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Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection

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Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities

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Nutrient-Limited Operational Strategies for the Microbial Production of Biochemicals

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Evolutionary engineering of Corynebacterium glutamicum

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Engineered citrate synthase alters Acetate Accumulation in Escherichia coli

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Heat-responsive and time-resolved transcriptome and metabolome analyses of Escherichia coli uncover thermo-tolerant mechanisms

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Evolution in Long-Term Stationary-Phase Batch Culture: Emergence of Divergent Escherichia coli Lineages over 1,200 Days

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Public goods and metabolic strategies

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Evolutionary pressures on microbial metabolic strategies in the chemostat

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Advanced continuous cultivation methods for systems microbiology

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

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Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes

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Safe and sustainable by design: A computer-based approach to redesign chemicals for reduced environmental hazards

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Comparative study between chemostat and batch reactors to quantify membrane permeability changes on bacteria exposed to silver nanoparticles

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Quantitative Trait Nucleotides Impacting the Technological Performances of Industrial Saccharomyces cerevisiae Strains

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The Transition Toward Nitrogen Deprivation in Diatoms Requires Chloroplast Stand-By and Deep Metabolic Reshuffling

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Trace Metal Requirements and Interactions in Symbiodinium kawagutii

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Evolthon: A community endeavor to evolve lab evolution

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Models for Gut-Mediated Horizontal Gene Transfer by Bacterial Plasmid Conjugation

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Accelerated adaptive laboratory evolution: A tool for evolutionary biotechnology

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Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength

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Carbon Availability Modifies Temperature Responses of Heterotrophic Microbial Respiration, Carbon Uptake Affinity, and Stable Carbon Isotope Discrimination

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Modeling the Growth of Organisms Validates a General Relation between Metabolic Costs and Natural Selection

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Effect of resource availability on evolution of virulence and competition in an environmentally transmitted pathogen

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An incoherent feedforward loop facilitates adaptive tuning of gene expression

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Species matter for predicting the functioning of evolving microbial communities – An eco-evolutionary model

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Long-term exposure of activated sludge in chemostats leads to changes in microbial communities composition and enhanced biodegradation of 4-chloroaniline and N-methylpiperazine

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Adaptation of Escherichia coli to long-term batch culture in various rich media

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Construction of mini‐chemostats for high‐throughput strain characterization

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Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination

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A multi-omics study to boost continuous bolaform sophorolipid production

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A High-Resolution View of Adaptive Event Dynamics in a Plasmid

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Evolutionary rescue of phosphomannomutase deficiency in yeast models of human disease

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Segregationally stabilised plasmids improve production of commodity chemicals in glucose-limited continuous fermentation

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Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution

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Emergence of Phenotypically Distinct Subpopulations Is a Factor in Adaptation of Recombinant Saccharomyces cerevisiae under Glucose-Limited Conditions

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Subpopulations in Strains of Staphylococcus aureus Provide Antibiotic Tolerance

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In search of the pH limit of growth in halo‐alkaliphilic cyanobacteria

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Continuous Cultivation of Yarrowia lipolytica: Potential, Challenges, and Case Studies

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A review of mass and energy flow through a lava flow system: insights provided from a non-equilibrium perspective

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Optimizing experimental conditions: the role of buffered environments in microbial isolation, physiological studies, and taxonomic characterization

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Population collapse and adaptive rescue during long‐term chemostat fermentation

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How Many Biochemistries Are Available To Build a Cell?

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A growth-coupling strategy for improving the stability of terpenoid bioproduction in Escherichia coli

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Single-Cell Technologies to Understand the Mechanisms of Cellular Adaptation in Chemostats

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Differential Gene Expression and Allele Frequency Changes Favour Adaptation of a Heterogeneous Yeast Population to Nitrogen-Limited Fermentations

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Continuous Production of Biogenic Magnetite Nanoparticles by the Marine Bacterium Magnetovibrio blakemorei Strain MV-1T with a Nitrous Oxide Injection Strategy

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The stressostat: A novel approach in adaptive laboratory evolution to improve end-product resistance

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Conversion of Escherichia coli into Mixotrophic CO2 Assimilation with Malate and Hydrogen Based on Recombinant Expression of 2-Oxoglutarate:Ferredoxin Oxidoreductase Using Adaptive Laboratory Evolution

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A synthetic biology approach for the design of genetic algorithms with bacterial agents

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Continuous Bioprocess Development: Methods for Control and Characterization of the Biological System

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Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demandPreprint

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Mesostats—A multiplexed, low-cost, do-it-yourself continuous culturing system for experimental evolution of mesocosms

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Development of novel probiotics for the intestinal diseases associated with mucin alterations by adaptive laboratory evolution

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Single-cell heterogeneity in ribosome content and the consequences for the growth lawsPreprint

Brettner, L. M., & Geiler‐Samerotte, K. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.19.590370 · Cited by 4

Adaptive genetics reveals constraints on protein structure/function by evolving E. coli under constant nutrient limitation

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Suppressing evolution in genetically engineered systems through repeated supplementation

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Metabolic trade-offs in response to increased acetate metabolism in Escherichia coliPreprint

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Segmental copy number amplifications are more stable than aneuploidies in the absence of selection

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Fitness tracking for adapting populations

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Construction and Validation of A Low-cost, Small-scale, Multiplex Continuous Culturing System for Microorganisms

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Genetic interaction network has a very limited impact on the evolutionary trajectories in continuous culture-grown populations of yeast

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Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection

Savageau, M. A. (2023) · Journal of Molecular Evolution · doi:10.1007/s00239-023-10127-y · Cited by 2

Genetic conflicts in budding yeast: The 2μ plasmid as a model selfish element

Hays, M. (2024) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2024.04.002 · Cited by 2

Pleiotropy allows recovery of phenotypic plasticity in constant environmentsPreprint

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Adaptive Laboratory Evolution of Pichia pastoris by Serial Batch Cultivation

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Glucose limitation in Lactococcus shapes a single-peaked fitness landscape exposing membrane occupancy as a constraintPreprint

Price, C. E., dos Santos, F. B., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F. J., Marrink, ‪. J., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/147926 · Cited by 1

A high resolution view of adaptive eventsPreprint

Han, M., Arbeithuber, B., Cremona, M. A., DeGiorgio, M., & Nekrutenko, A. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/429175 · Cited by 1

Understanding site choice and competition through the adaptive dynamics of microbial settling strategy in a chemostatPreprint

Cai, Y., & Geritz, S. A. H. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.13.189662 · Cited by 1

Molecular Systems Predict Equilibrium Distributions of Phenotype Diversity Available for SelectionPreprint

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Adaptive strategies under prolonged starvation and role of slow growth in bacterial fitnessPreprint

Nandy, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.14.472581 · Cited by 1

Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by transposons and microhomology-mediated recombinationPreprint

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Glyphosate resistance evolution to lethal and sublethal doses in chemostat populations of model organism Chlamydomonas reinhardtiiPreprint

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