Charles C Kim

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Improved analytical methods for microarray-based genome-composition analysis
    Charles C Kim
    Department of Microbiology and Immunology, 299 Campus Drive, Stanford University Medical Center, Stanford, CA 94305, USA
    Genome Biol 3:RESEARCH0065. 2002
  2. pmc Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse
    Trevor D Lawley
    Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
    PLoS Pathog 2:e11. 2006
  3. pmc Delineation of upstream signaling events in the salmonella pathogenicity island 2 transcriptional activation pathway
    Charles C Kim
    Microbiology and Immunology, 299 Campus Drive, Stanford University Medical Center, Stanford, CA 94305, USA
    J Bacteriol 186:4694-704. 2004
  4. pmc Modulation of virulence by two acidified nitrite-responsive loci of Salmonella enterica serovar Typhimurium
    Charles C Kim
    Microbiology and Immunology, Stanford University Medical Center, California 94305, USA
    Infect Immun 71:3196-205. 2003
  5. pmc Significance analysis of lexical bias in microarray data
    Charles C Kim
    Microbiology and Immunology, Stanford University Medical Center, Stanford, CA, 94305, USA
    BMC Bioinformatics 4:12. 2003
  6. pmc Identification of MglA-regulated genes reveals novel virulence factors in Francisella tularensis
    Anna Brotcke
    Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Fairchild Bldg D041, Stanford, CA 94305, USA
    Infect Immun 74:6642-55. 2006
  7. pmc Microarray-based detection of Salmonella enterica serovar Typhimurium transposon mutants that cannot survive in macrophages and mice
    Kaman Chan
    Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305 5124, USA
    Infect Immun 73:5438-49. 2005
  8. pmc Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray
    Kaman Chan
    Department of Microbiology and Immunology, Stanford University School of Medicine, California 94305 5124, USA
    J Bacteriol 185:553-63. 2003
  9. pmc LuxS is required for persistent pneumococcal carriage and expression of virulence and biosynthesis genes
    Elizabeth A Joyce
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
    Infect Immun 72:2964-75. 2004
  10. pmc Growth phase-dependent response of Helicobacter pylori to iron starvation
    D Scott Merrell
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
    Infect Immun 71:6510-25. 2003

Detail Information

Publications14

  1. pmc Improved analytical methods for microarray-based genome-composition analysis
    Charles C Kim
    Department of Microbiology and Immunology, 299 Campus Drive, Stanford University Medical Center, Stanford, CA 94305, USA
    Genome Biol 3:RESEARCH0065. 2002
    ..Current methodology uses empirical determination of cutoffs for classification into these categories, but this methodology is subject to several problems that can result in the misclassification of many genes...
  2. pmc Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse
    Trevor D Lawley
    Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
    PLoS Pathog 2:e11. 2006
    ....
  3. pmc Delineation of upstream signaling events in the salmonella pathogenicity island 2 transcriptional activation pathway
    Charles C Kim
    Microbiology and Immunology, 299 Campus Drive, Stanford University Medical Center, Stanford, CA 94305, USA
    J Bacteriol 186:4694-704. 2004
    ..Additionally, EnvZ, but not acetyl phosphate, is required for maximal expression of SPI2 in the intracellular environment, suggesting that the in vitro SPI2 activation pathway is the same as that used in vivo...
  4. pmc Modulation of virulence by two acidified nitrite-responsive loci of Salmonella enterica serovar Typhimurium
    Charles C Kim
    Microbiology and Immunology, Stanford University Medical Center, California 94305, USA
    Infect Immun 71:3196-205. 2003
    ..We conclude that these genes are regulated by physiological nitrogen oxides and that the absence of these bacterial genes in some way diminishes the ability of mice to clear a low dose infection...
  5. pmc Significance analysis of lexical bias in microarray data
    Charles C Kim
    Microbiology and Immunology, Stanford University Medical Center, Stanford, CA, 94305, USA
    BMC Bioinformatics 4:12. 2003
    ..A number of sophisticated methods for identification of significant lexical trends are currently available, but these methods are generally too cumbersome for practical use by most microarray users...
  6. pmc Identification of MglA-regulated genes reveals novel virulence factors in Francisella tularensis
    Anna Brotcke
    Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Fairchild Bldg D041, Stanford, CA 94305, USA
    Infect Immun 74:6642-55. 2006
    ..We have identified five new Francisella virulence genes, and our results suggest that characterizations of additional MglA-regulated genes will yield further insights into the pathogenesis of this bacterium...
  7. pmc Microarray-based detection of Salmonella enterica serovar Typhimurium transposon mutants that cannot survive in macrophages and mice
    Kaman Chan
    Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305 5124, USA
    Infect Immun 73:5438-49. 2005
    ..enterica serovar Typhimurium STM screen, illustrating the utility of this approach for the high-throughput identification of virulence factors important for survival in the host...
  8. pmc Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray
    Kaman Chan
    Department of Microbiology and Immunology, Stanford University School of Medicine, California 94305 5124, USA
    J Bacteriol 185:553-63. 2003
    ....
  9. pmc LuxS is required for persistent pneumococcal carriage and expression of virulence and biosynthesis genes
    Elizabeth A Joyce
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
    Infect Immun 72:2964-75. 2004
    ..Our analysis of an S. pneumoniae transcriptome revealed a function for LuxS in gene regulation that is not dependent upon high cell density and is likely involved in the maintenance of pneumococcal load in susceptible hosts...
  10. pmc Growth phase-dependent response of Helicobacter pylori to iron starvation
    D Scott Merrell
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
    Infect Immun 71:6510-25. 2003
    ..Finally, bioinformatic analysis of the predicted promoter regions of the differentially regulated genes led to identification of several putative Fur boxes, suggesting a direct role for Fur in iron-dependent regulation of these genes...
  11. pmc Delineation of diverse macrophage activation programs in response to intracellular parasites and cytokines
    Shuyi Zhang
    Department of Pathology, University of California San Francisco, CA, USA
    PLoS Negl Trop Dis 4:e648. 2010
    ....
  12. ncbi Traumatic brain injury induces macrophage subsets in the brain
    Christine L Hsieh
    San Francisco VA Medical Center, San Francisco, CA, USA
    Eur J Immunol 43:2010-22. 2013
    ..The Arg1(+) cells differed from Arg1(-) cells in multiple aspects, most notably in their chemokine repertoires. Thus, the macrophage response to TBI initially involves heterogeneous polarization toward at least two major subsets. ..
  13. pmc Experimental malaria infection triggers early expansion of natural killer cells
    Charles C Kim
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
    Infect Immun 76:5873-82. 2008
    ..These data indicate that the early response to P. chabaudi infection of the blood is marked by a primary wave of interferon with a subsequent response by NK cells...
  14. pmc Protective immunity against Helicobacter is characterized by a unique transcriptional signature
    Anne Mueller
    Department of Microbiology and Immunology, Stanford University School of Medicine, Sherman Fairchild Science Building D 033, 299 Campus Drive, Stanford, CA 94305 5402, USA
    Proc Natl Acad Sci U S A 100:12289-94. 2003
    ..We propose a mechanism of protection that involves the effector responses of either or both lymphocyte subclasses as well as the previously unappreciated paracrine functions of adipose tissue surrounding the resident lymphocytes...