Charles Kim, PhD

Title(s)Assistant Professor, Medicine
SchoolSchool of Medicine
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    University of California, San FranciscoPostdoctoral StudiesGraduate Division

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    Despite over a century of research since the discovery of Plasmodium parasites, malaria continues to be one of the top causes of infectious mortality in the world. An effective vaccine could significantly reduce malaria prevalence, but our lack of understanding of immune control mechanisms hinders the rational design of such a tool. To advance us toward this goal, we wish to understand how malaria infection is recognized by the host immune system, and how these recognition events subsequently promote activation of immune responses responsible for parasite elimination.

    We are employing a combination of immunology and systems biology approaches to understand these processes in the Plasmodium chabaudi mouse model of malaria infection. Our current interests are focused on the discovery of novel signaling pathways and regulatory network architecture in leukocytes of the innate immune system, combinatorial interactions between these pathways, identifying innate-adaptive interactions, and determining how these intracellular and intercellular interactions combine into a cohesive effector response capable of clearance of malaria parasites.


    University of Illinois, Urbana-Champaign, BS, 1997
    Stanford University, PhD, 2004
    University of California, San Francisco, Postdoctoral Fellow, 2005-2011

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    Immunological detection and control of experimental uncomplicated malaria
    NIH/NIAID R00AI085035Aug 3, 2011 - Jul 31, 2013
    Role: Principal Investigator
    Immunological detection and control of experimental uncomplicated malaria
    NIH/NIAID K99AI085035Jun 1, 2010 - May 31, 2011
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Baccarella A, Williams CR, Parrish JZ, Kim CC. Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance. BMC Bioinformatics. 2018 Nov 14; 19(1):423. PMID: 30428853.
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    2. Hoyer N, Zielke P, Hu C, Petersen M, Sauter K, Scharrenberg R, Peng Y, Kim CC, Han C, Parrish JZ, Soba P. Ret and Substrate-Derived TGF-ß Maverick Regulate Space-Filling Dendrite Growth in Drosophila Sensory Neurons. Cell Rep. 2018 Aug 28; 24(9):2261-2272.e5. PMID: 30157422.
      View in: PubMed
    3. Chitre AS, Kattah MG, Rosli YY, Pao M, Deswal M, Deeks SG, Hunt PW, Abdel-Mohsen M, Montaner LJ, Kim CC, Ma A, Somsouk M, McCune JM. A20 upregulation during treated HIV disease is associated with intestinal epithelial cell recovery and function. PLoS Pathog. 2018 03; 14(3):e1006806. PMID: 29505600.
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    4. Boiko N, Medrano G, Montano E, Jiang N, Williams CR, Madungwe NB, Bopassa JC, Kim CC, Parrish JZ, Hargreaves KM, Stockand JD, Eaton BA. TrpA1 activation in peripheral sensory neurons underlies the ionic basis of pain hypersensitivity in response to vinca alkaloids. PLoS One. 2017; 12(10):e0186888. PMID: 29084244.
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    5. Lindow JC, Wunder EA, Popper SJ, Min JN, Mannam P, Srivastava A, Yao Y, Hacker KP, Raddassi K, Lee PJ, Montgomery RR, Shaw AC, Hagan JE, Araújo GC, Nery N, Relman DA, Kim CC, Reis MG, Ko AI. Correction: Cathelicidin Insufficiency in Patients with Fatal Leptospirosis. PLoS Pathog. 2017 Sep; 13(9):e1006646. PMID: 28950012.
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    6. Fontana MF, de Melo GL, Anidi C, Hamburger R, Kim CY, Lee SY, Pham J, Kim CC. Correction: Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection. PLoS Pathog. 2017 Feb; 13(2):e1006192. PMID: 28146583.
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    7. Williams CR, Baccarella A, Parrish JZ, Kim CC. Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq. BMC Bioinformatics. 2017 Jan 17; 18(1):38. PMID: 28095772.
      View in: PubMed
    8. Fontana MF, de Melo GL, Anidi C, Hamburger R, Kim CY, Lee SY, Pham J, Kim CC. Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection. PLoS Pathog. 2016 Dec; 12(12):e1006046. PMID: 27923070.
