Tim F Cooper

Summary

Affiliation: University of Houston
Country: USA

Publications

  1. pmc Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli
    Tim F Cooper
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Proc Natl Acad Sci U S A 100:1072-7. 2003
  2. pmc Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli
    Tim F Cooper
    Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
    PLoS Genet 4:e35. 2008
  3. pmc Robust detection of hierarchical communities from Escherichia coli gene expression data
    Santiago Treviño
    Department of Physics, University of Houston, Houston, Texas, United States of America
    PLoS Comput Biol 8:e1002391. 2012
  4. doi request reprint Negative epistasis between beneficial mutations in an evolving bacterial population
    Aisha I Khan
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    Science 332:1193-6. 2011
  5. doi request reprint Mechanisms and selection of evolvability: experimental evidence
    Carolina Díaz Arenas
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    FEMS Microbiol Rev 37:572-82. 2013
  6. pmc Genetic background affects epistatic interactions between two beneficial mutations
    Yinhua Wang
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    Biol Lett 9:20120328. 2013
  7. doi request reprint Estimation of the rate and effect of new beneficial mutations in asexual populations
    Wei Zhang
    Department of Mathematics, University of Houston, Houston, TX 77204 3008, USA
    Theor Popul Biol 81:168-78. 2012
  8. pmc Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations
    Tim F Cooper
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    BMC Evol Biol 10:11. 2010
  9. pmc Effect of random and hub gene disruptions on environmental and mutational robustness in Escherichia coli
    Tim F Cooper
    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    BMC Genomics 7:237. 2006
  10. ncbi request reprint A negative relationship between mutation pleiotropy and fitness effect in yeast
    Tim F Cooper
    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    Evolution 61:1495-9. 2007

Collaborators

Detail Information

Publications13

  1. pmc Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli
    Tim F Cooper
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Proc Natl Acad Sci U S A 100:1072-7. 2003
    ..Our study demonstrates the utility of expression arrays for addressing evolutionary issues including the quantitative measurement of parallel evolution in independent lineages and the identification of beneficial mutations...
  2. pmc Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli
    Tim F Cooper
    Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
    PLoS Genet 4:e35. 2008
    ..More generally, we demonstrate that expression profiles can be profitably used to investigate epistatic interactions...
  3. pmc Robust detection of hierarchical communities from Escherichia coli gene expression data
    Santiago Treviño
    Department of Physics, University of Houston, Houston, Texas, United States of America
    PLoS Comput Biol 8:e1002391. 2012
    ..We find that noise mainly acts conservatively, increasing the relatedness required for a network link to be reliably assigned and decreasing the size of the core communities, rather than causing association of genes into new communities...
  4. doi request reprint Negative epistasis between beneficial mutations in an evolving bacterial population
    Aisha I Khan
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    Science 332:1193-6. 2011
    ..Sign epistasis was rare in this genome-wide study, in contrast to its prevalence in an earlier study of mutations in a single gene...
  5. doi request reprint Mechanisms and selection of evolvability: experimental evidence
    Carolina Díaz Arenas
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    FEMS Microbiol Rev 37:572-82. 2013
    ..We discuss recent theory and experiments that demonstrate the potential for traits that influence evolvability to arise and be selected...
  6. pmc Genetic background affects epistatic interactions between two beneficial mutations
    Yinhua Wang
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    Biol Lett 9:20120328. 2013
    ..Together, our results indicate the presence of interactions between focal mutations, but also caution that these interactions depend quantitatively on the wider genetic background...
  7. doi request reprint Estimation of the rate and effect of new beneficial mutations in asexual populations
    Wei Zhang
    Department of Mathematics, University of Houston, Houston, TX 77204 3008, USA
    Theor Popul Biol 81:168-78. 2012
    ..Application of our method to suitably designed experiments will allow estimation of how population evolvability depends on demographic and initial fitness parameters...
  8. pmc Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations
    Tim F Cooper
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    BMC Evol Biol 10:11. 2010
    ..To date, the influence of environmental variability on evolutionary dynamics has received relatively little experimental study...
  9. pmc Effect of random and hub gene disruptions on environmental and mutational robustness in Escherichia coli
    Tim F Cooper
    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    BMC Genomics 7:237. 2006
    ..Conversely, targeted removal of a hub gene is expected to have a large effect...
  10. ncbi request reprint A negative relationship between mutation pleiotropy and fitness effect in yeast
    Tim F Cooper
    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    Evolution 61:1495-9. 2007
    ..These results are consistent with pleiotropy having a direct role in affecting fitness...
  11. pmc Recombination speeds adaptation by reducing competition between beneficial mutations in populations of Escherichia coli
    Tim F Cooper
    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    PLoS Biol 5:e225. 2007
    ..Together, these results provide experimental support for the Fisher-Muller model and demonstrate that plasmid-mediated gene transfer can accelerate bacterial adaptation...
  12. pmc Parasites and mutational load: an experimental test of a pluralistic theory for the evolution of sex
    Tim F Cooper
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Proc Biol Sci 272:311-7. 2005
    ..These results suggest that, on average, deleterious mutations act multiplicatively with each other but in synergy with infection in determining fitness...
  13. ncbi request reprint Evolution of bacterial diversity and the origins of modularity
    Paul B Rainey
    School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
    Res Microbiol 155:370-5. 2004
    ....