Continuous multiplexed phage genome editing using recombitrons. [PDF]
Nat Biotechnol, 2023 Bacteriophages, which naturally shape bacterial communities, can be co-opted as a biological technology to help eliminate pathogenic bacteria from our bodies and food supply1.
Fishman CB +7 more
europepmc +2 more sources
PhamClust: a phage genome clustering tool using proteomic equivalence. [PDF]
mSystems, 2023 Bacteriophage comparative genomics is complex due to the mosaic nature of the genomes, and an underlying continuum of diversity confounds the identification of clear taxonomic boundaries.
Gauthier CH, Hatfull GF.
europepmc +2 more sources
The analysis of the function, diversity, and evolution of the Bacillus phage genome. [PDF]
BMC Microbiol, 2023 Background Phages play a pivotal role in the evolution of microbial populations. The interactions between phages and their hosts are complex and may vary in response to host physiology and environmental conditions.
Zhang Y +6 more
europepmc +2 more sources
PhaGAA: an integrated web server platform for phage genome annotation and analysis. [PDF]
Bioinformatics, 2023 Motivation Phage genome annotation plays a key role in the design of phage therapy. To date, there have been various genome annotation tools for phages, but most of these tools focus on mono-functional annotation and have complex operational processes ...
Wu J +8 more
europepmc +2 more sources
Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing. [PDF]
Nat Microbiol, 2022 CRISPR-Cas13 proteins are RNA-guided RNA nucleases that defend against incoming RNA and DNA phages by binding to complementary target phage transcripts followed by general, non-specific RNA degradation.
Adler BA +7 more
europepmc +2 more sources
Phage Genome Annotation: Where to Begin and End. [PDF]
Phage (New Rochelle), 2021 With the renewed interest in phage research, coupled with the rising accessibility to affordable sequencing, ever increasing numbers of phage genomes are being sequenced. Therefore, there is an increased need to assemble and annotate phage genomes. There
Shen A, Millard A.
europepmc +2 more sources
Strategies for Bacteriophage T5 Mutagenesis: Expanding the Toolbox for Phage Genome Engineering. [PDF]
Front Microbiol, 2021 Phage genome editing is crucial to uncover the molecular mechanisms of virus infection and to engineer bacteriophages with enhanced antibacterial properties.
Ramirez-Chamorro L +2 more
europepmc +2 more sources
Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. [PDF]
PLoS Comput Biol, 2020 In the modern genomic era, scientists without extensive bioinformatic training need to apply high-power computational analyses to critical tasks like phage genome annotation.
Ramsey J +8 more
europepmc +2 more sources
Structure and genome ejection mechanism of Staphylococcus aureus phage P68 [PDF]
Science Advances, 2019 Cryo-EM reveals the genome ejection mechanism of bacteriophage P68, a potential phage therapy agent against Staphylococcus aureus. Phages infecting Staphylococcus aureus can be used as therapeutics against antibiotic-resistant bacterial infections ...
D. Hrebik +5 more
openalex +2 more sources
Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades. [PDF]
Mol Biol Evol, 2018 The evolution of asexual organisms is driven not only by the inheritance of genetic modification but also by the acquisition of foreign DNA. The contribution of vertical and horizontal processes to genome evolution depends on their rates per year and is ...
Kupczok A +6 more
europepmc +2 more sources