J A Shapiro

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. ncbi Genome organization and reorganization in evolution: formatting for computation and function
    James A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
    Ann N Y Acad Sci 981:111-34. 2002
  2. ncbi Genome organization, natural genetic engineering and adaptive mutation
    J A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA
    Trends Genet 13:98-104. 1997
  3. ncbi Thinking about bacterial populations as multicellular organisms
    J A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, USA
    Annu Rev Microbiol 52:81-104. 1998
  4. ncbi Genome system architecture and natural genetic engineering in evolution
    J A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, USA
    Ann N Y Acad Sci 870:23-35. 1999
  5. ncbi Transposable elements as the key to a 21st century view of evolution
    J A Shapiro
    University of Chicago, Department of Biochemistry and Molecular Biology, Cummings Life Sciences Center, IL 60637 4931, USA
    Genetica 107:171-9. 1999
  6. ncbi Repetitive DNA, genome system architecture and genome reorganization
    James A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA
    Res Microbiol 153:447-53. 2002
  7. ncbi Differential fiu-lacZ fusion regulation linked to Escherichia coli colony development
    D L Newman
    Department of Biochemistry and Molecular Biology, University of Chicago, 920 E 58th Street, Chicago, IL 60637, USA
    Mol Microbiol 33:18-32. 1999
  8. ncbi Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology
    J A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, 929 E 57th Street, Chicago IL 60637, USA
    Stud Hist Philos Biol Biomed Sci 38:807-19. 2007
  9. ncbi A role for the Clp protease in activating Mu-mediated DNA rearrangements
    J A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637
    J Bacteriol 175:2625-31. 1993
  10. ncbi Retrotransposons and regulatory suites
    James A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA
    Bioessays 27:122-5. 2005

Collaborators

Detail Information

Publications15

  1. ncbi Genome organization and reorganization in evolution: formatting for computation and function
    James A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
    Ann N Y Acad Sci 981:111-34. 2002
    ..The concepts of cellular computation and decision-making, genome system architecture, and natural genetic engineering combine to provide a new way of framing evolutionary theories and understanding genome sequence information...
  2. ncbi Genome organization, natural genetic engineering and adaptive mutation
    J A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA
    Trends Genet 13:98-104. 1997
    ....
  3. ncbi Thinking about bacterial populations as multicellular organisms
    J A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, USA
    Annu Rev Microbiol 52:81-104. 1998
    ....
  4. ncbi Genome system architecture and natural genetic engineering in evolution
    J A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, USA
    Ann N Y Acad Sci 870:23-35. 1999
    ..This molecular genetic perspective places evolutionary change in the biologically responsive context of cellular biochemistry...
  5. ncbi Transposable elements as the key to a 21st century view of evolution
    J A Shapiro
    University of Chicago, Department of Biochemistry and Molecular Biology, Cummings Life Sciences Center, IL 60637 4931, USA
    Genetica 107:171-9. 1999
    ..By connecting transcriptional regulatory circuits to the action of natural genetic engineering systems, there is a plausible molecular basis for coordinated changes in the genome subject to biologically meaningful feedback...
  6. ncbi Repetitive DNA, genome system architecture and genome reorganization
    James A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA
    Res Microbiol 153:447-53. 2002
    ..Appreciating the functional significance of repetitive DNA provides new concepts of genome organization and genome reorganization in evolution...
  7. ncbi Differential fiu-lacZ fusion regulation linked to Escherichia coli colony development
    D L Newman
    Department of Biochemistry and Molecular Biology, University of Chicago, 920 E 58th Street, Chicago, IL 60637, USA
    Mol Microbiol 33:18-32. 1999
    ..A simple model for differential fiu'-'lacZ regulation is proposed whereby iron accessibility changes during colony morphogenesis...
  8. ncbi Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology
    J A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, 929 E 57th Street, Chicago IL 60637, USA
    Stud Hist Philos Biol Biomed Sci 38:807-19. 2007
    ..This remarkable series of observations requires us to revise basic ideas about biological information processing and recognise that even the smallest cells are sentient beings...
  9. ncbi A role for the Clp protease in activating Mu-mediated DNA rearrangements
    J A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637
    J Bacteriol 175:2625-31. 1993
    ..These results point to temporal changes in Clp proteolysis of the Mucts62 repressor as a key molecular event in the regulation of one class of genomic change in E. coli...
  10. ncbi Retrotransposons and regulatory suites
    James A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA
    Bioessays 27:122-5. 2005
    ..These chimeric transcripts display restricted expression in oocytes and preimplantation embryos and presumably originate from developmentally regulated LTR promoters. Some, but not all, chimeric transcripts encode novel protein products...
  11. ncbi A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering
    James A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, 920 E 58th Street, Chicago, IL 60637, USA
    Gene 345:91-100. 2005
    ..This review will take a broad overview of these developments and suggest some new ways of thinking about genomes as sophisticated informatic storage systems and about evolution as a systems engineering process...
  12. ncbi Why repetitive DNA is essential to genome function
    James A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, 920 E 58th Street, Chicago, IL 60637, USA
    Biol Rev Camb Philos Soc 80:227-50. 2005
    ..These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component...
  13. ncbi Revisiting the central dogma in the 21st century
    James A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science, Chicago, IL 60637, USA
    Ann N Y Acad Sci 1178:6-28. 2009
    ....
  14. ncbi Letting Escherichia coli teach me about genome engineering
    James A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science, Chicago, Illinois 60637, USA
    Genetics 183:1205-14. 2009
    ..All these experiences confirmed Barbara McClintock's view that cells frequently respond to stimuli by restructuring their genomes and provided novel insights into the natural genetic engineering processes involved in evolution...
  15. ncbi Mobile DNA and evolution in the 21st century
    James A Shapiro
    Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science W123B, 929 E 57th Street, Chicago, IL 60637, USA
    Mob DNA 1:4. 2010
    ....