Polygenic Adaptation and Clonal Interference Enable Sustained Diversity in Experimental Pseudomonas aeruginosa Populations

Pseudomonas aeruginosa biofilm formation on endotracheal tubes requires multiple two-component systems

(2020) Divakar Badal et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Parallel Evolution of Tobramycin Resistance across Species and Environments

(2020) Michelle R. Scribner et al.   mBio

Experimental Evolution In Vivo To Identify Selective Pressures during Pneumococcal Colonization

(2020) Vaughn S. Cooper et al.   mSystems

Polygenic adaptation: a unifying framework to understand positive selection

(2020) Neda Barghi et al.   NATURE REVIEWS GENETICS

One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity

(2020) Eisha Mhatre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Migration promotes mutator alleles in subdivided populations

(2019) Yevgeniy Raynes et al.   EVOLUTION

Within-Host Adaptation Mediated by Intergenic Evolution in Pseudomonas aeruginosa

(2019) S M Hossein Khademi et al.   Genome Biology and Evolution

Pseudomonas aeruginosa Interstrain Dynamics and Selection of Hyperbiofilm Mutants during a Chronic Infection

(2019) Erin S. Gloag et al.   mBio

Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle

(2019) Alfonso Santos-Lopez et al.   eLife

Experimental Evolution as a High-Throughput Screen for Genetic Adaptations

(2018) Vaughn S. Cooper   mSphere

Rapid diversification of Pseudomonas aeruginosa in cystic fibrosis lung-like conditions

(2018) Alana Schick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutational Evolution of Pseudomonas aeruginosa Resistance to Ribosome-Targeting Antibiotics

(2018) Fernando Sanz-García et al.   Frontiers in Genetics

Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species

(2017) Harry A. Thorpe et al.   GENETICS

Co-evolution with Staphylococcus aureus leads to lipopolysaccharide alterations in Pseudomonas aeruginosa

(2017) Mikael Tognon et al.   ISME Journal

The dynamics of molecular evolution over 60,000 generations

(2017) Benjamin H. Good et al.   NATURE

Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria

(2017) Alejandro Couce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hitchhiking and epistasis give rise to cohort dynamics in adapting populations

(2017) Sean W. Buskirk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Fitness Determinants during Energy-Limited Growth Arrest in Pseudomonas aeruginosa

(2017) David W. Basta et al.   mBio

History of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment

(2017) Phillip Yen et al.   PLOS BIOLOGY

Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species

(2017) Harry A. Thorpe et al.   GENETICS

Escaping the biofilm in more than one way: desorption, detachment or dispersion

(2016) Olga E Petrova et al.   CURRENT OPINION IN MICROBIOLOGY

Laboratory Evolution of Microbial Interactions in Bacterial Biofilms

(2016) Marivic Martin et al.   JOURNAL OF BACTERIOLOGY

Evolution of Ecological Diversity in Biofilms of Pseudomonas aeruginosa by Altered Cyclic Diguanylate Signaling

(2016) Kenneth M. Flynn et al.   JOURNAL OF BACTERIOLOGY

Major Transcriptome Changes Accompany the Growth of Pseudomonas aeruginosa in Blood from Patients with Severe Thermal Injuries

(2016) Cassandra Kruczek et al.   PLoS One

Within-host microevolution of Pseudomonas aeruginosa in Italian cystic fibrosis patients

(2015) Rasmus Lykke Marvig et al.   BMC MICROBIOLOGY

Sarcosine Catabolism in Pseudomonas aeruginosa Is Transcriptionally Regulated by SouR

(2015) Graham G. Willsey et al.   JOURNAL OF BACTERIOLOGY

Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations

(2015) Evgeni M. Frenkel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Deletion Mutant Library for Investigation of Functional Outputs of Cyclic Diguanylate Metabolism in Pseudomonas aeruginosa PA14

(2014) Dae-Gon Ha et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

(2014) Jeffrey E Barrick et al.   BMC GENOMICS

Marker genes for the metabolic adaptation of Pseudomonas aeruginosa to the hypoxic cystic fibrosis lung environment

(2014) Anja Eichner et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Strain-specific parallel evolution drives short-term diversification during Pseudomonas aeruginosa biofilm formation

(2014) K. E. McElroy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Importance of positioning for microbial evolution

