The Essential Genome of Escherichia coli K-12

Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

(2016) Nikki E. Freed et al.   BMC MICROBIOLOGY

Genes Required for the Fitness of Salmonella enterica Serovar Typhimurium during Infection of Immunodeficientgp91−/−phoxMice

(2016) Andrew J. Grant et al.   INFECTION AND IMMUNITY

Global Tn-seq analysis of carbohydrate utilization and vertebrate infectivity of Borrelia burgdorferi

(2016) Erin B. Troy et al.   MOLECULAR MICROBIOLOGY

Fluorescence-Based Flow Sorting in Parallel with Transposon Insertion Site Sequencing Identifies Multidrug Efflux Systems in Acinetobacter baumannii

(2016) Karl A. Hassan et al.   mBio

Mutations Affecting Potassium Import Restore the Viability of the Escherichia coli DNA Polymerase III holD Mutant

(2016) Adeline Durand et al.   PLoS Genetics

Defining key roles for auxiliary proteins in an ABC transporter that maintains bacterial outer membrane lipid asymmetry

(2016) Shuhua Thong et al.   eLife

Delivery of Cardiolipins to the Salmonella Outer Membrane Is Necessary for Survival within Host Tissues and Virulence

(2015) Zachary D. Dalebroux et al.   Cell Host & Microbe

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

(2015) Sina Solaimanpour et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Detecting Envelope Stress by Monitoring β-Barrel Assembly

(2014) Seung-Hyun Cho et al.   CELL

Identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems

(2014) Patrick D. Curtis et al.   MOLECULAR MICROBIOLOGY

ssb Gene Duplication Restores the Viability of ΔholC and ΔholD Escherichia coli Mutants

(2014) Stéphane Duigou et al.   PLoS Genetics

A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data

(2013) Michael A DeJesus et al.   BMC BIOINFORMATICS

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis

(2013) F. Sarmiento et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Serum Resistome of a Globally Disseminated Multidrug Resistant Uropathogenic Escherichia coli Clone

(2013) Minh-Duy Phan et al.   PLoS Genetics

EcoGene 3.0

(2012) Jindan Zhou et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Aldert Zomer et al.   PLoS One

Virulence determinants in the obligate intracellular pathogen Chlamydia trachomatis revealed by forward genetic approaches

(2012) B. D. Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Control of Virulence by Small RNAs in Streptococcus pneumoniae

(2012) Beth Mann et al.   PLoS Pathogens

Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis

(2012) Yanjia J. Zhang et al.   PLoS Pathogens

Translation of a minigene in the 5′ leader sequence of the enterohaemorrhagicEscherichia coli LEE1transcription unit affects expression of the neighbouring downstream gene

(2011) Md. Shahidul Islam et al.   BIOCHEMICAL JOURNAL

The essential genome of a bacterium

(2011) B. Christen et al.   Molecular Systems Biology

Complex transcriptional organization regulates an Escherichia coli locus implicated in lipopolysaccharide biogenesis

(2011) Alessandra M. Martorana et al.   RESEARCH IN MICROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Multiple regions along the Escherichia coli FtsK protein are implicated in cell division

(2010) Nelly Dubarry et al.   MOLECULAR MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

Update on the Keio collection of Escherichia coli single-gene deletion mutants

(2009) Natsuko Yamamoto et al.   Molecular Systems Biology

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

(2009) Tim van Opijnen et al.   NATURE METHODS

An ABC transport system that maintains lipid asymmetry in the Gram-negative outer membrane

(2009) J. C. Malinverni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung

(2009) J. D. Gawronski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Genetic Interaction Between the Escherichia coli AcpT Phosphopantetheinyl Transferase and the YejM Inner Membrane Protein

(2008) N. R. De Lay et al.   GENETICS

Small membrane proteins found by comparative genomics and ribosome binding site models

(2008) Matthew R. Hemm et al.   MOLECULAR MICROBIOLOGY