Publications (brief CV here)

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  • Peng F, Widmann S, Wunsche A, Duan K, Donovan KA, Dobson RCJ, Lenski RE,Cooper TF(2018) Effects of beneficial mutations in pykF gene vary over time and across replicate populations in a long-term experiment with bacteria. Mol. Biol. Evol. 35: 202-210. 

  • Wünsche A, Dinh DD, Satterwhite RS, Diaz Arenas C, Stoebel DM, Cooper TF. (2017) Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory. Nature Ecology and Evolution 1: 0061.

  •  Ray JCJ, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G. (2016) Cellular growth arrest and persistence from enzyme saturation. PLoS Comp. Biol 12 (3): e1004825.pdf

  • Wang Y, Arenas-Diaz C, Stoebel D, Flynn KM, Knapp E, Dillon MM, Wünsche A, Hatcher PJ, Moore FB-G , Cooper VS and Cooper TF (2016) Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness. PNAS 113: 5047-5052. PMID: 27091964

  • Phillips K, Castillo G, Wünsche A, Cooper TF (2016) Adaptation of Escherichia coli to glucose promotes evolvability in lactose. Evolution 70: 465-470. PMID: 26748670

  • Donovan KA, Atkinson SC, Kessans SA, Peng F, Cooper TF, Griffin MDW, Jameson GB, Dobson RCJ. (2016) Grappling with anisotropic data, pseudo-merohedral twinning and pseudo- translational non-crystallographic symmetry: A case study involving pyruvate kinase. Acta Crystallographica Section D 72(4): 512-519

  • Satterwhite R, Cooper TF (2015) Can generalists become masters of all trades? Constraints on Escherichia coli evolving on single- and mixed-resource environments. Evolution 69: 2067-2078. PMID: 26103008  

  • Monds RD, Lee TK, Colavin A, Ursell T, Cooper TF, Huang KC (2014) Systematic perturbation of cytoskeletal function reveals a linear scaling relationship between cell geometry and fitness. Cell Reports 9: 1528-1537. PMID: 25456141

  • Le Gac M, ooper TF, Cruveiller S, Claudine M, Schneider D (2013) Evolutionary history and genetic parallelism affect correlated responses to evolution. Mol. Ecol. 22: 3292-3303.

  • Liu J, Vipulanandan C, Cooper TF, Vipulanandan G (2013) Effects of Fe nanoparticles on bacterial growth and biosurfactant production. J. Nanoparticle Res. 15: 1-13. 

  • Flynn KM, Cooper TF, Moore FB-G, Cooper VS (2013) The environment affects epistatic interactions to alter the topology of an empirical fitness landscape. PLoS Genetics 9: e1003426

  • Wang Y, Diaz Arenas C, Stoebel DM, Cooper TF (2012) Genetic background affects epistatic interactions between two beneficial mutations. Biol. Lett. 9: 20120328. 

  • Gallet R, Cooper TF, Elena SF, Lenormand T (2012) Measuring selection coefficients below 10-3: Method, questions and prospects. Genetics. 190: 175-186.

  • Cooper TF (2012) Empirical insights into adaptive landscapes from bacterial experimental evolution in The Adaptive Landscape in Evolutionary Biology eds. E. Svensson, R. Calsbeek. Oxford, Oxford University Press.

  • Zhang W, Sehgal Z, Dinh DM, Azevedo RBR, Cooper TF, Azencott R (2012) Estimating the rate and effect of beneficial mutations in asexual populations. Theor Pop Biol. 81: 168-178.

  • Quan S, Ray, JCJ, Kwota Z, Duong T, Balazsi G, Cooper TF, Monds R (2012) Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli. PLoS Genetics 8: e1002444. pdf.

  • 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: 1433-1436.§

  • McDonald MJ, Cooper TF, Beaumont HBJ, Rainey PB (2011) The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens. Biol. Lett. 7: 98-100.

  • Cooper TF, Lenski RE (2010) Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations. BMC Evol. Biology. 10: e11. pdf. ***

  • Zhu T, Bailey MF, Cooper TF, Dobson RCJ (2010) The quaternary structure of pyruvate kinase type 1 from E. coli at low nanomolar concentrations. Biochimie. 92: 116-120.

  • Stanek MT, Cooper TF, Lenski RE (2009) Identification and dynamics of a beneficial mutation in a long-term experiment with Escherichia coli. BMC Evol. Biology. 9: 302. pdf.

  • Cooper TF, Remold SK, Lenski RE, Schneider D (2008) Expression Arrays reveal epistatic interactions between crp and mutations arising during 20,000 generations of evolution in Escherichia coli. PloS Genetics 4:e35. pdf.

  • Cooper TF (2007) Recombination speeds adaptation by reducing competition between competing mutations in populations of Escherichia coli. PLoS Biology 5: e225. pdf. *

  • Cooper TF, Ostrowski EA,Travisano M (2007) A negative relationship between mutation pleiotropy and fitness. Evolution 61: 1495-1499.

  • 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 7:237.

  • Cooper TF, Lenski RE, Elena SF (2005) Parasites and mutational load: an experimental test of a pluralistic theory for the evolution of sex. Proc. R. Soc. London B. 272: 311-317.

  • Cooper TF, Heinemann JA (2005) Selection for plasmid postsegregational killing depends on multiple infection: evidence for the selection of more virulent parasites through parasite-level competition. Proc. R. Soc. London B. 272: 403-410.

  • Cooper TF, Beaumont H, Rainey PB (2005) Biofilms as a test of the insurance hypothesis. Microbiology. 151: 2815-2816.

  • Rainey PB, Cooper TF (2004) Evolution of bacterial diversity and the origins of modularity. Res. Microbiol. 155: 370-375.

  • Cooper TF, Rozen DR, Lenski RE (2003) Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc. Natl. Acad. Sci. USA 100: 1072-1077.**

  • Cooper TF, Ofria C (2002) Evolution of stable ecosystems in populations of digital organisms. Alife 8: 227-232.

  • Cooper TF, Heinemann JA (2000) Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids. Proc. Natl. Acad. Sci. USA 97: 12643-12648.

  • Cooper TF, Heinemann JA (2000) Transfer of IncF and IncP plasmids and bacteriophage l occurs in the presence of antibiotics that prevent de-novo gene expression. Plasmid 43: 171-175.

*Subject of focus article in PLoS Biology and review in Nature Reviews Microbiology.

**Subject of review in Science and Highly recommended classification in Faculty of 1000.

***Highly recommended classification in Faculty of 1000.

§ Subject of articles in New York Times, Discover magazine, Nature and The Scientist.

§ Subject of accompanying commentary in Science.