Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states

Cited by (265)

Items 201–265 of 265

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5. Metabolic Engineering
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6. The organization of metabolic genotype space facilitates adaptive evolution in nitrogen metabolism
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7. E. coli metabolomics: capturing the complexity of a “simple” model
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10. Gene regulatory network inference: A semi-supervised approach
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11. Why optimal states recruit fewer reactions in metabolic networks
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12. Adaptive genetics reveals constraints on protein structure/function by evolving E. coli under constant nutrient limitation
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13. Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions
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14. Reverse Plasticity Underlies Rapid Evolution by Clonal Selection within Populations of Fibroblasts Propagated on a Novel Soft Substrate
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15. Integrating gene expression data into a genome-scale metabolic model to identify reprogramming during adaptive evolution
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16. Resource presentation dictates genetic and phenotypic adaptation in yeast
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17. Reconstruction of Local Biochemical Reaction Network Based on Human Chromosome 9 Sequence Data
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18. Differential remodeling of a T-cell transcriptome following CD8- versus CD3-induced signaling
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19. Model driven analysis of Escherichia coli metabolism
    Jennifer L. Reed · 2005 · eScholarship (California Digital Library)
20. Molecular bases for the loss of type VI secretion system activity during enteroaggregative E. coli experimental evolution
    Boris Taillefer, Jonas B. Desjardins, Eric Cascalès · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
21. Repeatability of gene expression evolution in experimental environmental adaptation
    Jiachen Li, Jianzhi Zhang · 2026 · Nature Communications
22. Unsupervised GRN Ensemble
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23. Host Evolution Improves Genetic Circuit Function in Complex Growth Environments
    Joanna T. Zhang, Andrew Lezia, Philip Emmanuele, Muyao Wu, Elina C. Olson, Aayush Somani, Adam M. Feist, Jeff Hasty · 2025 · ACS Synthetic Biology
24. Environmental versatility promotes modularity in genome-scale metabolic networks
    Areejit Samal, Andreas Wagner, Olivier Martin · 2011 · Zurich Open Repository and Archive (University of Zurich)
25. Genome Dynamics and Temperature Adaptation During Experimental Evolution of Obligate Intracellular Bacteria
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26. Heterogeneity in populations of enterohaemorrhagic Escherichia coli undergoing d-serine adaptation
    Nicky O’Boyle, Andrew J. Roe · 2020 · Current Genetics
27. A Systems Biology Approach to the Evolution of Codon Use Pattern
    Ines Thiele, Ines Thiele, Ronan Fleming, Richard Que, Aarash Bordbar, Bernhard Ørn Palsson · 2011 · Nature Precedings
28. Noise effect in metabolic networks
    Li Zheng-Yan, Xie Zheng-Wei, Chen Tong, Qi Ouyang · 2009 · Chinese Physics B
29. Accumulation of Single Nucleotide Polymorphism (SNP) Mutations in Escherichia coli Grown Under Food Production Conditions and Their Importance in Outbreak Strain Epidemiology
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30. The evolution of trait correlations constrains phenotypic adaptation to high CO 2 in a eukaryotic alga
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31. Acquired Radioresistance Through Adaptive Evolution with Gamma Radiation as Selection Pressure: Increased Expression and Induction of Anti-Stress Genes
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32. Experimental evolution reveals genetic routes for adaptive loss of the antibacterial type VI secretion system
    Boris Taillefer, Jonas B. Desjardins, Eric Cascalès · 2026 · Current Biology
33. Genetic analysis of grain protein concentration and related traits in the Illinois protein strain recombinant inbred population of maize
    Christine J. Lucas · 2014 · Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)
34. Physical Mechanisms Influencing Life Origin and Development. Physical–Biochemical Paradigm of Life
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35. Effects of resource packaging on the adaptative and pleiotropic consequences of evolution
    Neetika Ahlawat, Pavithra Venkataraman, Raman Gulab Brajesh, Supreet Saini · 2025 · npj Systems Biology and Applications
36. A rapid regulation with different response intensities of the pmoA gene guarantees process robustness towards methane surges in continuous and feast-famine bioreactors
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37. Integration of “Omics” Data with Genome‐Scale Metabolic Models
    Stephen Van Dien, Priti Pharkya, Robin E. Osterhout · 2012 · Wiley eBooks
38. Genome-Scale Assessment of Phenotypic Changes During Adaptive Evolution
    Stephen S. Fong · 2008 · Humana Press eBooks
39. Ploidy and the Predictability of Evolution in Fishers Geometric Model
    Sandeep Venkataram, Diamantis Sellis, Dmitri A. Petrov · 2013 · arXiv (Cornell University)
40. Network analysis reveals differential metabolic functionality in antibiotic-resistant Pseudomonas aeruginosa
    Laura J. Dunphy, Phillip Yen, Jason A. Papin · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
41. Combining transcriptomic and fitness data reveals additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum
    Eva L. Koch, Frédéric Guillaume · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
42. Adaptive and pleiotropic effects of evolution in synonymous sugar environments
    Neetika Ahlawat, Pavithra Venkataraman, Raman Gulab Brajesh, Supreet Saini · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
43. DETERMINING THE GENOTYPE-PHENOTYPE CONNECTION IN SYNTHETIC INDUCIBLE GENE EXPRESSION SYSTEMS
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44. Hypermutation and adaptation of experimentally evolved marine Vibrio bacteria
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45. Quantitative relationship between antibiotic exposure and the acquisition and transmission of resistance in bacteria in the laboratory
    Nadine Händel · 2015 · UvA-DARE (University of Amsterdam)
46. La superhélicité de l'ADN comme cible clef de l'adaptation au cours de 20000 générations d'évolution expérimentale chez Escherichia coli
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47. Genome-Scale Models and the Genetic Basis for E. coli Adaptation
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48. On Evolution - A Different Perspective
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49. Title: Ploidy and the Predictability of Evolution in Fisher’s Geometric Model Running Title: Ploidy and the Predictability of Evolution First Author:
    Sandeep Venkataram, Diamantis Sellis, Dmitri A. Petrov · 2013
50. Ensemble-based network aggregation improves the accuracy of
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51. Evolutionary Dynamics of Adaptive Populations: The Efiect of Phenotypic Plasticity, Imitation and Culture on Evolution
    Beverly Sackler · 2006
52. Repeatability of the Adaptation of Pseudomonas fluorescens to Low Glucose
    Oleksiy Teselkin · 2014 · uO Research (University of Ottawa)
53. Peer Reviewed Title: Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations
    R Andrew, Michelle Kenyon, Leutenegger Christian, Oliver K. Bernhard · 2009
54. Information theory and the phenotypic complexity of evolutionary adaptations and innovations
    Andreas Wagner · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
55. The Effects of Standing Genetic Variation on Adaptation to Novel Environments By Rohan Maddamsetti
    Providence Ri · 2008
56. Modulation of rhizosphere - associated microbiota by insect pest: a holobiont relationship
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57. Reverse plasticity underlies rapid evolution by clonal selection within populations of fibroblasts propagated on a novel soft substrate
    Purboja Purkayastha, Kavya Pendyala, Ayush S. Saxena, Hesamedin Hakimjavadi, Srikar Chamala, Purushottam D. Dixit, Charles F. Baer, Tanmay P. Lele · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
58. Understanding Bacterial Resistance and Dissemination: The Impact of Biocide Priming
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59. Metabolic Networks, Evolution
    Andreas Wagner · 2013 · Springer eBooks
60. Multi-dimensional antibiotic resistance time series reveals the phenotype-based fitness landscape for Escherichia coli
    Junichiro Iwasawa, Tomoya Maeda, Atsushi Shibai, Hazuki Kotani, Masako Kawada, Chikara Furusawa · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
61. MRI: an algorithm to identify metabolic reprogramming during adaptive laboratory evolution using gene expression data
    Shaghayegh Yazdanpanah, Ehsan Motamedian, Seyed Abbas Shojaosadati · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
62. Systems biology methods to study the epigenome and metabolic-epigenetic interactions
    P. B. Manjunatha, Rupa Bhowmick, Sriram Chandrasekaran · 2025 · Elsevier eBooks
63. Effet de la sélection fluctuante sur le pathogène du blé Zymoseptoria tritici par une approche d'évolution expérimentale
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64. Impact de l'alimentation et de l'effet souche sur l'adaptation de Escherichia coli dans son environnement naturel : le tube digestif
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65. Metabolite correlation networks reveal complex phenotypes of adaptation-driving mutations
    Sharon Samuel, Weronika Jasińska, Ezra Sternlicht, Matvey I. Nikelshparg, Daniel Kleiner, Shai Pilosof, Shimon Bershtein · 2026 · Nature Communications