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    9. Lindow JC, Wunder EA, Popper SJ, Min JN, Mannam P, Srivastava A, Yao Y, Hacker KP, Raddassi K, Lee PJ, Montgomery RR, Shaw AC, Hagan JE, Araújo GC, Nery N, Relman DA, Kim CC, Reis MG, Ko AI. Cathelicidin Insufficiency in Patients with Fatal Leptospirosis. PLoS Pathog. 2016 Nov; 12(11):e1005943. PMID: 27812211.
      View in: PubMed
    10. Fontana MF, Baccarella A, Craft JF, Boyle MJ, McIntyre TI, Wood MD, Thorn KS, Anidi C, Bayat A, Chung MR, Hamburger R, Kim CY, Pearman E, Pham J, Tang JJ, Boon L, Kamya MR, Dorsey G, Feeney ME, Kim CC. A Novel Model of Asymptomatic Plasmodium Parasitemia That Recapitulates Elements of the Human Immune Response to Chronic Infection. PLoS One. 2016; 11(9):e0162132. PMID: 27583554; PMCID: PMC5008831.
    11. Kim CC, Nakamura MC, Hsieh CL. Brain trauma elicits non-canonical macrophage activation states. J Neuroinflammation. 2016 05 24; 13(1):117. PMID: 27220367.
      View in: PubMed
    12. Lui H, Zhang J, Makinson SR, Cahill MK, Kelley KW, Huang HY, Shang Y, Oldham MC, Martens LH, Gao F, Coppola G, Sloan SA, Hsieh CL, Kim CC, Bigio EH, Weintraub S, Mesulam MM, Rademakers R, Mackenzie IR, Seeley WW, Karydas A, Miller BL, Borroni B, Ghidoni R, Farese RV, Paz JT, Barres BA, Huang EJ. Progranulin Deficiency Promotes Circuit-Specific Synaptic Pruning by Microglia via Complement Activation. Cell. 2016 May 05; 165(4):921-35. PMID: 27114033.
      View in: PubMed
    13. Robblee MM, Kim CC, Porter Abate J, Valdearcos M, Sandlund KL, Shenoy MK, Volmer R, Iwawaki T, Koliwad SK. Saturated Fatty Acids Engage an IRE1a-Dependent Pathway to Activate the NLRP3 Inflammasome in Myeloid Cells. Cell Rep. 2016 Mar 22; 14(11):2611-23. PMID: 26971994.
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    14. Williams CR, Baccarella A, Parrish JZ, Kim CC. Trimming of sequence reads alters RNA-Seq gene expression estimates. BMC Bioinformatics. 2016 Feb 25; 17:103. PMID: 26911985; PMCID: PMC4766705.
    15. Fontana MF, Baccarella A, Kellar D, Oniskey TK, Terinate P, Rosenberg SD, Huang EJ, Herbert DR, Kim CC. Myeloid expression of the AP-1 transcription factor JUNB modulates outcomes of type 1 and type 2 parasitic infections. Parasite Immunol. 2015 Sep; 37(9):470-8. PMID: 26178310; PMCID: PMC4573644.
    16. Huang X, He Y, Dubuc AM, Hashizume R, Zhang W, Reimand J, Yang H, Wang TA, Stehbens SJ, Younger S, Barshow S, Zhu S, Cooper MK, Peacock J, Ramaswamy V, Garzia L, Wu X, Remke M, Forester CM, Kim CC, Weiss WA, James CD, Shuman MA, Bader GD, Mueller S, Taylor MD, Jan YN, Jan LY. EAG2 potassium channel with evolutionarily conserved function as a brain tumor target. Nat Neurosci. 2015 Sep; 18(9):1236-46. PMID: 26258683; PMCID: PMC4639927.
    17. Huang BW, Pearman E, Kim CC. Mouse Models of Uncomplicated and Fatal Malaria. Bio Protoc. 2015 Jul 05; 5(13). PMID: 26236758.
