Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis

Comparisons of Shewanella strains based on genome annotations, modeling, and experiments

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

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Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

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

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

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Computational analysis of bacterial RNA-Seq data

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Identification of T6SS-dependent effector and immunity proteins by Tn-seq in Vibrio cholerae

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Approaches to querying bacterial genomes with transposon-insertion sequencing

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Metabolic Footprinting of Mutant Libraries to Map Metabolite Utilization to Genotype

(2012) Richard Baran et al.   ACS Chemical Biology

Inference of gene regulatory networks from genome-wide knockout fitness data

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Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis

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Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions

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Anomalies of the anaerobic tricarboxylic acid cycle inShewanella oneidensisrevealed by Tn-seq

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

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Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis

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Identification of MrtAB, an ABC Transporter Specifically Required for Yersinia pseudotuberculosis to Colonize the Mesenteric Lymph Nodes

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Construction and elementary mode analysis of a metabolic model for Shewanella oneidensis MR-1

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Recent advances in reconstruction and applications of genome-scale metabolic models

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Genome-wide metabolic network reconstruction of the picoalga Ostreococcus

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A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

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

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The Pfam protein families database

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Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

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An essential role for UshA in processing of extracellular flavin electron shuttles by Shewanella oneidensis

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High-throughput generation, optimization and analysis of genome-scale metabolic models

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Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples

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Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation

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

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

Quantitative phenotyping via deep barcode sequencing

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

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

Genome-scale gene/reaction essentiality and synthetic lethality analysis

(2009) Patrick F Suthers et al.   Molecular Systems Biology

Automated design of synthetic ribosome binding sites to control protein expression

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

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A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae

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