Journal
Phillips, KN., & Cooper, TF. (2021). The cost of evolved constitutive lac gene expression is usually, but not always, maintained during evolution of generalist populations.
Ecology and Evolution.
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Lai, HY., & Cooper, TF. (2021). Dynamics of bacterial adaptation.
Biochemical Society Transactions. 49(2), 945-951
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Karkare, K., Lai, HY., Azevedo, RBR., & Cooper, TF. (2021). Historical Contingency Causes Divergence in Adaptive Expression of the lac Operon.
Molecular Biology and Evolution. 38(7), 2869-2879
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Cesar, S., Anjur-Dietrich, M., Yu, B., Li, E., Rojas, E., Neff, N., . . . Huang, KC. (2020). Bacterial evolution in high-osmolarity environments.
mBio. 11(4), 1-17
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Wang, Y., & Cooper, TF. (2020). Environment-dependent costs and benefits of recombination in independently evolved populations of Escherichia coli*.
Evolution. 74(8), 1865-1873
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Phillips, KN., Widmann, S., Lai, HY., Nguyen, J., Ray, JCJ., Balázsi, G., . . . Cooper, TF. (2019). Diversity in lac operon regulation among diverse escherichia coli isolates depends on the broader genetic background but is not explained by genetic relatedness.
mBio. 10(6)
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Coombes, D., Moir, JWB., Poole, AM., Cooper, TF., & Dobson, RCJ. (2019). The fitness challenge of studying molecular adaptation.
Biochemical Society Transactions. 47(5), 1533-1542
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Hall, AE., Karkare, K., Cooper, VS., Bank, C., Cooper, TF., & Moore, FBG. (2019). Environment changes epistasis to alter trade-offs along alternative evolutionary paths.
Evolution. 73(10), 2094-2105
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Ram, Y., Dellus-Gur, E., Bibi, M., Karkare, K., Obolski, U., Feldman, MW., . . . Hadany, L. (2019). Predicting microbial growth in a mixed culture from growth curve data.
Proceedings of the National Academy of Sciences of the United States of America. 116(29), 14698-14707
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Wünsche, A., Dinh, DM., Satterwhite, RS., Arenas, CD., Stoebel, DM., & Cooper, TF. (2017). Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory.
Nature Ecology and Evolution. 1(4)
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Peng, F., Widmann, S., Wünsche, A., Duan, K., Donovan, KA., Dobson, RCJ., . . . Cooper, TF. (2018). Effects of Beneficial Mutations in pykF Gene Vary over Time and across Replicate Populations in a Long-Term Experiment with Bacteria.
Molecular Biology and Evolution. 35(1), 202-210
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Phillips, KN., Castillo, G., Wünsche, A., & Cooper, TF. (2016). Adaptation of Escherichia coli to glucose promotes evolvability in lactose.
Evolution. 70(2), 465-470
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Ray, JCJ., Wickersheim, ML., Jalihal, AP., Adeshina, YO., Cooper, TF., & Balázsi, G. (2016). Cellular Growth Arrest and Persistence from Enzyme Saturation.
PLoS Computational Biology. 12(3)
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Wang, Y., Arenas, CD., Stoebel, DM., Flynn, K., Knappc, E., Dillon, MM., . . . Cooper, TF. (2016). Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness.
Proceedings of the National Academy of Sciences of the United States of America. 113(18), 5047-5052
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Donovan, KA., Atkinson, SC., Kessans, SA., Peng, F., Cooper, TF., Griffin, MDW., . . . Dobson, RCJ. (2016). Grappling with anisotropic data, pseudo-merohedral twinning and pseudo-translational noncrystallographic symmetry: A case study involving pyruvate kinase.
Acta Crystallographica Section D: Structural Biology. 72(4), 512-519
[Journal article]Authored by: Cooper, T., Jameson, G.Read Online:
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Satterwhite, RS., & Cooper, TF. (2015). Constraints on adaptation of Escherichia coli to mixed-resource environments increase over time.
Evolution. 69(8), 2067-2078
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Monds, RD., Lee, TK., Colavin, A., Ursell, T., Quan, S., Cooper, TF., . . . Huang, KC. (2014). Systematic Perturbation of Cytoskeletal Function Reveals a Linear Scaling Relationship between Cell Geometry and Fitness.
Cell Reports. 9(4), 1528-1537
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Liu, J., Vipulanandan, C., Cooper, TF., & Vipulanandan, G. (2013). Effects of Fe nanoparticles on bacterial growth and biosurfactant production.
Journal of Nanoparticle Research. 15(1)
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Flynn, KM., Cooper, TF., Moore, FBG., & Cooper, VS. (2013). The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape.
PLoS Genetics. 9(4)
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Wang, Y., Díaz Arenas, C., Stoebel, DM., & Cooper, TF. (2013). Genetic background affects epistatic interactions between two beneficial mutations.
Biology Letters. 9(1)
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Díaz Arenas, C., & Cooper, TF. (2013). Mechanisms and selection of evolvability: Experimental Evidence.
FEMS Microbiology Reviews. 37(4), 572-582
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Le Gac, M., Cooper, TF., Cruveiller, S., Médigue, C., & Schneider, D. (2013). Evolutionary history and genetic parallelism affect correlated responses to evolution.
Molecular Ecology. 22(12), 3292-3303
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Gallet, R., Cooper, TF., Elena, SF., & Lenormand, T. (2012). Measuring selection coefficients below 10<sup>-3</sup>: Method, Questions, and Prospects.
Genetics. 190(1), 175-186
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Zhang, W., Sehgal, V., Dinh, DM., Azevedo, RBR., Cooper, TF., & Azencott, R. (2012). Estimation of the rate and effect of new beneficial mutations in asexual populations.
Theoretical Population Biology. 81(2), 168-178
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Quan, S., Ray, JCJ., Kwota, Z., Duong, T., Balázsi, G., Cooper, TF., . . . Monds, RD. (2012). Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli.
PLoS Genetics. 8(1)
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Treviño, S., Sun, Y., Cooper, TF., & Bassler, KE. (2012). Robust detection of hierarchical communities from escherichia coli gene expression data.
PLoS Computational Biology. 8(2)
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Khan, AI., Dinh, DM., Schneider, D., Lenski, RE., & Cooper, TF. (2011). Negative epistasis between beneficial mutations in an evolving bacterial population.
Science. 332(6034), 1193-1196
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de Visser, JAGM., Cooper, TF., & Elena, SF. (2011). The causes of epistasis.
Proceedings of the Royal Society B: Biological Sciences. 278(1725), 3617-3624
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Woods, RJ., Barrick, JE., Cooper, TF., Shrestha, U., Kauth, MR., & Lenski, RE. (2011). Second-order selection for evolvability in a large Escherichia coli population.
Science. 331(6023), 1433-1436
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McDonald, MJ., Cooper, TF., Beaumont, HJE., & Rainey, PB. (2011). The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens.
Biology Letters. 7(1), 98-100
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Zhu, T., Bailey, MF., Angley, LM., Cooper, TF., & Dobson, RCJ. (2010). The quaternary structure of pyruvate kinase type 1 from Escherichia coli at low nanomolar concentrations.
Biochimie. 92(1), 116-120
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Cooper, TF. (2010). Metabolism gets lucky.
Molecular Systems Biology. 6
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Cooper, TF., & Lenski, RE. (2010). Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations.
BMC Evolutionary Biology. 10(1)
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Stanek, MT., Cooper, TF., & Lenski, RE. (2009). Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli.
BMC Evolutionary Biology. 9(1)
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Cooper, TF. (2009). Evolutionary biology: Microbes exploit groundhog day.
Nature. 460(7252), 181
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Cooper, TF., Remold, SK., Lenski, RE., & Schneider, D. (2008). Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli.
PLoS Genetics. 4(2)
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Cooper, TF. (2007). Recombination speeds adaptation by reducing competition between beneficial mutations in populations of Escherichia coli.
PLoS Biology. 5(9), 1899-1905
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Cooper, TF., Ostrowski, EA., & Travisano, M. (2007). A negative relationship between mutation pleiotropy and fitness effect in yeast.
Evolution. 61(6), 1495-1499
[Journal article]Authored by: Cooper, T., Ostrowski, E.Read Online:
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Cooper, TF., Morby, AP., Gunn, A., & Schneider, D. (2006). Effect of random and hub gene disruptions on environmental and mutational robustness in Escherichia coli.
BMC Genomics. 7
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Cooper, TF., & Heinemann, JA. (2005). Selection for plasmid post-segregational killing depends on multiple infection: Evidence for the selection of more virulent parasites through parasite-level competition.
Proceedings of the Royal Society B: Biological Sciences. 272(1561), 403-410
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Cooper, TF., Lenski, RE., & Elena, SF. (2005). Parasites and mutational load: An experimental test of a pluralistic theory for the evolution of sex.
Proceedings of the Royal Society B: Biological Sciences. 272(1560), 311-317
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Cooper, TF., Beaumont, HJE., & Rainey, PB. (2005). Biofilm diversity as a test of the insurance hypothesis.
Microbiology. 151(9), 2815-2816
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Cooper, TF., Beaumont, HJE., & Rainey, PB. (2005). Biofilm diversity as a test of the insurance hypothesis..
Microbiology (Reading). 151(Pt 9), 2815-2816
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Rainey, PB., & Cooper, TF. (2004). Evolution of bacterial diversity and the origins of modularity.
Research in Microbiology. 155(5), 370-375
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Cooper, TF., Rozen, DE., & Lenski, RE. (2003). Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli.
Proceedings of the National Academy of Sciences of the United States of America. 100(3), 1072-1077
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Cooper, TF., & Heinemann, JA. (2000). Transfer of conjugative plasmids and bacteriophage λ occurs in the presence of antibiotics that prevent de novo gene expression.
Plasmid. 43(2), 171-175
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