      View in: PubMed
    18. Lin WY, Williams C, Yan C, Koledachkina T, Luedke K, Dalton J, Bloomsburg S, Morrison N, Duncan KE, Kim CC, Parrish JZ. The SLC36 transporter Pathetic is required for extreme dendrite growth in Drosophila sensory neurons. Genes Dev. 2015 Jun 01; 29(11):1120-35. PMID: 26063572; PMCID: PMC4470281.
    19. Sullivan RT, Kim CC, Fontana MF, Feeney ME, Jagannathan P, Boyle MJ, Drakeley CJ, Ssewanyana I, Nankya F, Mayanja-Kizza H, Dorsey G, Greenhouse B. FCRL5 Delineates Functionally Impaired Memory B Cells Associated with Plasmodium falciparum Exposure. PLoS Pathog. 2015 May; 11(5):e1004894. PMID: 25993340; PMCID: PMC4438005.
    20. Kim CC, Thai B, Yamaoka N, Aboutalib O. Hemispherical reflectance model for passive images in an outdoor environment. J Opt Soc Am A Opt Image Sci Vis. 2015 May 01; 32(5):1003-11. PMID: 26366926.
      View in: PubMed
    21. Fontana MF, Baccarella A, Pancholi N, Pufall MA, Herbert DR, Kim CC. JUNB is a key transcriptional modulator of macrophage activation. J Immunol. 2015 Jan 01; 194(1):177-86. PMID: 25472994; PMCID: PMC4431620.
    22. Jiménez-Díaz MB, Ebert D, Salinas Y, Pradhan A, Lehane AM, Myrand-Lapierre ME, O'Loughlin KG, Shackleford DM, Justino de Almeida M, Carrillo AK, Clark JA, Dennis AS, Diep J, Deng X, Duffy S, Endsley AN, Fedewa G, Guiguemde WA, Gómez MG, Holbrook G, Horst J, Kim CC, Liu J, Lee MC, Matheny A, Martínez MS, Miller G, Rodríguez-Alejandre A, Sanz L, Sigal M, Spillman NJ, Stein PD, Wang Z, Zhu F, Waterson D, Knapp S, Shelat A, Avery VM, Fidock DA, Gamo FJ, Charman SA, Mirsalis JC, Ma H, Ferrer S, Kirk K, Angulo-Barturen I, Kyle DE, DeRisi JL, Floyd DM, Guy RK. (+)-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. 2014 Dec 16; 111(50):E5455-62. PMID: 25453091; PMCID: PMC4273362.
    23. Baccarella A, Huang BW, Fontana MF, Kim CC. Loss of Toll-like receptor 7 alters cytokine production and protects against experimental cerebral malaria. Malar J. 2014 Sep 05; 13:354. PMID: 25192715; PMCID: PMC4164820.
    24. Chen F, Wu W, Millman A, Craft JF, Chen E, Patel N, Boucher JL, Urban JF, Kim CC, Gause WC. Neutrophils prime a long-lived effector macrophage phenotype that mediates accelerated helminth expulsion. Nat Immunol. 2014 Oct; 15(10):938-46. PMID: 25173346; PMCID: PMC4479254.
    25. Jagannathan P, Kim CC, Greenhouse B, Nankya F, Bowen K, Eccles-James I, Muhindo MK, Arinaitwe E, Tappero JW, Kamya MR, Dorsey G, Feeney ME. Loss and dysfunction of Vd2? ?d T cells are associated with clinical tolerance to malaria. Sci Transl Med. 2014 Aug 27; 6(251):251ra117. PMID: 25163477; PMCID: PMC4198150.
    26. Jiang N, Soba P, Parker E, Kim CC, Parrish JZ. The microRNA bantam regulates a developmental transition in epithelial cells that restricts sensory dendrite growth. Development. 2014 Jul; 141(13):2657-68. PMID: 24924190; PMCID: PMC4067962.
    27. Parrish JZ, Kim CC, Tang L, Bergquist S, Wang T, Derisi JL, Jan LY, Jan YN, Davis GW. Krüppel mediates the selective rebalancing of ion channel expression. Neuron. 2014 May 07; 82(3):537-44. PMID: 24811378; PMCID: PMC4104505.
