Prof Timothy Cooper staff profile picture

Contact details +6492136611

Prof Timothy Cooper

Professor of Molecular Biosciences

School of Natural and Computational Sciences

Research Expertise

Research Interests

Tim works on understanding the dynamics of microbial adaptation. These dynamics determine the ability of microbes to adapt and compete in both benign and stressful environments, like those presented by the use of antibiotics. His work focusses on the genetics of adaptation, especially on how interactions among genetic mutations and the environment influence evolutionary outcomes. 

Area of Expertise

Field of research codes
Biological Adaptation (060303): Biological Sciences (060000): Evolutionary Biology (060300): Genetics (060400): Microbial Genetics (060503): Microbiology (060500): Molecular Evolution (060409)

Keywords

Evolutionary biology, Microbiology, Experimental evolution

Research Projects

Summary of Research Projects

Position Current Completed
Project Leader 2 1

Research Outputs

Journal

Lai, HY., & Cooper, TF. (2021). Dynamics of bacterial adaptation. Biochemical Society Transactions. 49(2), 945-951
[Journal article]Authored by: Cooper, T.
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Karkare, K., Lai, H-Y., Azevedo, RBR., & Cooper, TF. (2021). Historical contingency causes divergence in adaptive expression of the lac operon.. Mol Biol Evol.
[Journal article]Authored by: Cooper, T.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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22
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.
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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.
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7
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.
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15
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.
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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.
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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.
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19
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.
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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.
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18
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.
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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.
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27
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.
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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.
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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.
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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.
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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.
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38
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.
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27
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.
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302
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.
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114
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.
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198
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.
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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.
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Cooper, TF. (2010). Metabolism gets lucky. Molecular Systems Biology. 6
[Journal article]Authored by: Cooper, T.
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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)
[Journal article]Authored by: Cooper, T.
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63
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.
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Cooper, TF. (2009). Evolutionary biology: Microbes exploit groundhog day. Nature. 460(7252), 181
[Journal article]Authored by: Cooper, T.
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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.
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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.
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133
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.
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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.
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27
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.
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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.
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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.
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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
[Journal article]Authored by: Cooper, T.
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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
[Journal article]Authored by: Cooper, T.
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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.
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326
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
[Journal article]Authored by: Cooper, T.
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Book

Cooper, TF. (2015). Experimental molecular evolution. In Molecular and Genome Evolution. (pp. 597 - 612). : Sinauer Associates Inc
[Chapter]Authored by: Cooper, T.
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Conference

Cooper, TF., Paixão, T., & Heinemann, JA.Within-host competition selects for plasmidencoded toxin-antitoxin systems. Proceedings of the Royal Society B: Biological Sciences. 277 (1697)(pp. 3149 - 3155). 0962-8452.
[Conference]Authored by: Cooper, T.
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Cooper, TF., & Heinemann, JA.Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids. Proceedings of the National Academy of Sciences of the United States of America. 97 (23)(pp. 12643 - 12648). 0027-8424.
[Conference]Authored by: Cooper, T.
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Teaching and Supervision

Courses Coordinated

  • 122.703 Gene Expression
  • 162.101 Cell Biology
  • 162.760 Research Methods and Communication in the Biosciences
  • 162.761 Research Methods and Written Communication in Biosciences
  • 162.762 Grant Writing and Oral Communication in Biosciences
  • 203.340 Applied Molecular Biology
  • 247.300 Research in Biosciences
Contact Supervisor

Summary of Doctoral Supervision

Position Current Completed
Main Supervisor 2 0
Co-supervisor 2 0

Current Doctoral Supervision

Main Supervisor of:

  • Kelly Hong - Doctor of Philosophy
    Antibiotic evolution
  • Huei-Yi Lai - Doctor of Philosophy
    Mechanisms of maintaining antibiotic resistance without antibiotic selection

Co-supervisor of:

  • Danielle Kok - Doctor of Philosophy
    ABAtE: Active Bacteriophages for AFB Eradication
  • Marketa Vlkova - Doctor of Philosophy
    Natural variation among E. coli isolates in transcriptional responses and memory