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References from Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1016/j.molcel.2017.12.023
10.1016/j.molcel.2017.12.023 · External reference
Intriguing interaction of bacteriophage-host association: An understanding in the era of omics
10.3389/fmicb.2017.00559 · 2017 · External reference
10.1038/nrmicro2620
10.1038/nrmicro2620 · External reference
10.1080/15476286.2020.1870844
10.1080/15476286.2020.1870844 · External reference
Next-Generation “-omics” Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa
10.1371/journal.pgen.1006134 · 2016 · External reference
10.1111/1462-2920.14979
10.1111/1462-2920.14979 · External reference
RNA-sequencing reveals the progression of Phage-Host interactions between φR1-37 and Yersinia enterocolitica
10.3390/v8040111 · 2016 · External reference
10.1038/nature08756
10.1038/nature08756 · External reference
A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome
10.1186/s12864-016-2539-z · 2016 · External reference
Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ
10.1080/15476286.2020.1827785 · 2021 · External reference
10.1016/j.mib.2014.06.010
10.1016/j.mib.2014.06.010 · External reference
10.1038/s41576-019-0150-2
10.1038/s41576-019-0150-2 · External reference
Realizing the potential of full-length transcriptome sequencing
10.1098/rstb.2019.0097 · 2019 · External reference
10.1038/s41564-019-0500-z
10.1038/s41564-019-0500-z · External reference
SMRT-Cappable-seq reveals complex operon variants in bacteria
2018 · External reference
Nanopore sequencing of RNA and cDNA molecules in Escherichia coli
2021 · External reference
Direct Metatranscriptome RNA-seq and Multiplex RT-PCR Amplicon Sequencing on Nanopore MinION – Promising Strategies for Multiplex Identification of Viable Pathogens in Food
2020 · External reference
Direct RNA nanopore sequencing of Pseudomonas aeruginosa clone C transcriptomes
2021 · External reference
Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing
2017 · External reference
Evaluating the genome and resistome of extensively drug-resistant Klebsiella pneumoniae using native DNA and RNA Nanopore sequencing
2020 · External reference
A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes
10.1038/s41467-019-11272-z · 2019 · External reference
10.1038/s41592-019-0617-2
10.1038/s41592-019-0617-2 · External reference
Nanopore ReCappable Sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs
10.1093/nar/gkac144 · 2022 · External reference
10.3390/biom5020647
10.3390/biom5020647 · External reference
10.1016/j.virol.2010.06.011
10.1016/j.virol.2010.06.011 · External reference
“Drc”, a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses
2020 · External reference
The bacteriophage N4-coded single-stranded DNA-binding protein (N4SSB) is the transcriptional activator of Escherichia coli RNA polymerase at N4 late promoters
10.1006/jmbi.1994.0098 · 1995 · External reference
10.1111/cmi.12330
10.1111/cmi.12330 · External reference
Survey of Pseudomonas aeruginosa and its phages: De novo peptide sequencing as a novel tool to assess the diversity of worldwide collected viruses
10.1111/j.1462-2920.2008.01862.x · 2009 · External reference
Feasibility of spray drying bacteriophages into respirable powders to combat pulmonary bacterial infections
10.1016/j.ejpb.2012.12.022 · 2013 · External reference
10.1093/bioinformatics/bty149
10.1093/bioinformatics/bty149 · External reference
Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement
10.1371/journal.pone.0112963 · 2014 · External reference
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
2017 · External reference
10.1093/bioinformatics/btu153
10.1093/bioinformatics/btu153 · External reference
10.1089/phage.2020.0006
10.1089/phage.2020.0006 · External reference
10.14806/ej.17.1.200
10.14806/ej.17.1.200 · External reference
10.1093/bioinformatics/bty191
10.1093/bioinformatics/bty191 · External reference
10.1093/bioinformatics/btp352
10.1093/bioinformatics/btp352 · External reference
10.1093/bioinformatics/btt656
10.1093/bioinformatics/btt656 · External reference
10.1093/bib/bbs017
10.1093/bib/bbs017 · External reference
10.1093/bioinformatics/btq033
10.1093/bioinformatics/btq033 · External reference
Regulatory roles of Escherichia coli 5’ UTR and ORF-internal RNAs detected by 3’ end mapping
10.7554/elife.69260 · 2021 · External reference
10.1093/nar/gkv416
10.1093/nar/gkv416 · External reference
SAPPHIRE: A neural network based classifier for σ70 promoter prediction in Pseudomonas
10.1186/s12859-020-03730-z · 2020 · External reference
Massively parallel characterization of engineered transcript isoforms using direct RNA sequencing
10.1038/s41467-022-28074-5 · 2022 · External reference
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
10.1186/gb-2007-8-2-r22 · 2007 · External reference
ARNold: A web tool for the prediction of rho-independent transcription terminators
10.4161/rna.8.1.13346 · 2011 · External reference
10.1186/1748-7188-6-26
10.1186/1748-7188-6-26 · External reference
10.1038/s41576-020-0254-8
10.1038/s41576-020-0254-8 · External reference
SEVAtile: a standardised DNA assembly method optimised for Pseudomonas. Microb
2021 · External reference
10.1038/nmeth765
10.1038/nmeth765 · External reference
Quantification of bacterial fluorescence using independent calibrants
10.1371/journal.pone.0199432 · 2018 · External reference
Tn7-Based Device for Calibrated Heterologous Gene Expression in Pseudomonas putida
10.1021/acssynbio.5b00058 · 2015 · External reference
10.1038/nmeth.2404
10.1038/nmeth.2404 · External reference
10.1093/nar/gks597
10.1093/nar/gks597 · External reference
10.1038/nrg2695
10.1038/nrg2695 · External reference
Galactic circos: User-friendly circos plots within the galaxy platform
10.1093/gigascience/giaa065 · 2020 · External reference
N4 virion RNA polymerase sites of transcription initiation
10.1016/s0092-8674(85)80032-5 · 1985 · External reference
10.1016/s0021-9258(18)63912-2
10.1016/s0021-9258(18)63912-2 · External reference
10.1080/10409238.2019.1651816
10.1080/10409238.2019.1651816 · External reference
10.1080/15476286.2020.1723328
10.1080/15476286.2020.1723328 · External reference
10.1093/nar/gkr1285
10.1093/nar/gkr1285 · External reference
10.1073/pnas.1416330112
10.1073/pnas.1416330112 · External reference
10.1038/nrmicro2560
10.1038/nrmicro2560 · External reference
10.1006/jmbi.1997.1251
10.1006/jmbi.1997.1251 · External reference
The Transcription Unit Architecture of Streptomyces lividans TK24
2019 · External reference
10.1016/s0022-2836(83)80282-4
10.1016/s0022-2836(83)80282-4 · External reference
10.1016/j.molcel.2016.11.002
10.1016/j.molcel.2016.11.002 · External reference
Diversity and Versatility in Small RNA-Mediated Regulation in Bacterial Pathogens
10.3389/fmicb.2021.719977 · 2021 · External reference
Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts
2018 · External reference
A grad-seq view of RNA and protein complexes in Pseudomonas aeruginosa under standard and bacteriophage predation conditions
10.1128/mbio.03454-20 · 2021 · External reference
Bacteriophages as sources of small non-coding RNA molecules
10.1016/j.plasmid.2020.102527 · 2021 · External reference
10.1128/jb.01007-13
10.1128/jb.01007-13 · External reference
