Research graph
References from Interrogating the Escherichia coli Epitranscriptome Via CRISPR Interference and Nanopore Native RNA Sequencing. Local targets link to admitted publications; unresolved targets remain external evidence.
Drummer‐Rapid Detection of RNA Modifications Through Comparative Nanopore Sequencing
10.1093/bioinformatics/btac274 · 2022 · External reference
Nonessential tRNA and rRNA Modifications Impact the Bacterial Response to Sub‐MIC Antibiotic Stress
10.1093/femsml/uqac019 · 2022 · External reference
RNA Editing in Bacteria: Occurrence, Regulation and Significance
10.1080/15476286.2018.1481698 · 2018 · External reference
Sites of Action of Two Ribosomal RNA Methylases Responsible for Resistance to Aminoglycosides
10.1016/0022-2836(87)90349-4 · 1987 · External reference
ResFinder 4.0 for Predictions of Phenotypes From Genotypes
10.1093/jac/dkaa345 · 2020 · External reference
Fast and Sensitive Protein Alignment Using DIAMOND
10.1038/nmeth.3176 · 2015 · External reference
MODOMICS: A Database of RNA Modifications and Related Information. 2023 Update
10.1093/nar/gkad1083 · 2024 · External reference
Plasmidfinder and In Silico pMLST: Identification and Typing of Plasmid Replicons in Whole‐Genome Sequencing (WGS)
10.1007/978-1-4939-9877-7_20 · 2020 · External reference
tRNA‐Mediated Codon‐Biased Translation in Mycobacterial Hypoxic Persistence
10.1038/ncomms13302 · 2016 · External reference
MaxQuant Enables High Peptide Identification Rates, Individualized p.p.b.‐Range Mass Accuracies and Proteome‐Wide Protein Quantification
10.1038/nbt.1511 · 2008 · External reference
A CRISPRi Screen in E. coli Reveals Sequence‐Specific Toxicity of dCas9
10.1038/s41467-018-04209-5 · 2018 · External reference
Twelve Years of SAMtools and BCFtools
10.1093/gigascience/giab008 · 2021 · External reference
Detection of Streptococcus Pyogenes M1Uk in Australia and Characterization of the Mutation Driving Enhanced Expression of Superantigen SpeA
10.1038/s41467-023-36717-4 · 2023 · External reference
Native RNA Nanopore Sequencing Reveals Antibiotic‐Induced Loss of rRNA Modifications in the A‐ and P‐Sites
10.1038/s41467-024-54368-x · 2024 · External reference
Widespread Occurrence of N6‐methyladenosine in Bacterial mRNA
10.1093/nar/gkv596 · 2015 · External reference
Gene Silencing With CRISPRi in Bacteria and Optimization of dCas9 Expression Levels
10.1016/j.ymeth.2019.07.024 · 2020 · External reference
Direct RNA Sequencing on Nanopore Arrays Redefines the Transcriptional Complexity of a Viral Pathogen
10.1038/s41467-019-08734-9 · 2019 · External reference
Transcriptome‐Wide Mapping of 5‐Methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C Within Archaeal mRNAs
10.1371/journal.pgen.1003602 · 2013 · External reference
Direct Nanopore Sequencing for the 17 RNA Modification Types in 36 Locations in the E. coli Ribosome Enables Monitoring of Stress‐Dependent Changes
10.1021/acschembio.3c00166 · 2023 · External reference
Highly Parallel Direct RNA Sequencing on an Array of Nanopores
10.1038/nmeth.4577 · 2018 · External reference
tRNA Modifications Regulate Translation During Cellular Stress
10.1016/j.febslet.2014.09.038 · 2014 · External reference
Enhanced Detection of RNA Modifications in Escherichia coli Utilizing Direct Rna Sequencing
10.1016/j.crmeth.2025.101168 · 2025 · External reference
Indigenous and Acquired Modifications in the Aminoglycoside Binding Sites of ≪I≫Pseudomonas Aeruginosa≪/I≫ rRNAs
10.4161/rna.25984 · 2013 · External reference
Proteomic Analysis of Human Plasma During Intermittent Fasting
10.1021/acs.jproteome.9b00090 · 2019 · External reference
Accurate and Fast Graph‐Based Pangenome Annotation and Clustering With ggCaller
10.1101/gr.277733.123 · 2023 · External reference
Complete Genomic and Transcriptional Landscape Analysis Using Third‐Generation Sequencing: A Case Study of Saccharomyces Cerevisiae CEN.PK113‐7D
10.1093/nar/gky014 · 2018 · External reference
Improved RNA Stability Estimation Through Bayesian Modeling Reveals Most Salmonella Transcripts Have Subminute Half‐Lives
10.1073/pnas.2308814121 · 2024 · External reference
Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome
10.1038/s41598-018-32615-8 · 2018 · External reference
Minimal, Encapsulated Proteomic‐Sample Processing Applied to Copy‐Number Estimation in Eukaryotic Cells
10.1038/nmeth.2834 · 2014 · External reference
RNA Modifications Detection by Comparative Nanopore Direct RNA Sequencing
10.1038/s41467-021-27393-3 · 2021 · External reference
Minimap2: Pairwise Alignment for Nucleotide Sequences
10.1093/bioinformatics/bty191 · 2018 · External reference
Epitranscriptome Sequencing Technologies: Decoding RNA Modifications
10.1038/nmeth.4110 · 2016 · External reference
Aminoglycoside Resistance 16S rRNA Methyltransferases Block Endogenous Methylation, Affect Translation Efficiency and Fitness of the Host
10.1261/rna.042572.113 · 2014 · External reference
Accurate Detection of m6A RNA Modifications in Native RNA Sequences
10.1038/s41467-019-11713-9 · 2019 · External reference
The Cfr rRNA Methyltransferase Confers Resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A Antibiotics
10.1128/aac.00131-06 · 2006 · External reference
A tRNA Modification With Aminovaleramide Facilitates AUA Decoding in Protein Synthesis
10.1038/s41589-024-01726-x · 2024 · External reference
Third‐Generation Sequencing Reveals Extensive Polycistronism and Transcriptional Overlapping in a Baculovirus
10.1038/s41598-018-26955-8 · 2018 · External reference
Inactivation of the RluD Pseudouridine Synthase Has Minimal Effects on Growth and Ribosome Function in Wild‐Type Escherichia coli and Salmonella enterica
10.1128/jb.00970-10 · 2011 · External reference
The Biogrid Database: A Comprehensive Biomedical Resource of Curated Protein, Genetic, and Chemical Interactions
10.1002/pro.3978 · 2021 · External reference
Nanopore Direct RNA Sequencing Maps the Complexity of Arabidopsis mRNA Processing and m6A Modification
10.7554/elife.49658 · 2020 · External reference
Salmon Provides Fast and Bias‐Aware Quantification of Transcript Expression
10.1038/nmeth.4197 · 2017 · External reference
Multifactorial Chromosomal Variants Regulate Polymyxin Resistance in Extensively Drug‐Resistant Klebsiella Pneumoniae
2018 · External reference
Evaluating the Genome and Resistome of Extensively Drug‐Resistant Klebsiella Pneumoniae Using Native DNA and RNA Nanopore Sequencing
10.1093/gigascience/giaa002 · 2020 · External reference
Comprehensive Functional Analysis of Escherichia coli Ribosomal RNA Methyltransferases
10.3389/fgene.2020.00097 · 2020 · External reference
Characterisation of in Vitro Resistance Selection Against Second‐/Last‐Line Antibiotics in Methicillin‐Resistant Staphylococcus aureus ATCC 43300 Strain
10.1093/jacamr/dlaf108 · 2025 · External reference
Protocol for Micro‐Purification, Enrichment, Pre‐Fractionation and Storage of Peptides for Proteomics Using Stagetips
10.1038/nprot.2007.261 · 2007 · External reference
Prokaryotic RNA Preparation Methods Useful for High Density Array Analysis: Comparison of Two Approaches
10.1093/nar/29.22.e112 · 2001 · External reference
The Birth of the Epitranscriptome: Deciphering the Function of RNA Modifications
10.1186/gb-2012-13-10-175 · 2012 · External reference
RluA Is the Major mRNA Pseudouridine Synthase in Escherichia coli
10.1371/journal.pgen.1011100 · 2024 · External reference
The ybiN Gene of Escherichia coli Encodes Adenine‐N6 Methyltransferase Specific for Modification of A1618 of 23 S Ribosomal RNA, a Methylated Residue Located Close to the Ribosomal Exit Tunnel
10.1016/j.jmb.2007.10.051 · 2008 · External reference
tRNA Modification Enzymes GidA and MnmE: Potential Role in Virulence of Bacterial Pathogens
10.3390/ijms151018267 · 2014 · External reference
Reading Canonical and Modified Nucleobases in 16S Ribosomal RNA Using Nanopore Native RNA Sequencing
10.1371/journal.pone.0216709 · 2019 · External reference
Direct Detection of RNA Modifications and Structure Using Single‐Molecule Nanopore Sequencing
10.1016/j.xgen.2022.100097 · 2022 · External reference
Mass Spectrometric Identification and Characterization of RNA‐Modifying Enzymes
10.1016/s0076-6879(07)25009-8 · 2007 · External reference
Analysis of Bacterial Transcriptome and Epitranscriptome Using Nanopore Direct RNA Sequencing
10.1093/nar/gkae601 · 2024 · External reference
Regulondb 11.0: Comprehensive High‐Throughput Datasets on Transcriptional Regulation in Escherichia coli K‐12
10.1099/mgen.0.000833 · 2022 · External reference
The Perseus Computational Platform for Comprehensive Analysis of (Prote)Omics Data
10.1038/nmeth.3901 · 2016 · External reference
ggseqlogo: A Versatile R Package for Drawing Sequence Logos
10.1093/bioinformatics/btx469 · 2017 · External reference
Engineering CRISPR Interference System in Klebsiella Pneumoniae for Attenuating Lactic Acid Synthesis
10.1186/s12934-018-0903-1 · 2018 · External reference
Pooled CRISPR Interference Screening Enables Genome‐Scale Functional Genomics Study in Bacteria With Superior Performance
10.1038/s41467-018-04899-x · 2018 · External reference
Patric, the Bacterial Bioinformatics Database and Analysis Resource
10.1093/nar/gkt1099 · 2014 · External reference
Nanopore Native RNA Sequencing of a Human Poly(A) Transcriptome
10.1038/s41592-019-0617-2 · 2019 · External reference
Gene Silencing Through CRISPR Interference in Bacteria: Current Advances and Future Prospects
10.3389/fmicb.2021.635227 · 2021 · External reference