(2014) W. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coexistence and Within-Host Evolution of Diversified Lineages of Hypermutable Pseudomonas aeruginosa in Long-term Cystic Fibrosis Infections

(2014) Sofía Feliziani et al.   PLoS Genetics

Genetic Diversity in the Interference Selection Limit

(2014) Benjamin H. Good et al.   PLoS Genetics

Synchronous Waves of Failed Soft Sweeps in the Laboratory: Remarkably Rampant Clonal Interference of Alleles at a Single Locus

(2013) M.-C. Lee et al.   GENETICS

Bacterial Community Morphogenesis Is Intimately Linked to the Intracellular Redox State

(2013) L. E. P. Dietrich et al.   JOURNAL OF BACTERIOLOGY

Extensive diversification is a common feature of Pseudomonas aeruginosa populations during respiratory infections in cystic fibrosis

(2013) Abdul Ashish et al.   Journal of Cystic Fibrosis

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Clonal Dissemination, Emergence of Mutator Lineages and Antibiotic Resistance Evolution in Pseudomonas aeruginosa Cystic Fibrosis Chronic Lung Infection

(2013) Carla López-Causapé et al.   PLoS One

Influence of Seasonality on the Genetic Diversity of Vibrio parahaemolyticus in New Hampshire Shellfish Waters as Determined by Multilocus Sequence Analysis

(2012) Crystal N. Ellis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Structural basis for oxygen sensing and signal transduction of the heme-based sensor protein Aer2 from Pseudomonas aeruginosa

(2012) Hitomi Sawai et al.   CHEMICAL COMMUNICATIONS

Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections

(2012) C. C. Traverse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics of Adaptation during Experimental Evolution of the Opportunistic Pathogen Pseudomonas aeruginosa

(2012) Alex Wong et al.   PLoS Genetics

Dynamics of Mutator and Antibiotic-Resistant Populations in a Pharmacokinetic/Pharmacodynamic Model of Pseudomonas aeruginosa Biofilm Treatment

(2011) María D. Macià et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Genotypic and Phenotypic Variation in Pseudomonas aeruginosa Reveals Signatures of Secondary Infection and Mutator Activity in Certain Cystic Fibrosis Patients with Chronic Lung Infections

(2011) Ashley E. Warren et al.   INFECTION AND IMMUNITY

Differences in Metabolism between the Biofilm and Planktonic Response to Metal Stress

(2011) Sean C. Booth et al.   JOURNAL OF PROTEOME RESEARCH

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

Modulation of Pseudomonas aeruginosa surface-associated group behaviors by individual amino acids through c-di-GMP signaling

(2011) Steve P. Bernier et al.   RESEARCH IN MICROBIOLOGY

Ecological succession in long-term experimentally evolved biofilms produces synergistic communities

(2010) Steffen R Poltak et al.   ISME Journal

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

(2010) T. M. Conrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pseudomonas aeruginosa PA14cupD transcription is activated by the RcsB response regulator, but repressed by its putative cognate sensor RcsC

(2009) Gianlucca G. Nicastro et al.   FEMS MICROBIOLOGY LETTERS

Mutualistic Biofilm Communities Develop with Porphyromonas gingivalis and Initial, Early, and Late Colonizers of Enamel

(2009) S. Periasamy et al.   JOURNAL OF BACTERIOLOGY

Dynamics of Adaptive Microevolution of HypermutablePseudomonas aeruginosaduring Chronic Pulmonary Infection in Patients with Cystic Fibrosis

(2009) Christina Hoboth et al.   JOURNAL OF INFECTIOUS DISEASES

Genetic adaptation of Pseudomonas aeruginosa during chronic lung infection of patients with cystic fibrosis: strong and weak mutators with heterogeneous genetic backgrounds emerge in mucA and/or lasR mutants

(2009) O. Ciofu et al.   MICROBIOLOGY-SGM

Vibrio biofilms: so much the same yet so different

(2009) Fitnat H. Yildiz et al.   TRENDS IN MICROBIOLOGY

A Simple Formula for Obtaining Markedly Improved Mutation Rate Estimates

(2008) Philip Gerrish   GENETICS

Suppression of  bipA Phenotypes in Escherichia coli by Abolishment of Pseudouridylation at Specific Sites on the 23S rRNA

(2008) K. Krishnan et al.   JOURNAL OF BACTERIOLOGY

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics