D M Wolf

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. ncbi Modularity of stress response evolution
    Amoolya H Singh
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 9 144, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 105:7500-5. 2008
  2. ncbi On the relationship between genomic regulatory element organization and gene regulatory dynamics
    D M Wolf
    NERSC Bioinformatics Group, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    J Theor Biol 195:167-86. 1998
  3. ncbi Memory in microbes: quantifying history-dependent behavior in a bacterium
    Denise M Wolf
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS ONE 3:e1700. 2008
  4. ncbi Fifteen minutes of fim: control of type 1 pili expression in E. coli
    Denise M Wolf
    Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    OMICS 6:91-114. 2002
  5. ncbi A microbial modified prisoner's dilemma game: how frequency-dependent selection can lead to random phase variation
    Denise M Wolf
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    J Theor Biol 234:255-62. 2005
  6. ncbi Motifs, modules and games in bacteria
    Denise M Wolf
    Department of Bioengineering, University of California, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Howard Hughes Medical Institute, 1 Cyclotron Road, MS 3 144, Berkeley, CA 94720, USA
    Curr Opin Microbiol 6:125-34. 2003
  7. ncbi Diversity in times of adversity: probabilistic strategies in microbial survival games
    Denise M Wolf
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    J Theor Biol 234:227-53. 2005
  8. ncbi Complexity in bacterial cell-cell communication: quorum signal integration and subpopulation signaling in the Bacillus subtilis phosphorelay
    Ilka B Bischofs
    Department of Bioengineering, University of California, 311 Hildebrand Hall, MC 5230, Berkeley, CA 94704 3224, USA
    Proc Natl Acad Sci U S A 106:6459-64. 2009
  9. ncbi Control, exploitation and tolerance of intracellular noise
    Christopher V Rao
    Department of Bioengineering, University of California, Berkeley, California 94720, USA
    Nature 420:231-7. 2002
  10. ncbi The Bacillus subtilis sin operon: an evolvable network motif
    Christopher A Voigt
    Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genetics 169:1187-202. 2005

Collaborators

Detail Information

Publications11

  1. ncbi Modularity of stress response evolution
    Amoolya H Singh
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 9 144, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 105:7500-5. 2008
    ..The architectures of these three pathways are therefore emblematic of different modes and constraints on evolution...
  2. ncbi On the relationship between genomic regulatory element organization and gene regulatory dynamics
    D M Wolf
    NERSC Bioinformatics Group, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    J Theor Biol 195:167-86. 1998
    ....
  3. ncbi Memory in microbes: quantifying history-dependent behavior in a bacterium
    Denise M Wolf
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS ONE 3:e1700. 2008
    ....
  4. ncbi Fifteen minutes of fim: control of type 1 pili expression in E. coli
    Denise M Wolf
    Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    OMICS 6:91-114. 2002
    ..In the process, we identify a general regulatory motif that tunes phenotype to an environmental variable, and explain a number of apparent experimental inconsistencies...
  5. ncbi A microbial modified prisoner's dilemma game: how frequency-dependent selection can lead to random phase variation
    Denise M Wolf
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    J Theor Biol 234:255-62. 2005
    ..Nature 398 (6726) (1999) 367), with random phase variation at optimal switching rates serving as the cooperation strategy...
  6. ncbi Motifs, modules and games in bacteria
    Denise M Wolf
    Department of Bioengineering, University of California, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Howard Hughes Medical Institute, 1 Cyclotron Road, MS 3 144, Berkeley, CA 94720, USA
    Curr Opin Microbiol 6:125-34. 2003
    ..This approach promises to generate a higher level understanding of cellular design, pathway evolution and cellular bioengineering...
  7. ncbi Diversity in times of adversity: probabilistic strategies in microbial survival games
    Denise M Wolf
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    J Theor Biol 234:227-53. 2005
    ..We show that even when RPV is not the ESS, it may minimize growth rate variance and the risk of extinction due to 'unlucky' environmental dynamics...
  8. ncbi Complexity in bacterial cell-cell communication: quorum signal integration and subpopulation signaling in the Bacillus subtilis phosphorelay
    Ilka B Bischofs
    Department of Bioengineering, University of California, 311 Hildebrand Hall, MC 5230, Berkeley, CA 94704 3224, USA
    Proc Natl Acad Sci U S A 106:6459-64. 2009
    ....
  9. ncbi Control, exploitation and tolerance of intracellular noise
    Christopher V Rao
    Department of Bioengineering, University of California, Berkeley, California 94720, USA
    Nature 420:231-7. 2002
    ..How can we explain the use, rejection and sensitivity to noise that is found in biological systems? An exploration of the sources and consequences of noise calls for the use of stochastic models...
  10. ncbi The Bacillus subtilis sin operon: an evolvable network motif
    Christopher A Voigt
    Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genetics 169:1187-202. 2005
    ..The dynamical plasticity of the protein-antagonist operon motif suggests that it is an evolutionarily convergent design selected not only for particular immediate function but also for its evolvability...
  11. ncbi Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for multiple alignment segmentation
    E P Xing
    Center for Bioinformatics and Computational Genomics, NERSC, Berkeley, CA 94720, USA
    J Theor Biol 212:129-39. 2001
    ..This algorithm facilitates the automation of sequence-based molecular structural and evolutionary analyses through statistical modeling and high performance computation...