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Charles Kim, PhD

TitleAssistant Professor
SchoolUCSF School of Medicine
DepartmentMedicine
Address1001 Potrero Ave
San Francisco CA 94110
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    University of California, San FranciscoPostdoctoral StudiesGraduate Division

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    RESEARCH INTERESTS

    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.


    EDUCATION AND TRAINING

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


    Collapse Research 
    Collapse Research Activities and Funding
    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. Williams CR, Baccarella A, Parrish JZ, Kim C. 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
    2. Fontana MF, de Melo GL, Anidi C, Hamburger R, Kim CY, Lee SY, Pham J, Kim C. 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.
      View in: PubMed
    3. 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 C, Reis MG, Ko AI. Cathelicidin Insufficiency in Patients with Fatal Leptospirosis. PLoS Pathog. 2016 Nov; 12(11):e1005943. PMID: 27812211.
      View in: PubMed
    4. Kim C, Nakamura MC, Hsieh CL. Brain trauma elicits non-canonical macrophage activation states. J Neuroinflammation. 2016; 13(1):117. PMID: 27220367.
      View in: PubMed
    5. 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 C, 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 5; 165(4):921-35. PMID: 27114033.
      View in: PubMed
    6. Robblee MM, Kim C, 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.
      View in: PubMed
    7. Williams CR, Baccarella A, Parrish JZ, Kim C. Trimming of sequence reads alters RNA-Seq gene expression estimates. BMC Bioinformatics. 2016; 17(1):103. PMID: 26911985.
      View in: PubMed
    8. Fontana MF, Baccarella A, Kellar D, Oniskey TK, Terinate P, Rosenberg SD, Huang EJ, Herbert DR, Kim C. 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 [Available on 09/01/16].
    9. 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 C, 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 [Available on 03/01/16].
    10. Huang BW, Pearman E, Kim C. Mouse Models of Uncomplicated and Fatal Malaria. Bio Protoc. 2015 Jul 5; 5(13). PMID: 26236758.
      View in: PubMed
    11. Lin WY, Williams C, Yan C, Koledachkina T, Luedke K, Dalton J, Bloomsburg S, Morrison N, Duncan KE, Kim C, Parrish JZ. The SLC36 transporter Pathetic is required for extreme dendrite growth in Drosophila sensory neurons. Genes Dev. 2015 Jun 1; 29(11):1120-35. PMID: 26063572; PMCID: PMC4470281 [Available on 12/01/15].
    12. Sullivan RT, Kim C, 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.
    13. Kim C, 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 1; 32(5):1003-11. PMID: 26366926.
      View in: PubMed
    14. Fontana MF, Baccarella A, Pancholi N, Pufall MA, Herbert DR, Kim C. JUNB is a key transcriptional modulator of macrophage activation. J Immunol. 2015 Jan 1; 194(1):177-86. PMID: 25472994; PMCID: PMC4431620 [Available on 01/01/16].
    15. 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 C, 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.
    16. Baccarella A, Huang BW, Fontana MF, Kim C. Loss of Toll-like receptor 7 alters cytokine production and protects against experimental cerebral malaria. Malar J. 2014; 13:354. PMID: 25192715; PMCID: PMC4164820.
    17. Chen F, Wu W, Millman A, Craft JF, Chen E, Patel N, Boucher JL, Urban JF, Kim C, 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.
    18. Jagannathan P, Kim C, 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.
    19. Jiang N, Soba P, Parker E, Kim C, 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.
    20. Parrish JZ, Kim C, 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 7; 82(3):537-44. PMID: 24811378; PMCID: PMC4104505.
    21. Krow-Lucal ER, Kim C, 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.
    22. Kim C, 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.
    23. Baccarella A, Fontana MF, Chen EC, Kim C. Toll-like receptor 7 mediates early innate immune responses to malaria. Infect Immun. 2013 Dec; 81(12):4431-42. PMID: 24042114; PMCID: PMC3837989.
    24. Hsieh CL, Kim C, 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.
    25. Broadhurst MJ, Ardeshir A, Kanwar B, Mirpuri J, Gundra UM, Leung JM, Wiens KE, Vujkovic-Cvijin I, Kim C, 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.
    26. Kim C, 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.
    27. Bezman NA, Kim C, 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.
    28. Sun JC, Lopez-Verges S, Kim C, DeRisi JL, Lanier LL. NK cells and immune "memory". J Immunol. 2011 Feb 15; 186(4):1891-7. PMID: 21289313; PMCID: PMC4410097.
    29. Loke P, Hammond SN, Leung JM, Kim C, 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; 4(6):e710. PMID: 20559541; PMCID: PMC2886038.
    30. Zhang S, Kim C, Batra S, McKerrow JH, Loke P. Delineation of diverse macrophage activation programs in response to intracellular parasites and cytokines. PLoS Negl Trop Dis. 2010; 4(3):e648. PMID: 20361029; PMCID: PMC2846935.
    31. Kim C, Wilson EB, DeRisi JL. Improved methods for magnetic purification of malaria parasites and haemozoin. Malar J. 2010; 9:17. PMID: 20074366; PMCID: PMC2817699.
    32. Kim C, Derisi JL. VersaCount: customizable manual tally software for cell counting. Source Code Biol Med. 2010; 5(1):1. PMID: 20180957; PMCID: PMC2829563.
    33. Parrish JZ, Xu P, Kim C, 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.
    34. Kim C, 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.
    35. Brotcke A, Weiss DS, Kim C, 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.
    36. Lawley TD, Chan K, Thompson LJ, Kim C, 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.
    37. Chan K, Kim C, 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.
    38. Kim C, 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.
    39. Goguet de la Salmonière YO, Kim C, 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.
    40. Joyce EA, Kawale A, Censini S, Kim C, 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.
    41. Merrell DS, Thompson LJ, Kim C, 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.
    42. Mueller A, O'Rourke J, Chu P, Kim C, 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.
    43. Kim C, 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.
    44. Kim C, Falkow S. Significance analysis of lexical bias in microarray data. BMC Bioinformatics. 2003 Apr 3; 4:12. PMID: 12697067; PMCID: PMC153504.
    45. Chan K, Baker S, Kim C, 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.
    46. Kim C, 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.
    47. Ghim SY, Kim C, 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.
    48. Combadière B, Reis e Sousa C, Trageser C, Zheng LX, Kim C, 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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