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Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

Zhou, A., Hillesland, K. L., He, Z., Schackwitz, W., Tu, Q., Zane, G. M., Ma, Q., Qu, Y., Stahl, D. A., Wall, J. D., et al. (2015) · The ISME Journal · doi:10.1038/ismej.2015.45 · Cited by 24 · see citing works

Re-engineering cellular physiology by rewiring high-level global regulatory genes

Fitzgerald, S. F., Dillon, S. C., Chao, T., Wiencko, H. L., Hokamp, K., Cameron, A. D. S., & Dorman, C. J. (2015) · Scientific Reports · doi:10.1038/srep17653 · Cited by 23 · see citing works

Escherichia coli Lacking RpoS Are Rare in Natural Populations of Non-Pathogens

Snyder, E., Gordon, D., & Stoebel, D. M. (2012) · G3 Genes Genomes Genetics · doi:10.1534/g3.112.003855 · Cited by 22 · see citing works

Synthetic biology-driven microbial production of folates: Advances and perspectives

Yang, H. M., Zhang, X., Liu, Y., Liu, L., Li, J., Du, G., & Chen, J. (2020) · Bioresource Technology · doi:10.1016/j.biortech.2020.124624 · Cited by 21 · see citing works

Determination of single nucleotide variants in Escherichia coli DH5α by using short-read sequencing

Song, Y., Lee, B.-R., Cho, S., Cho, Y., Kim, S.-W., Kang, T. J., Kim, S. C., & Cho, B. (2015) · FEMS Microbiology Letters · doi:10.1093/femsle/fnv073 · Cited by 21 · see citing works

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris

Zhou, A., Lau, R., Baran, R., Ma, J., von Netzer, F., Shi, W., Gorman‐Lewis, D., Kempher, M. L., He, Z., Qin, Y., et al. (2017) · mBio · doi:10.1128/mbio.01780-17 · Cited by 19 · see citing works

Adaptive laboratory evolution triggers pathogen-dependent broad-spectrum antimicrobial potency in Streptomyces

Harwani, D., Begani, J., Barupal, S., & Lakhani, J. (2022) · Journal of Genetic Engineering and Biotechnology · doi:10.1186/s43141-021-00283-3 · Cited by 18 · see citing works

Hypermutator emergence in experimental Escherichia coli populations is stress-type dependent

Callens, M., Rose, C. J., Finnegan, M., Gatchitch, F., Simon, L., Hamet, J., Pradier, L., Dubois, M., & Bedhomme, S. (2023) · Evolution Letters · doi:10.1093/evlett/qrad019 · Cited by 17 · see citing works

Evolving a mitigation of the stress response pathway to change the basic chemistry of life

Tolle, I., Oehm, S., Hoesl, M. G., Treiber-Kleinke, C., Peil, L., Bozukova, M., Albers, S., Bukari, A.-R. A., Semmler, T., Rappsilber, J., et al. (2023) · Frontiers in Synthetic Biology · doi:10.3389/fsybi.2023.1248065 · Cited by 17 · see citing works

Inactivation of Transcriptional Regulators during Within-Household Evolution of Escherichia coli

Kisiela, D., Radey, M. C., Paul, S., Porter, S. B., Polukhina, K., Tchesnokova, V. L., Shevchenko, S., Chan, D. W., Aziz, M., Johnson, T. J., et al. (2017) · Journal of Bacteriology · doi:10.1128/jb.00036-17 · Cited by 16 · see citing works

Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection

Steinrueck, M., & Guet, C. C. (2017) · eLife · doi:10.7554/elife.25100 · Cited by 17 · see citing works

Extracting Regulatory Networks of Escherichia coli from RegulonDB

Salgado, H., Martínez‐Flores, I., López-Fuentes, A., García-Sotelo, J. S., Porrón-Sotelo, L., Solano-Lira, H., Muñiz-Rascado, L., & Collado‐Vides, J. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-361-5_10 · Cited by 16 · see citing works

Regulation of solvent tolerance in P seudomonas putida S12 mediated by mobile elements

Hosseini, R., Kuepper, J., Köbbing, S., Blank, L. M., Wierckx, N. J. P., & de Winde, J. H. (2017) · Microbial Biotechnology · doi:10.1111/1751-7915.12495 · Cited by 16 · see citing works

The adaptive landscape of wildtype and glycosylation-deficient populations of the industrial yeast Pichia pastoris

Moser, J. W., Wilson, I. B. H., & Dragosits, M. (2017) · BMC Genomics · doi:10.1186/s12864-017-3952-7 · Cited by 13 · see citing works

An Introduction to Design of Microbial Strain using Synthetic Biology Toolboxes for Production of Biomolecules

Bhattacharjee, G., Gohil, N., & Singh, V. (2020) · Springer eBooks · doi:10.1007/978-981-15-2604-6_1 · Cited by 12 · see citing works

The timing of transcription of RpoS-dependent genes varies across multiple stresses in Escherichia coli K-12

