Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes

Long-Read Sequencing – A Powerful Tool in Viral Transcriptome Research

(2019) Zsolt Boldogkői et al.   TRENDS IN MICROBIOLOGY

Long reads: their purpose and place

(2018) Martin O Pollard et al.   HUMAN MOLECULAR GENETICS

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

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins

(2018) Alexander P. Hynes et al.   Nature Communications

Role of nucleotide identity in effective CRISPR target escape mutations

(2018) Tim Künne et al.   NUCLEIC ACIDS RESEARCH

Metapopulation Structure of CRISPR-Cas Immunity in Pseudomonas aeruginosa and Its Viruses

(2018) Whitney E. England et al.   mSystems

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Dynamics of Escherichia coli type I-E CRISPR spacers over 42 000 years

(2017) Ekaterina Savitskaya et al.   MOLECULAR ECOLOGY

Diversity and evolution of class 2 CRISPR–Cas systems

(2017) Sergey Shmakov et al.   NATURE REVIEWS MICROBIOLOGY

Optimal number of spacers in CRISPR arrays

(2017) Alexander Martynov et al.   PLoS Computational Biology

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

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

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

(2016) Jon McGinn et al.   MOLECULAR CELL

Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data

(2016) Yuzhen Ye et al.   RNA

Long-read sequencing and de novo assembly of a Chinese genome

(2016) Lingling Shi et al.   Nature Communications

The CRISPR-Cas immune system: Biology, mechanisms and applications

(2015) Devashish Rath et al.   BIOCHIMIE

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus–host coevolution

(2015) Eugene V. Koonin et al.   Molecular BioSystems

CRISPR adaptation biases explain preference for acquisition of foreign DNA

(2015) Asaf Levy et al.   NATURE

Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins

(2015) Joseph Bondy-Denomy et al.   NATURE

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome

(2015) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

(2014) Omer S. Alkhnbashi et al.   BIOINFORMATICS

Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs

(2014) Ambarish Biswas et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

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

CRISPRTarget

(2013) Ambarish Biswas et al.   RNA Biology

crRNA and tracrRNA guide Cas9-mediated DNA interference inStreptococcus thermophilus

(2013) Tautvydas Karvelis et al.   RNA Biology

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

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

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

(2012) Ido Yosef et al.   NUCLEIC ACIDS RESEARCH

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

CRISPR-based immune systems of the Sulfolobales: complexity and diversity

(2011) Roger A. Garrett et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Nature and Intensity of Selection Pressure on CRISPR-Associated Genes

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

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

The phage-host arms race: Shaping the evolution of microbes

(2010) Adi Stern et al.   BIOESSAYS

Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers

(2010) Soley Gudbergsdottir et al.   MOLECULAR MICROBIOLOGY

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

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY