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Charles C. Kim

Education

Ph.D. in Microbiology and Immunology, Stanford University, CA

Current position

Assistant Professor in Residence, Division of Experimental Medicine, Department of Medicine, University of California, San Francisco

Publications

  1. Lin, W. Y., Williams, C., Yan, C., Koledachkina, T., Luedke, K., Dalton, J., Bloomsburg, S., Morrison, N., Duncan, K. E., Kim, C. C. and Parrish, J. Z. (2015). The SLC36 transporter Pathetic is required for extreme dendrite growth in Drosophila sensory neurons. Genes Dev 29(11): 1120-1135.
  2. Sullivan, R. T.*, Kim, C. C.*, Fontana, M. F., Feeney, M. E., Jagannathan, P., Boyle, M. J., Drakeley, C. J., Ssewanyana, I., Nankya, F., Mayanja-Kizza, H., Dorsey, G. and Greenhouse, B. (2015). FCRL5 delineates functionally impaired memory B cells associated with Plasmodium falciparum exposure. PLoS Pathog 11(5): e1004894. (*Co-authors)
  3. Fontana, M. F., Baccarella, A., Pancholi, N., Pufall, M. A., Herbert, D. R. and Kim, C. C. (2015). JUNB is a key transcriptional modulator of macrophage activation. J Immunol 194(1): 177-186.
  4. Jimenez-Diaz, M. B., Ebert, D., Salinas, Y., Pradhan, A., Lehane, A. M., Myrand-Lapierre, M. E., O'Loughlin, K. G., Shackleford, D. M., Justino de Almeida, M., Carrillo, A. K., Clark, J. A., Dennis, A. S., Diep, J., Deng, X., Duffy, S., Endsley, A. N., Fedewa, G., Guiguemde, W. A., Gomez, M. G., Holbrook, G., Horst, J., Kim, C. C., Liu, J., Lee, M. C., Matheny, A., Martinez, M. S., Miller, G., Rodriguez-Alejandre, A., Sanz, L., Sigal, M., Spillman, N. J., Stein, P. D., Wang, Z., Zhu, F., Waterson, D., Knapp, S., Shelat, A., Avery, V. M., Fidock, D. A., Gamo, F. J., Charman, S. A., Mirsalis, J. C., Ma, H., Ferrer, S., Kirk, K., Angulo-Barturen, I., Kyle, D. E., DeRisi, J. L., Floyd, D. M. and Guy, R. K. (2014). (+)-SJ733, a clinical candidate for malaria that acts through ATP4 to induce rapid host-mediated clearance of Plasmodium. Proc Natl Acad Sci U S A 111(50): E5455-5462.
  5. Chen, F., Wu, W., Millman, A., Craft, J. F., Chen, E., Patel, N., Boucher, J. L., Urban, J. F., Jr., Kim, C. C. and Gause, W. C. (2014). Neutrophils prime a long-lived effector macrophage phenotype that mediates accelerated helminth expulsion. Nat Immunol 15(10): 938-946.
  6. Baccarella, A., Huang, B. W., Fontana, M. F. and Kim, C. C. (2014). Loss of Toll-like receptor 7 alters cytokine production and protects against experimental cerebral malaria. Malar J 13: 354.
  7. Jagannathan, P., Kim, C. C., Greenhouse, B., Nankya, F., Bowen, K., Eccles-James, I., Muhindo, M. K., Arinaitwe, E., Tappero, J. W., Kamya, M. R., Dorsey, G. and Feeney, M. E. (2014). Loss and dysfunction of Vdelta2(+) gammadelta T cells are associated with clinical tolerance to malaria. Sci Transl Med 6(251): 251ra117.
  8. Jiang, N., Soba, P., Parker, E., Kim, C. C. and Parrish, J. Z. (2014). The microRNA bantam regulates a developmental transition in epithelial cells that restricts sensory dendrite growth. Development 141(13): 2657-2668.
  9. Parrish, J. Z.*, Kim, C. C.*, Tang, L., Bergquist, S., Wang, T., Derisi, J. L., Jan, L. Y., Jan, Y. N. and Davis, G. W. (2014). Krüppel mediates the selective rebalancing of ion channel expression. Neuron 82(3): 537-544. (*Co-authors)
  10. Krow-Lucal, E. R., Kim, C. C., Burt, T. D. and McCune, J. M. (2014). Distinct functional programming of human fetal and adult monocytes. Blood 123(12): 1897-1904.
  11. Mostafavi, S., Ortiz-Lopez, A., Bogue, M. A., Hattori, K., Pop, C., Koller, D., Mathis, D., Benoist, C. and Immunological Genome, C. (2014). Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains. J Immunol 193(9): 4485-4496.
  12. Ericson, J. A., Duffau, P., Yasuda, K., Ortiz-Lopez, A., Rothamel, K., Rifkin, I. R., Monach, P. A. and ImmGen, C. (2014). Gene expression during the generation and activation of mouse neutrophils: implication of novel functional and regulatory pathways. PLoS One 9(10): e108553.
  13. Kim, C. C. and Lanier, L. L. (2013). Beyond the transcriptome: completion of act one of the Immunological Genome Project. Curr Opin Immunol 25(5): 593-597.
  14. Baccarella, A., Fontana, M. F., Chen, E. C. and Kim, C. C. (2013). Toll-like receptor 7 mediates early innate immune responses to malaria. Infect Immun 81(12): 4431-4442.
  15. Ergun, A., Doran, G., Costello, J. C., Paik, H. H., Collins, J. J., Mathis, D., Benoist, C. and ImmGen, C. (2013). Differential splicing across immune system lineages. Proc Natl Acad Sci U S A 110(35): 14324-14329.
  16. Mingueneau, M., Kreslavsky, T., Gray, D., Heng, T., Cruse, R., Ericson, J., Bendall, S., Spitzer, M. H., Nolan, G. P., Kobayashi, K., von Boehmer, H., Mathis, D., Benoist, C., Immunological Genome, C., Best, A. J., Knell, J., Goldrath, A., Joic, V., Koller, D., Shay, T., Regev, A., Cohen, N., Brennan, P., Brenner, M., Kim, F., Nageswara Rao, T., Wagers, A., Heng, T., Ericson, J., Rothamel, K., Ortiz-Lopez, A., Mathis, D., Benoist, C., Bezman, N. A., Sun, J. C., Min-Oo, G., Kim, C. C., Lanier, L. L., Miller, J., Brown, B., Merad, M., Gautier, E. L., Jakubzick, C., Randolph, G. J., Monach, P., Blair, D. A., Dustin, M. L., Shinton, S. A., Hardy, R. R., Laidlaw, D., Collins, J., Gazit, R., Rossi, D. J., Malhotra, N., Sylvia, K., Kang, J., Kreslavsky, T., Fletcher, A., Elpek, K., Bellemare-Pelletier, A., Malhotra, D. and Turley, S. (2013). The transcriptional landscape of alphabeta T cell differentiation. Nat Immunol 14(6): 619-632.
  17. Hsieh, C. L., Kim, C. C., Ryba, B. E., Niemi, E. C., Bando, J. K., Locksley, R. M., Liu, J., Nakamura, M. C. and Seaman, W. E. (2013). Traumatic brain injury induces macrophage subsets in the brain. Eur J Immunol 43(8): 2010-2022.
  18. Jojic, V., Shay, T., Sylvia, K., Zuk, O., Sun, X., Kang, J., Regev, A., Koller, D., Immunological Genome Project, C., Best, A. J., Knell, J., Goldrath, A., Joic, V., Koller, D., Shay, T., Regev, A., Cohen, N., Brennan, P., Brenner, M., Kim, F., Rao, T. N., Wagers, A., Heng, T., Ericson, J., Rothamel, K., Ortiz-Lopez, A., Mathis, D., Benoist, C., Bezman, N. A., Sun, J. C., Min-Oo, G., Kim, C. C., Lanier, L. L., Miller, J., Brown, B., Merad, M., Gautier, E. L., Jakubzick, C., Randolph, G. J., Monach, P., Blair, D. A., Dustin, M. L., Shinton, S. A., Hardy, R. R., Laidlaw, D., Collins, J., Gazit, R., Rossi, D. J., Malhotra, N., Sylvia, K., Kang, J., Kreslavsky, T., Fletcher, A., Elpek, K., Bellemarte-Pelletier, A., Malhotra, D. and Turley, S. (2013). Identification of transcriptional regulators in the mouse immune system. Nat Immunol 14(6): 633-643.
  19. Malhotra, N., Narayan, K., Cho, O. H., Sylvia, K. E., Yin, C., Melichar, H., Rashighi, M., Lefebvre, V., Harris, J. E., Berg, L. J., Kang, J. and Immunological Genome Project, C. (2013). A network of high-mobility group box transcription factors programs innate interleukin-17 production. Immunity 38(4): 681-693.
  20. Best, J. A., Blair, D. A., Knell, J., Yang, E., Mayya, V., Doedens, A., Dustin, M. L., Goldrath, A. W. and Immunological Genome Project, C. (2013). Transcriptional insights into the CD8(+) T cell response to infection and memory T cell formation. Nat Immunol 14(4): 404-412.
  21. Shay, T., Jojic, V., Zuk, O., Rothamel, K., Puyraimond-Zemmour, D., Feng, T., Wakamatsu, E., Benoist, C., Koller, D., Regev, A. and ImmGen, C. (2013). Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proc Natl Acad Sci U S A 110(8): 2946-2951.
  22. Cohen, N. R., Brennan, P. J., Shay, T., Watts, G. F., Brigl, M., Kang, J., Brenner, M. B. and ImmGen Project, C. (2013). Shared and distinct transcriptional programs underlie the hybrid nature of iNKT cells. Nat Immunol 14(1): 90-99.
  23. Kim, C. C., Nelson, C. S., Wilson, E. B., Hou, B., DeFranco, A. L. and DeRisi, J. L. (2012). Splenic red pulp macrophages produce type I interferons as early sentinels of malaria infection but are dispensable for control. PLoS One 7(10): e48126.
  24. Broadhurst, M. J., Ardeshir, A., Kanwar, B., Mirpuri, J., Gundra, U. M., Leung, J. M., Wiens, K. E., Vujkovic-Cvijin, I., Kim, C. C., Yarovinsky, F., Lerche, N. W., McCune, J. M. and Loke, P. (2012). Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon. PLoS Pathog 8(11): e1003000.
  25. Benoist, C., Lanier, L., Merad, M., Mathis, D. and Immunological Genome, P. (2012). Consortium biology in immunology: the perspective from the Immunological Genome Project. Nat Rev Immunol 12(10): 734-740.
  26. Gautier, E. L., Shay, T., Miller, J., Greter, M., Jakubzick, C., Ivanov, S., Helft, J., Chow, A., Elpek, K. G., Gordonov, S., Mazloom, A. R., Ma'ayan, A., Chua, W. J., Hansen, T. H., Turley, S. J., Merad, M., Randolph, G. J. and Immunological Genome, C. (2012). Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat Immunol 13(11): 1118-1128.
  27. Bezman, N. A.*, Kim, C. C.*, Sun, J. C.*, Min-Oo, G., Hendricks, D. W., Kamimura, Y., Best, J. A., Goldrath, A. W., Lanier, L. L. and Immunological Genome Project, C. (2012). Molecular definition of the identity and activation of natural killer cells. Nat Immunol 13(10): 1000-1009. (*Co-authors)
  28. Miller, J. C., Brown, B. D., Shay, T., Gautier, E. L., Jojic, V., Cohain, A., Pandey, G., Leboeuf, M., Elpek, K. G., Helft, J., Hashimoto, D., Chow, A., Price, J., Greter, M., Bogunovic, M., Bellemare-Pelletier, A., Frenette, P. S., Randolph, G. J., Turley, S. J., Merad, M. and Immunological Genome, C. (2012). Deciphering the transcriptional network of the dendritic cell lineage. Nat Immunol 13(9): 888-899.
  29. Narayan, K., Sylvia, K. E., Malhotra, N., Yin, C. C., Martens, G., Vallerskog, T., Kornfeld, H., Xiong, N., Cohen, N. R., Brenner, M. B., Berg, L. J., Kang, J. and Immunological Genome Project, C. (2012). Intrathymic programming of effector fates in three molecularly distinct gammadelta T cell subtypes. Nat Immunol 13(5): 511-518.
  30. Malhotra, D., Fletcher, A. L., Astarita, J., Lukacs-Kornek, V., Tayalia, P., Gonzalez, S. F., Elpek, K. G., Chang, S. K., Knoblich, K., Hemler, M. E., Brenner, M. B., Carroll, M. C., Mooney, D. J., Turley, S. J. and Immunological Genome Project, C. (2012). Transcriptional profiling of stroma from inflamed and resting lymph nodes defines immunological hallmarks. Nat Immunol 13(5): 499-510.
  31. Sun, J. C., Lopez-Verges, S., Kim, C. C., DeRisi, J. L. and Lanier, L. L. (2011). NK cells and immune "memory". J Immunol 186(4): 1891-1897.
  32. Loke, P., Hammond, S. N., Leung, J. M., Kim, C. C., Batra, S., Rocha, C., Balmaseda, A. and Harris, E. (2010). Gene expression patterns of dengue virus-infected children from nicaragua reveal a distinct signature of increased metabolism. PLoS Negl Trop Dis 4(6): e710.
  33. Zhang, S., Kim, C. C., Batra, S., McKerrow, J. H. and Loke, P. (2010). Delineation of diverse macrophage activation programs in response to intracellular parasites and cytokines. PLoS Negl Trop Dis 4(3): e648.
  34. Kim, C. C. and Derisi, J. L. (2010). VersaCount: customizable manual tally software for cell counting. Source Code Biol Med 5(1): 1.
  35. Kim, C. C., Wilson, E. B. and DeRisi, J. L. (2010). Improved methods for magnetic purification of malaria parasites and haemozoin. Malar J 9: 17. (Highly accessed)
  36. Parrish, J. Z., Xu, P., Kim, C. C., Jan, L. Y. and Jan, Y. N. (2009). The microRNA bantam functions in epithelial cells to regulate scaling growth of dendrite arbors in drosophila sensory neurons. Neuron 63(6): 788-802.
  37. Kim, C. C., Parikh, S., Sun, J. C., Myrick, A., Lanier, L. L., Rosenthal, P. J. and DeRisi, J. L. (2008). Experimental malaria infection triggers early expansion of natural killer cells. Infect Immun 76(12): 5873-5882.
  38. Brotcke, A., Weiss, D. S., Kim, C. C., Chain, P., Malfatti, S., Garcia, E. and Monack, D. M. (2006). Identification of MglA-regulated genes reveals novel virulence factors in Francisella tularensis. Infect Immun 74(12): 6642-6655.
  39. Lawley, T. D., Chan, K., Thompson, L. J., Kim, C. C., Govoni, G. R. and Monack, D. M. (2006). Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse. PLoS Pathog 2(2): e11.
  40. Chan, K., Kim, C. C. and Falkow, S. (2005). Microarray-based detection of Salmonella enterica serovar Typhimurium transposon mutants that cannot survive in macrophages and mice. Infect Immun 73(9): 5438-5449.
  41. Goguet de la Salmoniere, Y. O., Kim, C. C., Tsolaki, A. G., Pym, A. S., Siegrist, M. S. and Small, P. M. (2004). High-throughput method for detecting genomic-deletion polymorphisms. J Clin Microbiol 42(7): 2913-2918.
  42. Kim, C. C. and Falkow, S. (2004). Delineation of upstream signaling events in the salmonella pathogenicity island 2 transcriptional activation pathway. J Bacteriol 186(14): 4694-4704.
  43. Joyce, E. A., Kawale, A., Censini, S., Kim, C. C., Covacci, A. and Falkow, S. (2004). LuxS is required for persistent pneumococcal carriage and expression of virulence and biosynthesis genes. Infect Immun 72(5): 2964-2975.
  44. Merrell, D. S., Thompson, L. J., Kim, C. C., Mitchell, H., Tompkins, L. S., Lee, A. and Falkow, S. (2003). Growth phase-dependent response of Helicobacter pylori to iron starvation. Infect Immun 71(11): 6510-6525.
  45. Mueller, A., O'Rourke, J., Chu, P., Kim, C. C., Sutton, P., Lee, A. and Falkow, S. (2003). Protective immunity against Helicobacter is characterized by a unique transcriptional signature. Proc Natl Acad Sci U S A 100(21): 12289-12294.
  46. Kim, C. C., Monack, D. and Falkow, S. (2003). Modulation of virulence by two acidified nitrite-responsive loci of Salmonella enterica serovar Typhimurium. Infect Immun 71(6): 3196-3205.
  47. Kim, C. C. and Falkow, S. (2003). Significance analysis of lexical bias in microarray data. BMC Bioinformatics 4: 12.
  48. Chan, K., Baker, S., Kim, C. C., Detweiler, C. S., Dougan, G. and Falkow, S. (2003). Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray. J Bacteriol 185(2): 553-563.
  49. Kim, C. C., Joyce, E. A., Chan, K. and Falkow, S. (2002). Improved analytical methods for microarray-based genome-composition analysis. Genome Biol 3(11): RESEARCH0065.
  50. Ghim, S. Y., Kim, C. C., Bonner, E. R., D'Elia, J. N., Grabner, G. K. and Switzer, R. L. (1999). The Enterococcus faecalis pyr operon is regulated by autogenous transcriptional attenuation at a single site in the 5' leader. J Bacteriol 181(4): 1324-1329.
  51. Combadiere, B., Reis e Sousa, C., Trageser, C., Zheng, L. X., Kim, C. R. and Lenardo, M. J. (1998). Differential TCR signaling regulates apoptosis and immunopathology during antigen responses in vivo. Immunity 9(3): 305-313.
Protocols by Charles C. Kim
  1. Mouse Models of Uncomplicated and Fatal Malaria