David Krakauer

Summary

Affiliation: Santa Fe Institute
Country: USA

Publications

  1. pmc Noisy clues to the origin of life
    David C Krakauer
    Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
    Proc Biol Sci 269:2423-8. 2002
  2. ncbi request reprint Evolution. Insights into innovation
    Douglas H Erwin
    Department of Paleobiology, Smithsonian Institution, Washington, DC 20560, USA
    Science 304:1117-9. 2004
  3. ncbi request reprint Social structure, robustness, and policing cost in a cognitively sophisticated species
    Jessica C Flack
    Santa Fe Institute, Santa Fe, New Mexico 87501, USA
    Am Nat 165:E126-39. 2005
  4. pmc The greater than twofold cost of integration for retroviruses
    David C Krakauer
    Santa Fe Institute, 1399 Hyde Park Road, NM 87501, USA
    Proc Biol Sci 273:1159-63. 2006
  5. doi request reprint The challenges and scope of theoretical biology
    David C Krakauer
    Santa Fe Institute, Santa Fe, NM, USA
    J Theor Biol 276:269-76. 2011
  6. pmc Defining genes: a computational framework
    Peter F Stadler
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, 04107 Leipzig, Germany
    Theory Biosci 128:165-70. 2009
  7. pmc A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes
    Fabrizio Lillo
    Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
    Biol Direct 2:22. 2007
  8. doi request reprint Diversity, dilemmas, and monopolies of niche construction
    David C Krakauer
    Santa Fe Institute, Santa Fe, New Mexico 87501, USA
    Am Nat 173:26-40. 2009
  9. pmc The immuno-dynamics of conflict intervention in social systems
    David C Krakauer
    Santa Fe Institute, Santa Fe, New Mexico, United States of America
    PLoS ONE 6:e22709. 2011
  10. ncbi request reprint Levels of selection in positive-strand virus dynamics
    D C Krakauer
    Santa Fe Institute, Santa Fe, NM 87501, USA
    J Evol Biol 16:64-73. 2003

Research Grants

  1. MATHEMATICAL TOOLS AND MODELING FOR BIOLOGISTS
    David Krakauer; Fiscal Year: 2005

Detail Information

Publications22

  1. pmc Noisy clues to the origin of life
    David C Krakauer
    Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
    Proc Biol Sci 269:2423-8. 2002
    ..Hence, two factors formerly considered inimical to the origin of life-developmental noise and drift in small populations-can in combination give rise to conditions favourable to robust replication...
  2. ncbi request reprint Evolution. Insights into innovation
    Douglas H Erwin
    Department of Paleobiology, Smithsonian Institution, Washington, DC 20560, USA
    Science 304:1117-9. 2004
  3. ncbi request reprint Social structure, robustness, and policing cost in a cognitively sophisticated species
    Jessica C Flack
    Santa Fe Institute, Santa Fe, New Mexico 87501, USA
    Am Nat 165:E126-39. 2005
    ..Our data and simple model suggest that third-party policing effectiveness and cost are dependent on power structure and might emerge only in societies with high variance in power...
  4. pmc The greater than twofold cost of integration for retroviruses
    David C Krakauer
    Santa Fe Institute, 1399 Hyde Park Road, NM 87501, USA
    Proc Biol Sci 273:1159-63. 2006
    ....
  5. doi request reprint The challenges and scope of theoretical biology
    David C Krakauer
    Santa Fe Institute, Santa Fe, NM, USA
    J Theor Biol 276:269-76. 2011
    ..We argue that evolutionary history is not only a source of uncertainty, but also provides the basis, through conserved traits, for very general explanations for biological regularities, and the prospect of unified theories of life...
  6. pmc Defining genes: a computational framework
    Peter F Stadler
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, 04107 Leipzig, Germany
    Theory Biosci 128:165-70. 2009
    ..The definition seeks to satisfy the practical requirements imposed by annotation, capture logical aspects of regulation, and encompass the evolutionary property of homology...
  7. pmc A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes
    Fabrizio Lillo
    Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
    Biol Direct 2:22. 2007
    ..We investigate the length, phase and orientation properties of overlap in 58 prokaryotic species evaluating neutral and selective mechanisms of evolution...
  8. doi request reprint Diversity, dilemmas, and monopolies of niche construction
    David C Krakauer
    Santa Fe Institute, Santa Fe, New Mexico 87501, USA
    Am Nat 173:26-40. 2009
    ..We discuss the implications of niche-construction theory on the evolution of life cycles and development, behavioral plasticity, the division of labor, and long-term macroevolutionary trends...
  9. pmc The immuno-dynamics of conflict intervention in social systems
    David C Krakauer
    Santa Fe Institute, Santa Fe, New Mexico, United States of America
    PLoS ONE 6:e22709. 2011
    ..Our analyses further suggest that it can be profitable to conceive of conflict management strategies at the behavioral level as mechanisms of social immunity...
  10. ncbi request reprint Levels of selection in positive-strand virus dynamics
    D C Krakauer
    Santa Fe Institute, Santa Fe, NM 87501, USA
    J Evol Biol 16:64-73. 2003
    ..Data from poliovirus suggest that viruses might be unable to resolve the vertical conflicts of interests among different levels of selection...
  11. ncbi request reprint Module dynamics of the GnRH signal transduction network
    David C Krakauer
    Santa Fe Institute, NM 87501, USA
    J Theor Biol 218:457-70. 2002
    ..We propose that the cell computes by exploiting variation in the time scales of protein activation (phosphorylation) and gene expression...
  12. ncbi request reprint Red queen dynamics of protein translation
    David C Krakauer
    Santa Fe Institute, Hyde Park Road, Santa Fe, NM, 87501, USA
    J Theor Biol 218:97-109. 2002
    ....
  13. ncbi request reprint Encoding power in communication networks
    J C Flack
    Santa Fe Institute, Santa Fe, New Mexico 87501, USA
    Am Nat 168:E87-102. 2006
    ....
  14. ncbi request reprint Nonequilibrium phase transitions in biomolecular signal transduction
    Eric Smith
    Santa Fe Institute, Santa Fe, New Mexico 87501, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 84:051917. 2011
    ....
  15. pmc Evidence of strategic periodicities in collective conflict dynamics
    Simon DeDeo
    Santa Fe Institute, Santa Fe, NM 87501, USA
    J R Soc Interface 8:1260-73. 2011
    ....
  16. ncbi request reprint Evolution. Transitions from nonliving to living matter
    Steen Rasmussen
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Science 303:963-5. 2004
  17. pmc The evolution of developmental patterning under genetic duplication constraints
    Miguel A Fuentes
    Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
    J R Soc Interface 5:237-45. 2008
    ..This preference leads to an overall decrease in the density of redundant genotypes as developmental robustness neutralizes the advantages of genetic robustness...
  18. ncbi request reprint Policing stabilizes construction of social niches in primates
    Jessica C Flack
    Santa Fe Institute, Santa Fe, New Mexico 87501, USA
    Nature 439:426-9. 2006
    ..The structure of such networks plays a critical role in infant survivorship, emergence and spread of cooperative behaviour, social learning and cultural traditions...
  19. pmc Robustness mechanisms in primate societies: a perturbation study
    Jessica C Flack
    Santa Fe Institute, NM 87501, USA
    Proc Biol Sci 272:1091-9. 2005
    ....
  20. pmc Robustness and complexity co-constructed in multimodal signalling networks
    Nihat Ay
    Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
    Philos Trans R Soc Lond B Biol Sci 362:441-7. 2007
    ....
  21. ncbi request reprint Geometric robustness theory and biological networks
    Nihat Ay
    Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D 04103 Leipzig, Germany
    Theory Biosci 125:93-121. 2007
    ..We discuss the relationship between robustness measures and related measures of complexity and how robustness always implies a minimal level of complexity...
  22. pmc Redundancy, antiredundancy, and the robustness of genomes
    David C Krakauer
    Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
    Proc Natl Acad Sci U S A 99:1405-9. 2002
    ..We suggest that antiredundancy deserves greater attention in relation to cancer, mitochondrial disease, and virus infection...

Research Grants1

  1. MATHEMATICAL TOOLS AND MODELING FOR BIOLOGISTS
    David Krakauer; Fiscal Year: 2005
    ..The proposal describes a series of short courses and workshops across both disciplines and details the plan for the first of three workshops that are concerned with issues at the interface of theoretical and experimental biology. ..