Reconciling high-throughput gene essentiality data with metabolic network reconstructions

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis

(2017) Jennifer A. Bartell et al.   Nature Communications

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

(2017) Zhuo Wang et al.   PLoS Computational Biology

Co-infecting microorganisms dramatically alter pathogen gene essentiality during polymicrobial infection

(2017) Carolyn B. Ibberson et al.   Nature Microbiology

Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides

(2017) Brian T. Burger et al.   mSystems

The design and analysis of transposon insertion sequencing experiments

(2016) Michael C. Chao et al.   NATURE REVIEWS MICROBIOLOGY

Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont

(2016) J. Elijah Powell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis

(2016) Jared T. Broddrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inherent Variability of Growth Media Impacts the Ability of Salmonella Typhimurium to Interact with Host Cells

(2016) Sushmita Sridhar et al.   PLoS One

Glycerophospholipid synthesis and functions in Pseudomonas

(2015) Tatiana Kondakova et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Pseudomonas aeruginosa essentials: an update on investigation of essential genes

(2015) Mario Juhas   MICROBIOLOGY-SGM

Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes

(2015) Yoann Le Breton et al.   Scientific Reports

optGpSampler: An Improved Tool for Uniformly Sampling the Solution-Space of Genome-Scale Metabolic Networks

(2014) Wout Megchelenbrink et al.   PLoS One

Genome-Wide Saturation Mutagenesis of Burkholderia pseudomallei K96243 Predicts Essential Genes and Novel Targets for Antimicrobial Development

(2014) M. G. Moule et al.   mBio

Requirements for Pseudomonas aeruginosa Acute Burn and Chronic Surgical Wound Infection

(2014) Keith H. Turner et al.   PLoS Genetics

A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis

(2013) Soma Ghosh et al.   BMC Systems Biology

Tn-Seq Analysis of Vibrio cholerae Intestinal Colonization Reveals a Role for T6SS-Mediated Antibacterial Activity in the Host

(2013) Yang Fu et al.   Cell Host & Microbe

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

(2013) Tim van Opijnen et al.   NATURE REVIEWS MICROBIOLOGY

A Comprehensive Analysis of In Vitro and In Vivo Genetic Fitness of Pseudomonas aeruginosa Using High-Throughput Sequencing of Transposon Libraries

(2013) David Skurnik et al.   PLoS Pathogens

Inhibition of bacterial thioredoxin reductase: an antibiotic mechanism targeting bacteria lacking glutathione

(2012) Jun Lu et al.   FASEB JOURNAL

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A metabolic network approach for the identification and prioritization of antimicrobial drug targets

(2012) Arvind K. Chavali et al.   TRENDS IN MICROBIOLOGY

In Vivo-Validated Essential Genes Identified in Acinetobacter baumannii by Using Human Ascites Overlap Poorly with Essential Genes Detected on Laboratory Media

(2012) T. C. Umland et al.   mBio

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pseudomonas aeruginosa Reference Strain PA14 Displays Increased Virulence Due to a Mutation in ladS

(2011) Helga Mikkelsen et al.   PLoS One

Essence of life: essential genes of minimal genomes

(2011) Mario Juhas et al.   TRENDS IN CELL BIOLOGY

Genome-Scale Identification of Resistance Functions in Pseudomonas aeruginosa Using Tn-seq

(2011) L. A. Gallagher et al.   mBio

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

Triclosan Resistance of Pseudomonas aeruginosa PAO1 Is Due to FabV, a Triclosan-Resistant Enoyl-Acyl Carrier Protein Reductase

(2009) L. Zhu et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome Diversity of Pseudomonas aeruginosa PAO1 Laboratory Strains

(2009) J. Klockgether et al.   JOURNAL OF BACTERIOLOGY