Mutational hotspots lead to robust but suboptimal adaptive outcomes in certain environments

A reversible mutation in a genomic hotspot saves bacterial swarms from extinction

(2023) Idan Hefetz et al.   iScience

Transient mutation bias increases the predictability of evolution on an empirical genotype–phenotype landscape

(2023) James S. Horton et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Shifts in mutation spectra enhance access to beneficial mutations

(2023) Mrudula Sane et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutation bias shapes the spectrum of adaptive substitutions

(2022) Alejandro V. Cano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Near-Deterministic Mutational Hotspot in Pseudomonas fluorescens Is Constructed by Multiple Interacting Genomic Features

(2022) M J Shepherd et al.   MOLECULAR BIOLOGY AND EVOLUTION

Localized pmrB hypermutation drives the evolution of colistin heteroresistance

(2022) Natalia Kapel et al.   Cell Reports

Wide-ranging consequences of priority effects governed by an overarching factor

(2022) Callie Rodgers Chappell et al.   eLife

A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes

(2021) James S. Horton et al.   Nature Communications

Predicting Evolution Using Regulatory Architecture

(2020) Philippe Nghe et al.   Annual Review of Biophysics

Inactivation of Glutamine Synthetase-Coding Gene glnA Increases Susceptibility to Quinolones Through Increasing Outer Membrane Protein F in Salmonella enterica Serovar Typhi

(2020) Ana R. Millanao et al.   Frontiers in Microbiology

Priority effects and ecological restoration

(2020) Emanuela W. A. Weidlich et al.   RESTORATION ECOLOGY

Hotspots of Human Mutation

(2020) Alex V. Nesta et al.   TRENDS IN GENETICS

Predicting mutational routes to new adaptive phenotypes

(2019) Peter A Lind et al.   eLife

Repeated Phenotypic Evolution by Different Genetic Routes in Pseudomonas fluorescens SBW25

(2019) Jenna Gallie et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis

(2019) Joshua L. Payne et al.   PLOS BIOLOGY

The impact of growth rate and environmental factors on mutation rates and spectra in Escherichia coli

(2018) Ram P. Maharjan et al.   Environmental Microbiology Reports

The complex underpinnings of genetic background effects

(2018) Martin N. Mullis et al.   Nature Communications

Mutational Biases Influence Parallel Adaptation

(2017) Arlin Stoltzfus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification and analysis of mutational hotspots in oncogenes and tumour suppressors

(2017) Hanadi Baeissa et al.   Oncotarget

A shifting mutational landscape in 6 nutritional states: Stress-induced mutagenesis as a series of distinct stress input–mutation output relationships

(2017) Ram P. Maharjan et al.   PLOS BIOLOGY

Environment determines evolutionary trajectory in a constrained phenotypic space

(2017) David T Fraebel et al.   eLife

Predicting evolution

(2017) Michael Lässig et al.   Nature Ecology & Evolution

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

(2016) Kathleen Sprouffske et al.   BMC BIOINFORMATICS

Evolutionary convergence in experimental Pseudomonas populations

(2016) Peter A Lind et al.   ISME Journal

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

(2016) Marta Lourenço et al.   PLoS Genetics

Sensory properties of the PIIsignalling protein family

(2015) Karl Forchhammer et al.   FEBS Journal

The many roles of glutamate in metabolism

(2015) Mark C. Walker et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

The Effect of Selection Environment on the Probability of Parallel Evolution

(2015) Susan F. Bailey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

(2015) Tiffany B. Taylor et al.   SCIENCE

Replaying the tape of life in the twenty-first century

(2015) Virginie Orgogozo   Interface Focus

The biosurfactant viscosin produced byPseudomonas fluorescens SBW25 aids spreading motility and plant growth promotion

(2014) Abdullah S. Alsohim et al.   ENVIRONMENTAL MICROBIOLOGY

Mini-Tn7 vectors for studying post-transcriptional gene expression in Pseudomonas

(2014) Yunhao Liu et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

(2014) Tom Vogwill et al.   MOLECULAR BIOLOGY AND EVOLUTION

Environmental variability counteracts priority effects to facilitate species coexistence: evidence from nectar microbes

(2014) C. M. Tucker et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

THE LOCI OF REPEATED EVOLUTION: A CATALOG OF GENETIC HOTSPOTS OF PHENOTYPIC VARIATION

(2013) Arnaud Martin et al.   EVOLUTION

Does your gene need a background check? How genetic background impacts the analysis of mutations, genes, and evolution

(2013) Christopher H. Chandler et al.   TRENDS IN GENETICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations

(2010) Tim F Cooper et al.   BMC EVOLUTIONARY BIOLOGY

NtrC-Dependent Regulatory Network for Nitrogen Assimilation in Pseudomonas putida

(2009) A. B. Hervas et al.   JOURNAL OF BACTERIOLOGY

High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection

(2009) S. Chattopadhyay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

(2009) Mark W Silby et al.   GENOME BIOLOGY

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

Dual Involvement of CbrAB and NtrBC in the Regulation of Histidine Utilization in Pseudomonas fluorescens SBW25

(2008) Xue-Xian Zhang et al.   GENETICS

Predicting evolution from genomics: experimental evolution of bacteriophage T7

(2008) J J Bull et al.   HEREDITY

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

(2008) Y. Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA