Diversity and evolution of class 2 CRISPR–Cas systems
Class 2 CRISPR–Cas systems are characterized by effector modules that consist of a single
multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the …
multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the …
RNA-guided genetic silencing systems in bacteria and archaea
Clustered regularly interspaced short palindromic repeat (CRISPR) are essential
components of nucleic-acid-based adaptive immune systems that are widespread in …
components of nucleic-acid-based adaptive immune systems that are widespread in …
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
AP Camargo, S Nayfach, IMA Chen… - Nucleic acids …, 2023 - academic.oup.com
Viruses are widely recognized as critical members of all microbiomes. Metagenomics
enables large-scale exploration of the global virosphere, progressively revealing the …
enables large-scale exploration of the global virosphere, progressively revealing the …
iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria
The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied
through metagenomics. While metagenomes enable high-throughput exploration of the viral …
through metagenomics. While metagenomes enable high-throughput exploration of the viral …
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
Bacteriophages have important roles in the ecology of the human gut microbiome but are
under-represented in reference databases. To address this problem, we assembled the …
under-represented in reference databases. To address this problem, we assembled the …
A genomic catalog of Earth's microbiomes
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has
enabled insights into the ecology and evolution of environmental and host-associated …
enabled insights into the ecology and evolution of environmental and host-associated …
Programmable RNA targeting with the single-protein CRISPR effector Cas7-11
A Özcan, R Krajeski, E Ioannidi, B Lee, A Gardner… - Nature, 2021 - nature.com
CRISPR–Cas interference is mediated by Cas effector nucleases that are either components
of multisubunit complexes—in class 1 CRISPR–Cas systems—or domains of a single …
of multisubunit complexes—in class 1 CRISPR–Cas systems—or domains of a single …
Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes
Competitive coevolution between microbes and viruses has led to the diversification of
CRISPR–Cas defense systems against infectious agents. By analyzing metagenomic …
CRISPR–Cas defense systems against infectious agents. By analyzing metagenomic …
Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering
Microbial systems underpin many biotechnologies, including CRISPR, but the exponential
growth of sequence databases makes it difficult to find previously unidentified systems. In …
growth of sequence databases makes it difficult to find previously unidentified systems. In …
The human gut virome is highly diverse, stable, and individual specific
The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain
uncharacterized, and their roles in shaping the gut microbiome and in impacting on human …
uncharacterized, and their roles in shaping the gut microbiome and in impacting on human …