Adams, J., Hoang, J., Petroni, E., Ashby, E. C., Hardin, J., & Stoebel, D. M. (2023) · mSystems · doi:10.1128/msystems.00663-23 · Cited by 11 · see citing works

Transposable Elements Mediate Adaptive Debilitation of Flagella in Experimental Escherichia coli Populations

Plague, G. R., Boodram, K. S., Dougherty, K. M., Bregg, S., Gilbert, D. P., Bakshi, H., & da Costa, D. P. (2017) · Journal of Molecular Evolution · doi:10.1007/s00239-017-9797-5 · Cited by 10 · see citing works

Demonstration of sequential adaptation strategy for developing salt tolerance in bacteria for wastewater treatment: A study using Escherichia coli as model

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Subfunctionalization influences the expansion of bacterial multidrug antibiotic resistance

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Transposable Elements: A Toolkit for Stress and Environmental Adaptation in Bacteria

Ullastres, A., Merenciano, M., Guio, L., & González, J. (2016) · doi:10.1002/9781119004813.ch11 · Cited by 11 · see citing works

Sequence-dependent model of genes with dual σ factor preference

Baptista, I. S. C., Kandavalli, V. K., Chauhan, V., Bahrudeen, M. N. M., Almeida, B. L. B., Palma, C. S. D., Dash, S., & Ribeiro, A. S. (2022) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2022.194812 · Cited by 9 · see citing works

Effect of dithiocyano-methane on hexose monophosphate pathway in the respiratory metabolism of Escherichia coli

Chen, Y., Ke, W., Qin, H., Chen, S., Qin, L., Yang, Y., Yu, H., & Tan, Y. (2020) · AMB Express · doi:10.1186/s13568-020-01142-z · Cited by 7 · see citing works

Advance of tolerance engineering on microbes for industrial production

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Novel approach to quantitative spatial gene expression uncovers genetic stochasticity in the developing Drosophila eye

Ali, S., Signor, S. A., Kozlov, K. N., & Nuzhdin, S. V. (2019) · Evolution & Development · doi:10.1111/ede.12283 · Cited by 6 · see citing works

Piecewise linear approximations to model the dynamics of adaptation to osmotic stress by food-borne pathogens

Métris, A., George, S., & Ropers, D. (2016) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2016.06.022 · Cited by 6 · see citing works

Parallel Genome-Wide Fixation of Ancestral Alleles in Partially Outcrossing Experimental Populations ofCaenorhabditis elegans

Chandler, C. H. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.012914 · Cited by 6 · see citing works

A glimpse of potential transposable element impact on adaptation of the industrial yeast Saccharomyces cerevisiae

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Chloramphenicol Selection of IS10 Transposition in the cat Promoter Region of Widely Used Cloning Vectors

González-Prieto, C., Agúndez, L., & Llosa, M. (2015) · PLoS ONE · doi:10.1371/journal.pone.0138615 · 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

Adaptive laboratory evolution in a novel parallel shaken pH‐auxostat

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Gene regulation in Bacteroides fragilis : adaptive control in a dynamic host environment

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Impacts of Stress Caused by Copper Sulfate (CuSO4) on the Genome of the Tambaqui (Colossoma macropomum): Quantification of Rex1 and Heterochromatic Profile

da Silva, H. C. M., Ribeiro, L. B., da Mota, A. J., Feldberg, E., & Matoso, D. A. (2022) · Brazilian Archives of Biology and Technology · doi:10.1590/1678-4324-2023220170 · Cited by 2 · see citing works

Compensatory evolution via cryptic genetic variation: Distinct trajectories to phenotypic and fitness recoveryPreprint

Chari, S., Marier, C., Porter, C., Northrop, E., Belinky, A., & Dworkin, I. M. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/200725 · Cited by 2 · see citing works

Screening Adaptive Microbial Hydrolytic Enzymes for Cleaner Production in Resource-Limited Settings

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Genomic signatures highlight stress-response evasion and translational tuning as key drivers of Escherichia coli adaptation to fluorinated tryptophans

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The Regulation of Prokaryotic Transposable Elements by the RNA Binding Protein Hfq

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Sathiasothy, S. (2011) · MacSphere (McMaster University) · doi:10.71548/24805

Az Escherichia coli K-12 inszerciós elemeinek hatása a genom stabilitására

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On Evolution - A Different Perspective

Murali, P. (2014)

information on the genotype of these organisms. The information obtained by whole genome sequencing complemented with hypothesis-driven experiments will advance our understanding of the evolvability of an organism both within the confines of the laboratory as well as in their natural environments.

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Repeatability of the Adaptation of Pseudomonas fluorescens to Low Glucose

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Persister formation in Borrelia burgdorferi, Staphylococcus aureus, and Escherichia coli

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Genetic basis of persister formation in Escherichia coli

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Novel approach to quantitative spatial gene expression uncovers genetic stochasticity in the developing Drosophila eyePreprint

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