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Repeated evolution and the impact of evolutionary history on adaptation

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Development of a comparative genomic fingerprinting assay for rapid and high resolution genotyping of Arcobacter butzleri

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Resistance to rifampicin: a review

(2014) Beth P Goldstein   JOURNAL OF ANTIBIOTICS

The CpxR/CpxA Two-component Regulatory System Up-regulates the Multidrug Resistance Cascade to FacilitateEscherichia coliResistance to a Model Antimicrobial Peptide

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Testing the Role of Genetic Background in Parallel Evolution Using the Comparative Experimental Evolution of Antibiotic Resistance

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Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

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Linking System-Wide Impacts of RNA Polymerase Mutations to the Fitness Cost of Rifampin Resistance in Pseudomonas aeruginosa

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Prediction of antibiotic resistance by gene expression profiles

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Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids

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The Cpx Stress Response Confers Resistance to Some, but Not All, Bactericidal Antibiotics

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Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

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(2013) David L. Stern   NATURE REVIEWS GENETICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

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Evolutionary insight from whole-genome sequencing of experimentally evolved microbes

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Evolutionary rescue and the limits of adaptation

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The probability of genetic parallelism and convergence in natural populations

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Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

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Cost of Adaptation and Fitness Effects of Beneficial Mutations inPseudomonas fluorescens

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Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

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Antibiotic Sensitivity Profiles Determined with an Escherichia coli Gene Knockout Collection: Generating an Antibiotic Bar Code

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Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models

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Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

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Genomewide Identification of Genetic Determinants of Antimicrobial Drug Resistance in Pseudomonas aeruginosa

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Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

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The Sequence Alignment/Map format and SAMtools

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(2009) Ken Chen et al.   NATURE METHODS

Convergent evolution of metabolic roles in bacterial co-symbionts of insects

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The Properties of Adaptive Walks in Evolving Populations of Fungus

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The Distribution of Fitness Effects of Beneficial Mutations in Pseudomonas aeruginosa

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Complex Ciprofloxacin Resistome Revealed by Screening a Pseudomonas aeruginosa Mutant Library for Altered Susceptibility

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Heterogeneous Adaptive Trajectories of Small Populations on Complex Fitness Landscapes

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The Neglected Intrinsic Resistome of Bacterial Pathogens

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The Population Genetics of dN/dS

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