Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy

A virus or more in (nearly) every cell: ubiquitous networks of virus–host interactions in extreme environments

(2018) Jacob H. Munson-McGee et al.   ISME Journal

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

CRISPR–Cas: Complex Functional Networks and Multiple Roles beyond Adaptive Immunity

(2018) Guilhem Faure et al.   JOURNAL OF MOLECULAR BIOLOGY

DNA double-strand break repair is involved in desiccation resistance of Sinorhizobium meliloti, but is not essential for its symbiotic interaction with Medicago truncatula

(2017) Pierre Dupuy et al.   MICROBIOLOGY-SGM

Five big mysteries about CRISPR’s origins

(2017) Heidi Ledford   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria

(2017) Aude Bernheim et al.   Nature Communications

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

Contribution of reactive oxygen species to thymineless death in Escherichia coli

(2017) Yuzhi Hong et al.   Nature Microbiology

CRISPRDetect: A flexible algorithm to define CRISPR arrays

(2016) Ambarish Biswas et al.   BMC GENOMICS

Prompt repair of hydrogen peroxide-induced DNA lesions prevents catastrophic chromosomal fragmentation

(2016) Tulip Mahaseth et al.   DNA REPAIR

Evolutionary Ecology of Prokaryotic Immune Mechanisms

(2016) Stineke van Houte et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems

(2016) Adrian G. Patterson et al.   MOLECULAR CELL

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

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

(2016) David Burstein et al.   Nature Communications

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

(2016) Benjamin R. K. Roller et al.   Nature Microbiology

A new view of the tree of life

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

Comparison of subset selection methods in linear regression in the context of health-related quality of life and substance abuse in Russia

(2015) Olga Morozova et al.   BMC Medical Research Methodology

Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense

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

An updated evolutionary classification of CRISPR–Cas systems

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

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

The basic building blocks and evolution of CRISPR–Cas systems

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

An ontology for microbial phenotypes

(2014) Marcus C Chibucos et al.   BMC MICROBIOLOGY

BREX is a novel phage resistance system widespread in microbial genomes

(2014) T. Goldfarb et al.   EMBO JOURNAL

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

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

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context

(2013) J. Iranzo et al.   JOURNAL OF BACTERIOLOGY

Comparative genomics of defense systems in archaea and bacteria

(2013) Kira S. Makarova et al.   NUCLEIC ACIDS RESEARCH

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

(2013) Jenna Morgan Lang et al.   PLoS One

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

(2013) Wenyan Jiang et al.   PLoS Genetics

CRISPR Interference Can Prevent Natural Transformation and Virulence Acquisition during In Vivo Bacterial Infection

(2012) David Bikard et al.   Cell Host & Microbe

Viral Diversity Threshold for Adaptive Immunity in Prokaryotes

(2012) A. D. Weinberger et al.   mBio

MissForest--non-parametric missing value imputation for mixed-type data

(2011) D. J. Stekhoven et al.   BIOINFORMATICS

Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems

(2011) Kim-Anh Lê Cao et al.   BMC BIOINFORMATICS

Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage

(2011) Rika E. Anderson et al.   FEMS MICROBIOLOGY ECOLOGY

The influence of external factors on bacteriophages—review

(2011) E. Jończyk et al.   FOLIA MICROBIOLOGICA

Bacteriophage resistance mechanisms

(2010) Simon J. Labrie et al.   NATURE REVIEWS MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The formation of double-strand breaks at multiply damaged sites is driven by the kinetics of excision/incision at base damage in eukaryotic cells

(2009) Stanislav G. Kozmin et al.   NUCLEIC ACIDS RESEARCH

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2009) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic Logistic Regression for Binary Dependent Variables

(2009) Anthony R. Ives et al.   SYSTEMATIC BIOLOGY

Worlds within worlds: evolution of the vertebrate gut microbiota

(2008) Ruth E. Ley et al.   NATURE REVIEWS MICROBIOLOGY