    28. Krow-Lucal ER, Kim CC, Burt TD, McCune JM. Distinct functional programming of human fetal and adult monocytes. Blood. 2014 Mar 20; 123(12):1897-904. PMID: 24518760; PMCID: PMC3962163.
    29. Kim CC, Lanier LL. Beyond the transcriptome: completion of act one of the Immunological Genome Project. Curr Opin Immunol. 2013 Oct; 25(5):593-7. PMID: 24168965; PMCID: PMC3855358.
    30. Baccarella A, Fontana MF, Chen EC, Kim CC. Toll-like receptor 7 mediates early innate immune responses to malaria. Infect Immun. 2013 Dec; 81(12):4431-42. PMID: 24042114; PMCID: PMC3837989.
    31. Hsieh CL, Kim CC, Ryba BE, Niemi EC, Bando JK, Locksley RM, Liu J, Nakamura MC, Seaman WE. Traumatic brain injury induces macrophage subsets in the brain. Eur J Immunol. 2013 Aug; 43(8):2010-22. PMID: 23630120; PMCID: PMC4210355.
    32. Broadhurst MJ, Ardeshir A, Kanwar B, Mirpuri J, Gundra UM, Leung JM, Wiens KE, Vujkovic-Cvijin I, Kim CC, Yarovinsky F, Lerche NW, McCune JM, Loke P. Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon. PLoS Pathog. 2012; 8(11):e1003000. PMID: 23166490; PMCID: PMC3499566.
    33. Kim CC, Nelson CS, Wilson EB, Hou B, DeFranco AL, DeRisi JL. Splenic red pulp macrophages produce type I interferons as early sentinels of malaria infection but are dispensable for control. PLoS One. 2012; 7(10):e48126. PMID: 23144737; PMCID: PMC3483282.
    34. Bezman NA, Kim CC, Sun JC, Min-Oo G, Hendricks DW, Kamimura Y, Best JA, Goldrath AW, Lanier LL. Molecular definition of the identity and activation of natural killer cells. Nat Immunol. 2012 Oct; 13(10):1000-9. PMID: 22902830; PMCID: PMC3572860.
    35. Sun JC, Lopez-Verges S, Kim CC, DeRisi JL, Lanier LL. NK cells and immune "memory". J Immunol. 2011 Feb 15; 186(4):1891-7. PMID: 21289313; PMCID: PMC4410097.
    36. Loke P, Hammond SN, Leung JM, Kim CC, Batra S, Rocha C, Balmaseda A, Harris E. Gene expression patterns of dengue virus-infected children from nicaragua reveal a distinct signature of increased metabolism. PLoS Negl Trop Dis. 2010 Jun 15; 4(6):e710. PMID: 20559541; PMCID: PMC2886038.
    37. Zhang S, Kim CC, Batra S, McKerrow JH, Loke P. Delineation of diverse macrophage activation programs in response to intracellular parasites and cytokines. PLoS Negl Trop Dis. 2010 Mar 30; 4(3):e648. PMID: 20361029; PMCID: PMC2846935.
    38. Kim CC, Wilson EB, DeRisi JL. Improved methods for magnetic purification of malaria parasites and haemozoin. Malar J. 2010 Jan 14; 9:17. PMID: 20074366; PMCID: PMC2817699.
    39. Kim CC, Derisi JL. VersaCount: customizable manual tally software for cell counting. Source Code Biol Med. 2010 Jan 13; 5(1):1. PMID: 20180957; PMCID: PMC2829563.
    40. Parrish JZ, Xu P, Kim CC, Jan LY, Jan YN. The microRNA bantam functions in epithelial cells to regulate scaling growth of dendrite arbors in drosophila sensory neurons. Neuron. 2009 Sep 24; 63(6):788-802. PMID: 19778508; PMCID: PMC2772869.
    41. Kim CC, Parikh S, Sun JC, Myrick A, Lanier LL, Rosenthal PJ, DeRisi JL. Experimental malaria infection triggers early expansion of natural killer cells. Infect Immun. 2008 Dec; 76(12):5873-82. PMID: 18824529; PMCID: PMC2583561.
