Type IV CRISPR–Cas systems are highly diverse and involved in competition between plasmids

Multidrug-resistant plasmids repress chromosomally encoded T6SS to enable their dissemination

(2019) Gisela Di Venanzio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes

(2019) Daniel J. Nasko et al.   mBio

Direct removal of RNA polymerase barriers to replication by accessory replicative helicases

(2019) Michelle Hawkins et al.   NUCLEIC ACIDS RESEARCH

(Ph)ighting Phages: How Bacteria Resist Their Parasites

(2019) Jakob T. Rostøl et al.   Cell Host & Microbe

CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species

(2019) Nathan D. McDonald et al.   BMC GENOMICS

The next generation of CRISPR–Cas technologies and applications

(2019) Adrian Pickar-Oliver et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Origins and evolution of CRISPR-Cas systems

(2019) Eugene V. Koonin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A type III-A CRISPR-Cas system employs degradosome nucleases to ensure robust immunity

(2019) Lucy Chou-Zheng et al.   eLife

Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration

(2019) Sanne E. Klompe et al.   NATURE

CRISPR–Cas in mobile genetic elements: counter-defence and beyond

(2019) Guilhem Faure et al.   NATURE REVIEWS MICROBIOLOGY

Structural basis of Type IV CRISPR RNA biogenesis by a Cas6 endoribonuclease

(2019) Hannah N. Taylor et al.   RNA Biology

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance

(2019) Tanita Wein et al.   Nature Communications

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

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

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

(2018) Pawel S Krawczyk et al.   NUCLEIC ACIDS RESEARCH

Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis

(2018) Sergey A. Shmakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families

(2018) Shiraz A. Shah et al.   RNA Biology

Mobile DNAs as Ecologically and Evolutionarily Independent Units of Life

(2018) Timothy M. Ghaly et al.   TRENDS IN MICROBIOLOGY

High-resolution identification of multiple Salmonella serovars in a single sample using CRISPR-SeroSeq

(2018) Cameron P. Thompson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Integrative analysis of fitness and metabolic effects of plasmids in Pseudomonas aeruginosa PAO1

(2018) Alvaro San Millan et al.   ISME Journal

Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum

(2018) Ahsen Özcan et al.   Nature Microbiology

Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back

(2017) Eugene V. Koonin et al.   Genome Biology and Evolution

The helicase DinG responds to stress due to DNA double strand breaks

(2017) Stephan A. Frye et al.   PLoS One

Antagonism correlates with metabolic similarity in diverse bacteria

(2017) Jakob Russel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems

(2017) Sukrit Silas et al.   eLife

The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs

(2017) Adair L. Borges et al.   Annual Review of Virology

CRISPRDetect: A flexible algorithm to define CRISPR arrays

(2016) Ambarish Biswas et al.   BMC GENOMICS

CRISPR-Cas Systems Optimize Their Immune Response by Specifying the Site of Spacer Integration

(2016) Jon McGinn et al.   MOLECULAR CELL

Applications of CRISPR technologies in research and beyond

(2016) Rodolphe Barrangou et al.   NATURE BIOTECHNOLOGY

Asymmetric positioning of Cas1–2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system

(2016) K.N.R. Yoganand et al.   NUCLEIC ACIDS RESEARCH

Type 3 Fimbriae Encoded on Plasmids Are Expressed from a Unique Promoter without Affecting Host Motility, Facilitating an Exceptional Phenotype That Enhances Conjugal Plasmid Transfer

(2016) Jonas Stenløkke Madsen et al.   PLoS One

The role of Cas8 in type I CRISPR interference

(2015) Simon Cass et al.   BIOSCIENCE REPORTS

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

An updated evolutionary classification of CRISPR–Cas systems

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

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

CRISPR adaptive immune systems of Archaea

(2014) Gisle Vestergaard et al.   RNA Biology

A Linear-Time Algorithm for Gaussian and Non-Gaussian Trait Evolution Models

(2014) Lam si Tung Ho et al.   SYSTEMATIC BIOLOGY

Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes

(2014) Jennifer R Huddleston   Infection and Drug Resistance

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

(2013) Lei S. Qi et al.   CELL

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A novel interference mechanism by a type IIIB CRISPR-Cmr module inSulfolobus

(2013) Ling Deng et al.   MOLECULAR MICROBIOLOGY

A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity

(2013) Kimberley D. Seed et al.   NATURE

Transcription-replication encounters, consequences and genomic instability

(2013) Anne Helmrich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Protospacer recognition motifs

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

Type I-E CRISPR-Cas Systems Discriminate Target from Non-Target DNA through Base Pairing-Independent PAM Recognition

(2013) Edze R. Westra et al.   PLoS Genetics

Crystal Structure of the Largest Subunit of a Bacterial RNA-guided Immune Complex and Its Role in DNA Target Binding

(2012) Sabin Mulepati et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3

(2012) Edze R. Westra et al.   MOLECULAR CELL

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

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

Staphylococcus aureusDinG, a helicase that has evolved into a nuclease

(2011) Anne-Marie McRobbie et al.   BIOCHEMICAL JOURNAL

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

Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system

(2011) Tomas Sinkunas et al.   EMBO JOURNAL

More closely related species are more ecologically similar in an experimental test

(2011) J. H. Burns et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Archaeal CRISPR-based immune systems: exchangeable functional modules

(2011) Roger A. Garrett et al.   TRENDS IN MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism

(2009) Shiraz Ali Shah et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

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

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo

(2009) Hasna Boubakri et al.   EMBO JOURNAL

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

(2009)   MICROBIOLOGY-SGM

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

(2008) A. F. Andersson et al.   SCIENCE