Publications (brief CV here)
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.
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.
Diaz Arenas C, Cooper TF (2012) Mechanisms and selection of evolvability: experimental evidence. FEMS Micro. Rev. 37: 572-582.
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.
de Visser AJ, Cooper TF, Elena S (2011) The causes of epistasis. Proc. R. Soc. Lond. B. 278: 3617-3624.
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 (2010) Metabolism gets lucky. Mol. Sys. Biol. 6: 439. (N&V)
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.
Cooper TF (2009) Microbes exploit groundhog day. Nature: 460: 181. (N&V)
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, 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.