Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter

Global Organization and Proposed Megataxonomy of the Virus World

(2020) Eugene V. Koonin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Phage diversity, genomics and phylogeny

(2020) Moïra B. Dion et al.   NATURE REVIEWS MICROBIOLOGY

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes

(2020) Sergey A. Shmakov et al.   Communications Biology

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

The ecology and evolution of microbial CRISPR-Cas adaptive immune systems

(2019) Edze R. Westra et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy

(2019) Jake L. Weissman et al.   ISME Journal

CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog

(2019) Paola Soto-Perez et al.   Cell Host & Microbe

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

The independent loss model with ordered insertions for the evolution of CRISPR spacers

(2018) F. Baumdicker et al.   THEORETICAL POPULATION BIOLOGY

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Insights into the Human Virome Using CRISPR Spacers from Microbiomes

(2018) Claudio Hidalgo-Cantabrana et al.   Viruses-Basel

Bacteriophages Contribute to Shaping Clostridioides (Clostridium) difficile Species

(2018) Louis-Charles Fortier   Frontiers in Microbiology

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

(2018) Andrey N. Shkoporov et al.   Nature Communications

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

(2017) Francisco Martinez-Hernandez et al.   Nature Communications

Viral communities of the human gut: metagenomic analysis of composition and dynamics

(2017) Varun Aggarwala et al.   Mobile DNA

MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes

(2017) Abraham G. Moller et al.   PeerJ

Phage-host interactions in Streptococcus thermophilus: Genome analysis of phages isolated in Uruguay and ectopic spacer acquisition in CRISPR array

(2017) Rodrigo Achigar et al.   Scientific Reports

CRISPRDetect: A flexible algorithm to define CRISPR arrays

(2016) Ambarish Biswas et al.   BMC GENOMICS

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Virus Variation Resource – improved response to emergent viral outbreaks

(2016) Eneida L. Hatcher et al.   NUCLEIC ACIDS RESEARCH

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Rapid evolution of the human gut virome

(2013) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for the widespread distribution of CRISPR-Cas system in the PhylumCyanobacteria

(2013) Fei Cai et al.   RNA Biology

The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

(2010) Josiane E. Garneau et al.   NATURE

Bacteriophage resistance mechanisms

(2010) Simon J. Labrie et al.   NATURE REVIEWS MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS