Identification of Natural CRISPR Systems and Targets in the Human Microbiome

CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers

(2020) Franziska Wimmer et al.   Frontiers in Microbiology

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

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

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

CRISPR still needs microbiologists

(2018)   Nature Microbiology

Characterizing the activity of abundant, diverse and active CRISPR-Cas systems in lactobacilli

(2018) Alexandra B. Crawley et al.   Scientific Reports

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life

(2018) Tommi Vatanen et al.   Nature Microbiology

Five big mysteries about CRISPR’s origins

(2017) Heidi Ledford   NATURE

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

(2017) Sergey A. Shmakov et al.   mBio

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

(2017) Abraham G. Moller et al.   PeerJ

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems

(2016) Adrian G. Patterson et al.   MOLECULAR CELL

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

(2016) David Burstein et al.   Nature Communications

Haemophilus haemolyticus Interaction with Host Cells Is Different to Nontypeable Haemophilus influenzae and Prevents NTHi Association with Epithelial Cells

(2016) Janessa L. Pickering et al.   Frontiers in Cellular and Infection Microbiology

DNA methylation in bacteria: from the methyl group to the methylome

(2015) María A Sánchez-Romero et al.   CURRENT OPINION IN MICROBIOLOGY

Phage-bacteria interaction network in human oral microbiome

(2015) Jinfeng Wang et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories

(2015) Christine L Sun et al.   ISME Journal

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

An updated evolutionary classification of CRISPR–Cas systems

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

Revisiting phage therapy: new applications for old resources

(2015) Franklin L. Nobrega et al.   TRENDS IN MICROBIOLOGY

Bacteriophage and their potential roles in the human oral cavity

(2015) Anna Edlund et al.   Journal of Oral Microbiology

Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs

(2014) Anna A Gogleva et al.   BMC GENOMICS

Characterization of bacteriophage communities and CRISPR profiles from dental plaque

(2014) Mayuri Naidu et al.   BMC MICROBIOLOGY

Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens

(2014) Asma Hatoum-Aslan et al.   CURRENT OPINION IN MICROBIOLOGY

Human oral viruses are personal, persistent and gender-consistent

(2014) Shira R Abeles et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

CRISPR–Cas systems: beyond adaptive immunity

(2014) Edze R. Westra et al.   NATURE REVIEWS MICROBIOLOGY

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

(2013) K. Vasu et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A CRISPR/Cas system mediates bacterial innate immune evasion and virulence

(2013) Timothy R. Sampson et al.   NATURE

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

(2013) Connor T. Skennerton et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics of defense systems in archaea and bacteria

(2013) Kira S. Makarova et al.   NUCLEIC ACIDS RESEARCH

DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array

(2013) I. Yosef et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR-Cas and restriction–modification systems are compatible and increase phage resistance

(2013) Marie-Ève Dupuis et al.   Nature Communications

Alternative Roles for CRISPR/Cas Systems in Bacterial Pathogenesis

(2013) Timothy R. Sampson et al.   PLoS Pathogens

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses

(2012) David T. Pride et al.   ENVIRONMENTAL MICROBIOLOGY

The interconnection between biofilm formation and horizontal gene transfer

(2012) Jonas Stenløkke Madsen et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

(2012) A. Stern et al.   GENOME RESEARCH

The human microbiome: A hot spot of microbial horizontal gene transfer

(2012) Li Liu et al.   GENOMICS

The highly dynamic CRISPR1 system ofStreptococcus agalactiaecontrols the diversity of its mobilome

(2012) Maria-José Lopez-Sanchez et al.   MOLECULAR MICROBIOLOGY

A framework for human microbiome research

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

(2012) Ariel D. Weinberger et al.   PLoS Computational Biology

Diverse CRISPRs Evolving in Human Microbiomes

(2012) Mina Rho et al.   PLoS Genetics

The human commensal Bacteroides fragilis binds intestinal mucin

(2011) Julie Y. Huang et al.   ANAEROBE

Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems

(2011) Kira S Makarova et al.   Biology Direct

Non-Identity-Mediated CRISPR-Bacteriophage Interaction Mediated via the Csy and Cas3 Proteins

(2011) K. C. Cady et al.   JOURNAL OF BACTERIOLOGY

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

CRISPR/Cas System and Its Role in Phage-Bacteria Interactions

(2010) Hélène Deveau et al.   Annual Review of Microbiology

Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time

(2010) D. T. Pride et al.   GENOME RESEARCH

The CRISPR System: Small RNA-Guided Defense in Bacteria and Archaea

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

Self-targeting by CRISPR: gene regulation or autoimmunity?

(2010) Adi Stern et al.   TRENDS IN GENETICS

CRISPR-based adaptive and heritable immunity in prokaryotes

(2009) John van der Oost et al.   TRENDS IN BIOCHEMICAL SCIENCES

Comparative analysis of CRISPR loci in lactic acid bacteria genomes

(2008) Philippe Horvath et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Interaction between Bacteriophage DMS3 and Host CRISPR Region Inhibits Group Behaviors of Pseudomonas aeruginosa

(2008) M. E. Zegans et al.   JOURNAL OF BACTERIOLOGY

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

(2008) S. J. J. Brouns et al.   SCIENCE

CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA

(2008) Luciano A. Marraffini et al.   SCIENCE