Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes

(2018) Antoine Vigouroux et al.   Molecular Systems Biology

Deep learning improves prediction of CRISPR–Cpf1 guide RNA activity

(2018) Hui Kwon Kim et al.   NATURE BIOTECHNOLOGY

Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance

(2018) Tianmin Wang et al.   Nature Communications

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

(2018) Lun Cui et al.   Nature Communications

High‐throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae

(2017) Xue Liu et al.   Molecular Systems Biology

Refined sgRNA efficacy prediction improves large- and small-scale CRISPR–Cas9 applications

(2017) Maurice Labuhn et al.   NUCLEIC ACIDS RESEARCH

In Silico Meets In Vivo : Towards Computational CRISPR-Based sgRNA Design

(2017) Guo-hui Chuai et al.   TRENDS IN BIOTECHNOLOGY

sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity

(2017) Raj Chari et al.   ACS Synthetic Biology

Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens

(2017) Olaya Rendueles et al.   PLoS Pathogens

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

(2016) Jason M. Peters et al.   CELL

CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes

(2016) Bastiaan Evers et al.   NATURE BIOTECHNOLOGY

Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes

(2016) David W Morgens et al.   NATURE BIOTECHNOLOGY

Applications of CRISPR technologies in research and beyond

(2016) Rodolphe Barrangou et al.   NATURE BIOTECHNOLOGY

A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors

(2016) Ryan J Park et al.   NATURE GENETICS

Consequences of Cas9 cleavage in the chromosome ofEscherichia coli

(2016) Lun Cui et al.   NUCLEIC ACIDS RESEARCH

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

(2016) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

A Role for REP Sequences in Regulating Translation

(2015) Wenxing Liang et al.   MOLECULAR CELL

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Tn-Seq Explorer: A Tool for Analysis of High-Throughput Sequencing Data of Transposon Mutant Libraries

(2015) Sina Solaimanpour et al.   PLoS One

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

A CRISPR-Based Screen Identifies Genes Essential for West-Nile-Virus-Induced Cell Death

(2015) Hongming Ma et al.   Cell Reports

Phage-Encoded Colanic Acid-Degrading Enzyme Permits Lytic Phage Infection of a Capsule-Forming Resistant Mutant Escherichia coli Strain

(2014) Min Soo Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

(2014) Maureen K. Thomason et al.   JOURNAL OF BACTERIOLOGY

Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases

(2014) Robert J Citorik et al.   NATURE BIOTECHNOLOGY

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

(2014) David Bikard et al.   NATURE BIOTECHNOLOGY

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

(2013) Lei S. Qi et al.   CELL

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

One-Step Cloning and Chromosomal Integration of DNA

(2013) François St-Pierre et al.   ACS Synthetic Biology

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

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

EcoGene 3.0

(2012) Jindan Zhou et al.   NUCLEIC ACIDS RESEARCH

Improved plasmid-based system for fully regulated off-to-on gene expression in Escherichia coli: Application to production of toxic proteins

(2012) John E. Cronan   PLASMID

Regulation of the Escherichia coli HipBA Toxin-Antitoxin System by Proteolysis

(2012) Sonja Hansen et al.   PLoS One

ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data

(2012) Aldert Zomer et al.   PLoS One

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Tools from viruses: Bacteriophage successes and beyond

(2012) Marine Henry et al.   VIROLOGY

The Rcs phosphorelay: more than just a two-component pathway

(2010) David J Clarke   Future Microbiology

The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

(2010) Josiane E. Garneau et al.   NATURE

A Forward-Genetic Screen and Dynamic Analysis of Lambda Phage Host-Dependencies Reveals an Extensive Interaction Network and a New Anti-Viral Strategy

(2010) Nathaniel D. Maynard et al.   PLoS Genetics

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

(2008) S. J. J. Brouns et al.   SCIENCE