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

Hartono, S., Meijerink, M. F. A., Abee, T., Smid, E. J., & van Mastrigt, O. (2023) · New Biotechnology · doi:10.1016/j.nbt.2023.10.010 · Cited by 7 · see citing works

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

Cheng, Y., Huang, W., Lo, S.-C., Huang, E., Chiang, E. I., Huang, C., & Yang, Y. (2023) · Microorganisms · doi:10.3390/microorganisms11020253 · Cited by 8 · see citing works

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

Gargantilla-Becerra, Á., Gutiérrez, M., & Lahoz-Beltrá, R. (2021) · International Journal of Parallel Emergent and Distributed Systems · doi:10.1080/17445760.2021.1879072 · Cited by 7 · see citing works

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

Blount, B. A., Lu, X., Driessen, M. R. M., Jovicevic, D., Sanchez, M. I., Ciurkot, K., Zhao, Y., Lauer, S. L., McKiernan, R. M., Gowers, G.-O. F., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.15.500197 · Cited by 5 · see citing works

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

Hansson, E. M., Childs, D. Z., & Beckerman, A. P. (2022) · PLoS ONE · doi:10.1371/journal.pone.0272052 · Cited by 4 · see citing works

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

Kulkarni, R. S. (2022) · Medical Hypotheses · doi:10.1016/j.mehy.2022.110999 · Cited by 4 · see citing works

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 · see citing works

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

Schwartz, K., Kinnersley, M. A., Lindsey, C. R., Sherlock, G. J., & Rosenzweig, F. (2025) · BMC Biology · doi:10.1186/s12915-025-02331-7 · Cited by 4 · see citing works

Suppressing evolution in genetically engineered systems through repeated supplementation

Layman, N. C., Tuschhoff, B. M., Basinski, A. J., Remien, C. H., Bull, J. J., & Nuismer, S. L. (2020) · Evolutionary Applications · doi:10.1111/eva.13119 · Cited by 2 · see citing works

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

Pentz, J. T., Koehler, S. I., Middlebrook, E. A., Mak, K. Y., Hovde, B. T., & Hanschen, E. R. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.20.624476 · Cited by 3 · see citing works

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

De, T., Nun, N. B., Spealman, P., Suresh, I., Avecilla, G., Abdul‐Rahman, F., Ram, Y., & Gresham, D. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag095 · Cited by 2 · see citing works

Fitness tracking for adapting populations

Gresham, D. (2015) · Nature · doi:10.1038/nature14207 · Cited by 2 · see citing works

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

Tonoyan, L., Guihéneuf, F., Friel, R., & O’Flaherty, V. (2020) · BIO-PROTOCOL · doi:10.21769/bioprotoc.3813 · Cited by 2 · see citing works

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

Klim, J., Zielenkiewicz, U., Skoneczny, M., Skoneczna, A., Kurlandzka, A., & Kaczanowski, S. (2021) · BMC Ecology and Evolution · doi:10.1186/s12862-021-01830-9 · Cited by 2 · see citing works

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 · see citing works

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 · see citing works

Pleiotropy allows recovery of phenotypic plasticity in constant environmentsPreprint

Kingma, E. M., Diepeveen, E. T., de la Cruz, L. I., & Laan, L. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.02.123208 · Cited by 2 · see citing works

Adaptive Laboratory Evolution of Pichia pastoris by Serial Batch Cultivation

Moritz, C., Gassler, T., Altvater, M., & Mattanovich, D. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4779-0_26 · Cited by 1 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Molecular Systems Predict Equilibrium Distributions of Phenotype Diversity Available for SelectionPreprint

Valderrama-Gómez, M. Á., & Savageau, M. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.27.446045 · Cited by 1 · see citing works

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 · see citing works

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

Hays, M., Schwartz, K., Schmidtke, D. T., Aggeli, D., & Sherlock, G. J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.11.491585 · Cited by 1 · see citing works

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

Hansson, E. M., Childs, D. Z., & Beckerman, A. P. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.26.582134 · Cited by 1 · see citing works

Study of the evolutionary dynamics of plant beneficial bacteria

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Microbial Experimental Evolution

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Nanoparticles Toxicity on Escherichia coli: Batch and Kinetic Approach

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Factors that enhance the ability of Pseudomonas aeruginosa to resist the action of antibiotics

Matrood, W. A. (2016) · Liverpool John Moores University · doi:10.24377/ljmu.t.00004727

Adaptive evolution of transcription factor binding affinitiesPreprint

Hong, J., Brandt, N. J., Yang, A. W. H., Hughes, T., & Gresham, D. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/118455

Study of Cells in the Steady‐State Growth Space

Erm, S., Abner, K., Seiman, A., Adamberg, K., & Vilu, R. (2017) · doi:10.1002/9783527699902.ch9

Theoretical and conceptual derivation of threshold phenomena and metabolic switching models in a chemostat system

Thierie, J. (2018) · Journal of Computational Biology and Bioinformatics Research · doi:10.5897/jcbbr2018.0117

Adaptation of Escherichia coli to the mouse gut

Batista, J. M. B. (2016) · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)

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

Gargantilla-Becerra, Á., Gutiérrez, M., & Lahoz-Beltrá, R. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2101.07540

Emergence of phenotypically distinct subpopulations is a factor in adaptation of recombinant Saccharomyces cerevisiae under glucose-limited conditionsPreprint

Wright, N. R., Wulff, T., Workman, C. T., Rønnest, N. P., & Sonnenschein, N. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.18.427050

Understanding and engineering the factors that control fatty acid biosynthesis in escherichia coli

Gallagher, D. T. (2018) · Spiral (Imperial College London) · doi:10.25560/86387

The Use of Chemostats in Microbial Systems Biology

Ziv, N., Brandt, N. J., & Gresham, D. (2013) · Journal of Visualized Experiments · doi:10.3791/50168-v · Cited by 26 · see citing works

[45] Chemostats used for studying natural selection and adaptive evolution

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The enduring utility of continuous culturing in experimental evolution

Gresham, D., & Dunham, M. J. (2014) · Genomics · doi:10.1016/j.ygeno.2014.09.015 · Cited by 120 · see citing works

Video Article Design and Use of Multiplexed Chemostat Arrays

Miller, A. W., Befort, C., Kerr, E. O., & Dunham, M. J. (2013)

Procedure for Adaptive Laboratory Evolution of Microorganisms Using a Chemostat

Jeong, H., Lee, S. J., & Kim, P. (2016) · Journal of Visualized Experiments · doi:10.3791/54446 · Cited by 12 · see citing works