40 novel candidate non-coding RNAs were identified beyond those previously annotated. Proteomic analysis was combined with transcriptome data to confirm and refine the annotation of a number of hpothetical genes. ssRNA-seq was also combined with microarray and proteome analysis to further define the S. Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA-seq provides a novel and powerful approach to the characterization of the bacterial transcriptome.
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