Prophages are associated with extensive CRISPR–Cas auto-immunity

Targeting of temperate phages drives loss of type I CRISPR–Cas systems

(2020) Clare Rollie et al.   NATURE

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

(2020) Franziska Wimmer et al.   Frontiers in Microbiology

Co-evolution within structured bacterial communities results in multiple expansion of CRISPR loci and enhanced immunity

(2020) Nora C Pyenson et al.   eLife

Machine-learning approach expands the repertoire of anti-CRISPR protein families

(2020) Ayal B. Gussow et al.   Nature Communications

Imprecise Spacer Acquisition Generates CRISPR-Cas Immune Diversity through Primed Adaptation

(2019) Simon A. Jackson et al.   Cell Host & Microbe

Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas

(2019) Adam E. Dolan et al.   MOLECULAR CELL

Cas4–Cas1 fusions drive efficient PAM selection and control CRISPR adaptation

(2019) Cristóbal Almendros et al.   NUCLEIC ACIDS RESEARCH

Catalytically Active Cas9 Mediates Transcriptional Interference to Facilitate Bacterial Virulence

(2019) Hannah K. Ratner et al.   MOLECULAR CELL

Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d

(2019) Bo Zhang et al.   Nature Communications

A Simple Criterion for Inferring CRISPR Array Direction

(2019) Ognjen Milicevic et al.   Frontiers in Microbiology

Bioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer Approaches

(2019) Yanbin Yin et al.   mSystems

Detection of spacer precursors formed in vivo during primed CRISPR adaptation

(2019) Anna A. Shiriaeva et al.   Nature Communications

Type I-F CRISPR-Cas resistance against virulent phages results in abortive infection and provides population-level immunity

(2019) Bridget N. J. Watson et al.   Nature Communications

Protein Inhibitors of CRISPR-Cas9

(2018) Joseph Bondy-Denomy   ACS Chemical Biology

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

Incomplete prophage tolerance by type III-A CRISPR-Cas systems reduces the fitness of lysogenic hosts

(2018) Gregory W. Goldberg et al.   Nature Communications

PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures

(2018) Daniel Gleditzsch et al.   RNA Biology

Discovery of widespread Type I and Type V CRISPR-Cas inhibitors

(2018) Nicole D. Marino et al.   SCIENCE

Systematic discovery of natural CRISPR-Cas12a inhibitors

(2018) Kyle E. Watters et al.   SCIENCE

Deciphering, Communicating, and Engineering the CRISPR PAM

(2017) Ryan T. Leenay et al.   JOURNAL OF MOLECULAR BIOLOGY

The spacer size of I-B CRISPR is modulated by the terminal sequence of the protospacer

(2017) Ming Li et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas: Adapting to change

(2017) Simon A. Jackson et al.   SCIENCE

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

(2017) Sergey A. Shmakov et al.   mBio

CRISPRDetect: A flexible algorithm to define CRISPR arrays

(2016) Ambarish Biswas et al.   BMC GENOMICS

Type I CRISPR-Cas targets endogenous genes and regulates virulence to evade mammalian host immunity

(2016) Rongpeng Li et al.   CELL RESEARCH

Friendly Fire: Biological Functions and Consequences of Chromosomal Targeting by CRISPR-Cas Systems

(2016) Gary E. Heussler et al.   JOURNAL OF BACTERIOLOGY

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation

(2016) Tim Künne et al.   MOLECULAR CELL

Altered stoichiometryEscherichia coliCascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation

(2016) Konstantin Kuznedelov et al.   NUCLEIC ACIDS RESEARCH

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Highly efficient primed spacer acquisition from targets destroyed by theEscherichia colitype I-E CRISPR-Cas interfering complex

(2016) Ekaterina Semenova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR–Cas system

(2016) Raymond H. J. Staals et al.   Nature Communications

Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species

(2016) April Pawluk et al.   Nature Microbiology

Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems

(2015) Jiuyu Wang et al.   CELL

Foreign DNA capture during CRISPR–Cas adaptive immunity

(2015) James K. Nuñez et al.   NATURE

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

Harnessing Type I and Type III CRISPR-Cas systems for genome editing

(2015) Yingjun Li et al.   NUCLEIC ACIDS RESEARCH

CRISPR-based screening of genomic island excision events in bacteria

(2015) Kurt Selle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Efficient programmable gene silencing by Cascade

(2014) Devashish Rath et al.   NUCLEIC ACIDS RESEARCH

Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression

(2014) Michelle L. Luo et al.   NUCLEIC ACIDS RESEARCH

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

Degenerate target sites mediate rapid primed CRISPR adaptation

(2014) P. C. Fineran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

(2013) Vikram Pattanayak et al.   NATURE BIOTECHNOLOGY

Unexpectedly broad target recognition of the CRISPR-mediated virus defence system in the archaeon Sulfolobus solfataricus

(2013) Andrea Manica et al.   NUCLEIC ACIDS RESEARCH

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Protospacer recognition motifs

(2013) Shiraz A. Shah et al.   RNA Biology

Cytotoxic Chromosomal Targeting by CRISPR/Cas Systems Can Reshape Bacterial Genomes and Expel or Remodel Pathogenicity Islands

(2013) Reuben B. Vercoe et al.   PLoS Genetics

The CRISPRs, They Are A-Changin': How Prokaryotes Generate Adaptive Immunity

(2012) Edze R. Westra et al.   Annual Review of Genetics

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

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

Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence

(2011) E. Semenova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The Escherichia coli CRISPR System Protects from   Lysogenization, Lysogens, and Prophage Induction

(2010) R. Edgar et al.   JOURNAL OF BACTERIOLOGY

Self-targeting by CRISPR: gene regulation or autoimmunity?

(2010) Adi Stern et al.   TRENDS IN GENETICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex

(2009) Caryn R. Hale et al.   CELL

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

(2009)   MICROBIOLOGY-SGM

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

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