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

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

(2016) Jason M. Peters et al.   CELL

The design and analysis of transposon insertion sequencing experiments

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

Gene Essentiality Is a Quantitative Property Linked to Cellular Evolvability

(2015) Gaowen Liu et al.   CELL

General and condition-specific essential functions ofPseudomonas aeruginosa

(2015) Samuel A. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering

(2014) M. Juhas et al.   MICROBIOLOGY-SGM

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

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

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

The predictability of molecular evolution during functional innovation

(2014) D. Blank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shigellareroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth

(2014) David Kentner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing

(2014) Justin R. Pritchard et al.   PLoS Genetics

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

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

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

High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data

(2013) Michael C. Chao et al.   NUCLEIC ACIDS RESEARCH

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships

(2013) Nives Škunca et al.   PLoS Computational Biology

Gene Fitness Landscapes of Vibrio cholerae at Important Stages of Its Life Cycle

(2013) Heather D. Kamp et al.   PLoS Pathogens

Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis

(2012) Brian A Klein et al.   BMC GENOMICS

High-throughput comparison of gene fitness among related bacteria

(2012) Rocio Canals et al.   BMC GENOMICS

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

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Outer Membrane Protein A (OmpA): A New Player in Shigella flexneri Protrusion Formation and Inter-Cellular Spreading

(2012) Cecilia Ambrosi et al.   PLoS One

Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability

(2012) Tobias Bergmiller et al.   PLoS Genetics

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

The essential genome of a bacterium

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

The Sequence Alignment/Map format and SAMtools

(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

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

Reduction of acetate accumulation in Escherichia coli cultures for increased recombinant protein production

(2007) Matthew S. Wong et al.   METABOLIC ENGINEERING