The evolutionary history and diagnostic utility of the CRISPR-Cas system withinSalmonella entericassp.enterica

Evolutionary causes and consequences of diversified CRISPR immune profiles in natural populations

(2015) Whitney E. England et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The basic building blocks and evolution of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica

(2014) Pimlapas Leekitcharoenphon et al.   PLoS One

Molecular methods for serovar determination of Salmonella

(2013) Chunlei Shi et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters

(2013) Ruth E. Timme et al.   Genome Biology and Evolution

Pathogen typing in the genomics era: MLST and the future of molecular epidemiology

(2013) Marcos Pérez-Losada et al.   INFECTION GENETICS AND EVOLUTION

A CRISPR view of genome sequences

(2013) Amy K. Cain et al.   NATURE REVIEWS MICROBIOLOGY

On the Evolutionary History, Population Genetics and Diversity among Isolates of Salmonella Enteritidis PFGE Pattern JEGX01.0004

(2013) Marc W. Allard et al.   PLoS One

Structure and Genetic Content of the Megaplasmids of Neurotoxigenic Clostridium butyricum Type E Strains from Italy

(2013) Angelo Iacobino et al.   PLoS One

Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona

(2013) Zhemin Zhou et al.   PLoS Genetics

Dealing with the Evolutionary Downside of CRISPR Immunity: Bacteria and Beneficial Plasmids

(2013) Wenyan Jiang et al.   PLoS Genetics

CRISPR-Cas systems and RNA-guided interference

(2013) Rodolphe Barrangou   Wiley Interdisciplinary Reviews-RNA

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

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

High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

(2012) Marc W Allard et al.   BMC GENOMICS

The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella enterica subsp. enterica serovar Enteritidis

(2012) Nikki Shariat et al.   FOOD MICROBIOLOGY

Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak

(2012) Anthony P. Underwood et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli

(2012) Ido Yosef et al.   NUCLEIC ACIDS RESEARCH

CRISPR Typing and Subtyping for Improved Laboratory Surveillance of Salmonella Infections

(2012) Laëtitia Fabre et al.   PLoS One

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

(2012) Mark Achtman et al.   PLoS Pathogens

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type

(2011) Henk C. den Bakker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars ofSalmonella entericasubsp.enterica

(2011) Fenyun Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

(2011) Henk C den Bakker et al.   BMC GENOMICS

Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference

(2011) Natalia Beloglazova et al.   EMBO JOURNAL

Nature and Intensity of Selection Pressure on CRISPR-Associated Genes

(2011) N. Takeuchi et al.   JOURNAL OF BACTERIOLOGY

Comparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution

(2011) W. F. Fricke et al.   JOURNAL OF BACTERIOLOGY

Evolution and classification of the CRISPR–Cas systems

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

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Evolutionary Dynamics of Clustered Irregularly Interspaced Short Palindromic Repeat Systems in the Ocean Metagenome

(2010) V. A. Sorokin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

(2010) Luciano A. Marraffini et al.   NATURE REVIEWS GENETICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

The Small, Slow and Specialized CRISPR and Anti-CRISPR of Escherichia and Salmonella

(2010) Marie Touchon et al.   PLoS One

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

Nasty Viruses, Costly Plasmids, Population Dynamics, and the Conditions for Establishing and Maintaining CRISPR-Mediated Adaptive Immunity in Bacteria

(2010) Bruce R. Levin   PLoS Genetics

Viral biogeography revealed by signatures inSulfolobus islandicusgenomes

(2009) Nicole L. Held et al.   ENVIRONMENTAL MICROBIOLOGY

CRISPR-based adaptive and heritable immunity in prokaryotes

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

A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE

(2008) Michael P. Cummings et al.   EVOLUTION

Comparative analysis of CRISPR loci in lactic acid bacteria genomes

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

A bacterial metapopulation adapts locally to phage predation despite global dispersal

(2007) V. Kunin et al.   GENOME RESEARCH