Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems

The Biology of CRISPR-Cas: Backward and Forward

(2018) Frank Hille et al.   CELL

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

(2018) Cindy J. Castelle et al.   CELL

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

(2018) Cindy J. Castelle et al.   NATURE REVIEWS MICROBIOLOGY

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Towards a balanced view of the bacterial tree of life

(2017) Frederik Schulz et al.   Microbiome

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

The chemistry of Cas9 and its CRISPR colleagues

(2017) Janice S. Chen et al.   Nature Reviews Chemistry

New CRISPR–Cas systems from uncultivated microbes

(2016) David Burstein et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

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

(2016) David Burstein et al.   Nature Communications

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense

(2015) Edze R. Westra et al.   CURRENT BIOLOGY

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

(2015) Sergey Shmakov et al.   MOLECULAR CELL

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

CRISPR adaptation biases explain preference for acquisition of foreign DNA

(2015) Asaf Levy et al.   NATURE

CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus

(2015) David Paez-Espino et al.   mBio

Diverse uncultivated ultra-small bacterial cells in groundwater

(2015) Birgit Luef et al.   Nature Communications

Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harboring a CRISPR-like Cas4 protein

(2015) Steven P. T. Hooton et al.   Frontiers in Microbiology

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity

(2014) James K Nuñez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China

(2012) Zhao-Qi Song et al.   ENVIRONMENTAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Self-targeting by CRISPR: gene regulation or autoimmunity?

(2010) Adi Stern et al.   TRENDS IN GENETICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

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

On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing

(2007) Ibtissem Grissa et al.   BIOCHIMIE