[HTML][HTML] Bacteriophages of Shiga Toxin-Producing Escherichia coli and Their Contribution to Pathogenicity
L Rodríguez-Rubio, N Haarmann, M Schwidder… - Pathogens, 2021 - mdpi.com
Shiga toxins (Stx) of Shiga toxin-producing Escherichia coli (STEC) are generally encoded
in the genome of lambdoid bacteriophages, which spend the most time of their life cycle …
in the genome of lambdoid bacteriophages, which spend the most time of their life cycle …
Current and promising approaches to identify horizontal gene transfer events in metagenomes
GM Douglas, MGI Langille - Genome biology and evolution, 2019 - academic.oup.com
High-throughput shotgun metagenomics sequencing has enabled the profiling of myriad
natural communities. These data are commonly used to identify gene families and pathways …
natural communities. These data are commonly used to identify gene families and pathways …
Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages
Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and
diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a …
diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a …
RiboReport-benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
R Gelhausen, T Müller, SL Svensson… - Briefings in …, 2022 - academic.oup.com
Small proteins encoded by short open reading frames (ORFs) with 50 codons or fewer are
emerging as an important class of cellular macromolecules in diverse organisms. However …
emerging as an important class of cellular macromolecules in diverse organisms. However …
[HTML][HTML] Are antisense proteins in prokaryotes functional?
Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes.
Across bacterial species hundreds of short open reading frames antisense to annotated …
Across bacterial species hundreds of short open reading frames antisense to annotated …
[HTML][HTML] Optimality in the standard genetic code is robust with respect to comparison code sets
S Wichmann, Z Ardern - Biosystems, 2019 - Elsevier
The genetic code and its evolution have been studied by many different approaches. One
approach is to compare the properties of the standard genetic code (SGC) to theoretical …
approach is to compare the properties of the standard genetic code (SGC) to theoretical …
OLGenie: estimating natural selection to predict functional overlapping genes
Purifying (negative) natural selection is a hallmark of functional biological sequences, and
can be detected in protein-coding genes using the ratio of nonsynonymous to synonymous …
can be detected in protein-coding genes using the ratio of nonsynonymous to synonymous …
[HTML][HTML] Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers
Abstract Analysis of genome wide transcription start sites (TSSs) revealed an unexpected
complexity since not only canonical TSS of annotated genes are recognized by RNA …
complexity since not only canonical TSS of annotated genes are recognized by RNA …
[HTML][HTML] Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data
Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation,
including finding many unannotated genes. However, protocols for RIBO-Seq and …
including finding many unannotated genes. However, protocols for RIBO-Seq and …
Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome
All genomes include gene families with very limited taxonomic distributions that potentially
represent new genes and innovations in protein-coding sequence, raising questions on the …
represent new genes and innovations in protein-coding sequence, raising questions on the …