Journal
Kuzdzal-Fick, JJ., Moreno, A., Broersma, CME., Cooper, TF., & Ostrowski, EA. (2022). From individual behaviors to collective outcomes: fruiting body formation in Dictyostelium as a group-level phenotype..
Evolution.
[Journal article]Authored by: Cooper, T., Ostrowski, E.Read Online:

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Smith, CE., Smith, ANH., Cooper, TF., & Moore, FBG. (2022). Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns.
Proceedings of the Royal Society B: Biological Sciences. 289(1982)
[Journal article]Authored by: Cooper, T., Smith, A.Read Online:

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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. 11(18), 12497-12507
[Journal article]Authored by: Cooper, T.Read Online:

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Lai, HY., & Cooper, TF. (2021). Dynamics of bacterial adaptation.
Biochemical Society Transactions. 49(2), 945-951
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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)
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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)
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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)
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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)
[Journal article]Authored by: Cooper, T.Read Online:

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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)
[Journal article]Authored by: Cooper, T.Read Online:

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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)
[Journal article]Authored by: Cooper, T.Read Online:

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Díaz Arenas, C., & Cooper, TF. (2013). Mechanisms and selection of evolvability: Experimental Evidence.
FEMS Microbiology Reviews. 37(4), 572-582
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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)
[Journal article]Authored by: Cooper, T.Read Online:

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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)
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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Cooper, TF. (2010). Metabolism gets lucky.
Molecular Systems Biology. 6
[Journal article]Authored by: Cooper, T.Read Online:

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)
[Journal article]Authored by: Cooper, T.Read Online:

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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)
[Journal article]Authored by: Cooper, T.Read Online:

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Cooper, TF. (2009). Evolutionary biology: Microbes exploit groundhog day.
Nature. 460(7252), 181
[Journal article]Authored by: Cooper, T.Read Online:

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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)
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

Cooper, TF., Beaumont, HJE., & Rainey, PB. (2005). Biofilm diversity as a test of the insurance hypothesis..
Microbiology (Reading). 151(Pt 9), 2815-2816
[Journal article]Authored by: Cooper, T.Read Online:

Rainey, PB., & Cooper, TF. (2004). Evolution of bacterial diversity and the origins of modularity.
Research in Microbiology. 155(5), 370-375
[Journal article]Authored by: Cooper, T.Read Online:

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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
[Journal article]Authored by: Cooper, T.Read Online:

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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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