    42. Brotcke A, Weiss DS, Kim CC, Chain P, Malfatti S, Garcia E, Monack DM. Identification of MglA-regulated genes reveals novel virulence factors in Francisella tularensis. Infect Immun. 2006 Dec; 74(12):6642-55. PMID: 17000729; PMCID: PMC1698089.
    43. Lawley TD, Chan K, Thompson LJ, Kim CC, Govoni GR, Monack DM. Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse. PLoS Pathog. 2006 Feb; 2(2):e11. PMID: 16518469; PMCID: PMC1383486.
    44. Chan K, Kim CC, Falkow S. Microarray-based detection of Salmonella enterica serovar Typhimurium transposon mutants that cannot survive in macrophages and mice. Infect Immun. 2005 Sep; 73(9):5438-49. PMID: 16113260; PMCID: PMC1231100.
    45. Kim CC, Falkow S. Delineation of upstream signaling events in the salmonella pathogenicity island 2 transcriptional activation pathway. J Bacteriol. 2004 Jul; 186(14):4694-704. PMID: 15231802; PMCID: PMC438577.
    46. Goguet de la Salmonière YO, Kim CC, Tsolaki AG, Pym AS, Siegrist MS, Small PM. High-throughput method for detecting genomic-deletion polymorphisms. J Clin Microbiol. 2004 Jul; 42(7):2913-8. PMID: 15243038; PMCID: PMC446289.
    47. Joyce EA, Kawale A, Censini S, Kim CC, Covacci A, Falkow S. LuxS is required for persistent pneumococcal carriage and expression of virulence and biosynthesis genes. Infect Immun. 2004 May; 72(5):2964-75. PMID: 15102809; PMCID: PMC387900.
    48. Merrell DS, Thompson LJ, Kim CC, Mitchell H, Tompkins LS, Lee A, Falkow S. Growth phase-dependent response of Helicobacter pylori to iron starvation. Infect Immun. 2003 Nov; 71(11):6510-25. PMID: 14573673; PMCID: PMC219544.
    49. Mueller A, O'Rourke J, Chu P, Kim CC, Sutton P, Lee A, Falkow S. Protective immunity against Helicobacter is characterized by a unique transcriptional signature. Proc Natl Acad Sci U S A. 2003 Oct 14; 100(21):12289-94. PMID: 14528007; PMCID: PMC218751.
    50. Kim CC, Monack D, Falkow S. Modulation of virulence by two acidified nitrite-responsive loci of Salmonella enterica serovar Typhimurium. Infect Immun. 2003 Jun; 71(6):3196-205. PMID: 12761099; PMCID: PMC155741.
    51. Kim CC, Falkow S. Significance analysis of lexical bias in microarray data. BMC Bioinformatics. 2003 Apr 03; 4:12. PMID: 12697067; PMCID: PMC153504.
    52. Chan K, Baker S, Kim CC, Detweiler CS, Dougan G, Falkow S. Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray. J Bacteriol. 2003 Jan; 185(2):553-63. PMID: 12511502; PMCID: PMC145314.
    53. Kim CC, Joyce EA, Chan K, Falkow S. Improved analytical methods for microarray-based genome-composition analysis. Genome Biol. 2002 Oct 29; 3(11):RESEARCH0065. PMID: 12429064; PMCID: PMC133449.
    54. Ghim SY, Kim CC, Bonner ER, D'Elia JN, Grabner GK, Switzer RL. The Enterococcus faecalis pyr operon is regulated by autogenous transcriptional attenuation at a single site in the 5' leader. J Bacteriol. 1999 Feb; 181(4):1324-9. PMID: 9973361; PMCID: PMC93512.
    55. Combadière B, Reis e Sousa C, Trageser C, Zheng LX, Kim CR, Lenardo MJ. Differential TCR signaling regulates apoptosis and immunopathology during antigen responses in vivo. Immunity. 1998 Sep; 9(3):305-13. PMID: 9768750.
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