Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq

Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity

(2020) Wenyan Jiang et al.   CELL

A decade of advances in transposon-insertion sequencing

(2020) Amy K. Cain et al.   NATURE REVIEWS GENETICS

Pneumolysin: Pathogenesis and Therapeutic Target

(2020) Andrew T. Nishimoto et al.   Frontiers in Microbiology

Synthetic gene-regulatory networks in the opportunistic human pathogen Streptococcus pneumoniae

(2020) Robin A. Sorg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events

(2020) Jun Kurushima et al.   eLife

Optimization and Characterization of a Galleria mellonella Larval Infection Model for Virulence Studies and the Evaluation of Therapeutics Against Streptococcus pneumoniae

(2019) Freya Cools et al.   Frontiers in Microbiology

Three New Integration Vectors and Fluorescent Proteins for Use in the Opportunistic Human Pathogen Streptococcus pneumoniae

(2019) Keller et al.   Genes

Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi

(2019) Henry H. Lee et al.   Nature Microbiology

Therapeutic Synergy Between Antibiotics and Pulmonary Toll-Like Receptor 5 Stimulation in Antibiotic-Sensitive or -Resistant Pneumonia

(2019) Laura Matarazzo et al.   Frontiers in Immunology

Modulating pathogenesis with Mobile-CRISPRi

(2019) Jiuxin Qu et al.   JOURNAL OF BACTERIOLOGY

Streptococcus pneumoniae: transmission, colonization and invasion

(2018) Jeffrey N. Weiser et al.   NATURE REVIEWS MICROBIOLOGY

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

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

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

(2017) Xue Liu et al.   Molecular Systems Biology

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

(2016) Jason M. Peters et al.   CELL

Infection of zebrafish embryos with live fluorescent Streptococcus pneumoniae as a real-time pneumococcal meningitis model

(2016) Kin Ki Jim et al.   Journal of Neuroinflammation

Single Cell Bottlenecks in the Pathogenesis of Streptococcus pneumoniae

(2016) Masamitsu Kono et al.   PLoS Pathogens

Community Behavior and Spatial Regulation within a Bacterial Microcolony in Deep Tissue Sites Serves to Protect against Host Attack

(2015) Kimberly M. Davis et al.   Cell Host & Microbe

Experimental approaches to phenotypic diversity in infection

(2015) Saskia Kreibich et al.   CURRENT OPINION IN MICROBIOLOGY

The Plasma S-adenosylmethionine Level is Associated With the Severity of Hepatitis B-Related Liver Disease

(2015) Ting Li et al.   MEDICINE

Sequence tag–based analysis of microbial population dynamics

(2015) Sören Abel et al.   NATURE METHODS

Essential roles of methionine andS-adenosylmethionine in the autarkic lifestyle ofMycobacterium tuberculosis

(2015) Michael Berney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microscale insights into pneumococcal antibiotic mutant selection windows

(2015) Robin A. Sorg et al.   Nature Communications

Analysis of Bottlenecks in Experimental Models of Infection

(2015) Sören Abel et al.   PLoS Pathogens

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Influenza Promotes Pneumococcal Growth during Coinfection by Providing Host Sialylated Substrates as a Nutrient Source

(2014) Steven J. Siegel et al.   Cell Host & Microbe

The co-pathogenesis of influenza viruses with bacteria in the lung

(2014) Jonathan A. McCullers   NATURE REVIEWS MICROBIOLOGY

CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems

(2014) Lihua J. Zhu et al.   PLoS One

The Role of Host and Microbial Factors in the Pathogenesis of Pneumococcal Bacteraemia Arising from a Single Bacterial Cell Bottleneck

(2014) Alice Gerlini et al.   PLoS Pathogens

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Lei S. Qi et al.   CELL

Adult zebrafish model for pneumococcal pathogenesis

(2013) Anni Saralahti et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Within-Host Selection Is Limited by an Effective Population of Streptococcus pneumoniae during Nasopharyngeal Colonization

(2013) Yuan Li et al.   INFECTION AND IMMUNITY

Interleukin-22 Reduces Lung Inflammation during Influenza A Virus Infection and Protects against Secondary Bacterial Infection

(2013) S. Ivanov et al.   JOURNAL OF VIROLOGY

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

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

A fine scale phenotype-genotype virulence map of a bacterial pathogen

(2012) T. van Opijnen et al.   GENOME RESEARCH

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Structural basis for TetM-mediated tetracycline resistance

(2012) A. Donhofer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Novel Mechanism of Programmed Cell Death in Bacteria by Toxin–Antitoxin Systems Corrupts Peptidoglycan Synthesis

(2011) Hannes Mutschler et al.   PLOS BIOLOGY

Mucosal Administration of Flagellin Protects Mice from Streptococcus pneumoniae Lung Infection

(2010) N. Munoz et al.   INFECTION AND IMMUNITY

Genome-Wide Identification ofStreptococcus pneumoniaeGenes Essential for Bacterial Replication during Experimental Meningitis

(2010) T. E. Molzen et al.   INFECTION AND IMMUNITY

Pathogenesis, treatment, and prevention of pneumococcal pneumonia

(2009) Tom van der Poll et al.   LANCET

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms

(2009) Tim van Opijnen et al.   NATURE METHODS

Animal Models of Streptococcus pneumoniae Disease

(2008) D. Chiavolini et al.   CLINICAL MICROBIOLOGY REVIEWS

Calcium efflux is essential for bacterial survival in the eukaryotic host

(2008) Jason W. Rosch et al.   MOLECULAR MICROBIOLOGY

Genetic Requirement for Pneumococcal Ear Infection

(2008) Huaiqing Chen et al.   PLoS One