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    James Ryan, MD

    TitleAssociate Professor
    SchoolUCSF School of Medicine
    DepartmentMedicine
    Address3333 California Street
    San Francisco CA 94118
    Phone415-750-2104
    vCardDownload vCard

      Collapse Biography 
      Collapse Education and Training
      University of California, San FranciscoPost-Doc Fellow/Scholar Medicine1991
      University of California, San FranciscoResidency

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      Collapse Bibliographic 
      Collapse Publications
      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. Cozen ML, Ryan JC, Shen H, Cheung R, Kaplan DE, Pocha C, Brau N, Aytaman A, Schmidt WN, Pedrosa M, Anand BS, Chang KM, Morgan T, Monto A. Improved Survival Among all Interferon-a-Treated Patients in HCV-002, a Veterans Affairs Hepatitis C Cohort of 2211 Patients, Despite Increased Cirrhosis Among Nonresponders. Dig Dis Sci. 2016 Jun; 61(6):1744-56. PMID: 27059981.
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      2. Ryan JC, Wu Q, Shoemaker RC. Transcriptomic signatures in whole blood of patients who acquire a chronic inflammatory response syndrome (CIRS) following an exposure to the marine toxin ciguatoxin. BMC Med Genomics. 2015; 8:15. PMID: 25889530; PMCID: PMC4392619.
      3. Mancia A, Abelli L, Kucklick JR, Rowles TK, Wells RS, Balmer BC, Hohn AA, Baatz JE, Ryan JC. Microarray applications to understand the impact of exposure to environmental contaminants in wild dolphins (Tursiops truncatus). Mar Genomics. 2015 Feb; 19:47-57. PMID: 25479946.
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      4. Shoemaker RC, House D, Ryan JC. Structural brain abnormalities in patients with inflammatory illness acquired following exposure to water-damaged buildings: a volumetric MRI study using NeuroQuant®. Neurotoxicol Teratol. 2014 Sep-Oct; 45:18-26. PMID: 24946038.
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      5. Mancia A, Ryan JC, Van Dolah FM, Kucklick JR, Rowles TK, Wells RS, Rosel PE, Hohn AA, Schwacke LH. Machine learning approaches to investigate the impact of PCBs on the transcriptome of the common bottlenose dolphin (Tursiops truncatus). Mar Environ Res. 2014 Sep; 100:57-67. PMID: 24695049.
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      6. Ho EY, Cozen ML, Shen H, Lerrigo R, Trimble E, Ryan JC, Corvera CU, Monto A. Expanded use of aggressive therapies improves survival in early and intermediate hepatocellular carcinoma. HPB (Oxford). 2014 Aug; 16(8):758-67. PMID: 24467780; PMCID: PMC4113259.
      7. Hartigan-O'Connor DJ, Lin D, Ryan JC, Shvachko VA, Cozen ML, Segal MR, Terrault NA, Lanier LL, Manos MM, McCune JM. Monocyte activation by interferon a is associated with failure to achieve a sustained virologic response after treatment for hepatitis C virus infection. J Infect Dis. 2014 May 15; 209(10):1602-12. PMID: 24325966; PMCID: PMC3997582.
      8. Rathburn CK, Sharp NJ, Ryan JC, Neely MG, Cook M, Chapman RW, Burnett LE, Burnett KG. Transcriptomic responses of juvenile Pacific whiteleg shrimp, Litopenaeus vannamei, to hypoxia and hypercapnic hypoxia. Physiol Genomics. 2013 Sep 3; 45(17):794-807. PMID: 23821614.
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      9. Cozen ML, Ryan JC, Shen H, Lerrigo R, Yee RM, Sheen E, Wu R, Monto A. Nonresponse to interferon-a based treatment for chronic hepatitis C infection is associated with increased hazard of cirrhosis. PLoS One. 2013; 8(4):e61568. PMID: 23637856; PMCID: PMC3636226.
      10. Yee RM, Lehil MS, Rongey C, Shen H, Cozen ML, Monto A, Ryan JC. Impaired lymphocyte reactivity measured by immune function testing in untransplanted patients with cirrhosis. Clin Vaccine Immunol. 2013 Apr; 20(4):526-9. PMID: 23389930; PMCID: PMC3623409.
      11. Mancia A, Ryan JC, Chapman RW, Wu Q, Warr GW, Gulland FM, Van Dolah FM. Health status, infection and disease in California sea lions (Zalophus californianus) studied using a canine microarray platform and machine-learning approaches. Dev Comp Immunol. 2012 Apr; 36(4):629-37. PMID: 22067742.
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      12. Johnson JG, Morey JS, Neely MG, Ryan JC, Van Dolah FM. Transcriptome remodeling associated with chronological aging in the dinoflagellate, Karenia brevis. Mar Genomics. 2012 Mar; 5:15-25. PMID: 22325718.
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      13. Ryan JC. Development of a measure of work motivation for a meta-theory of motivation. Psychol Rep. 2011 Jun; 108(3):743-55. PMID: 21879620.
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      14. Shegarfi H, Dai KZ, Daws MR, Ryan JC, Vaage JT, Rolstad B, Naper C. The rat NK cell receptors Ly49s4 and Ly49i4 recognize nonclassical MHC-I molecules on Listeria monocytogenes-infected macrophages. J Leukoc Biol. 2011 Apr; 89(4):617-23. PMID: 21248147.
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      15. Shegarfi H, Dai KZ, Inngjerdingen M, Ryan JC, Vaage JT, Rolstad B, Naper C. The activating rat Ly49s5 receptor responds to increased levels of MHC class Ib molecules on Listeria monocytogenes-infected enteric epithelial cells. Eur J Immunol. 2010 Dec; 40(12):3535-43. PMID: 21108473.
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      16. Ryan JC, Cross CA, Van Dolah FM. Effects of COX inhibitors on neurodegeneration and survival in mice exposed to the marine neurotoxin domoic acid. Neurosci Lett. 2011 Jan 3; 487(1):83-7. PMID: 20934488.
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      17. Ryan JC, Morey JS, Bottein MY, Ramsdell JS, Van Dolah FM. Gene expression profiling in brain of mice exposed to the marine neurotoxin ciguatoxin reveals an acute anti-inflammatory, neuroprotective response. BMC Neurosci. 2010; 11:107. PMID: 20796285; PMCID: PMC2939656.
      18. Shoemaker RC, House D, Ryan JC. Defining the neurotoxin derived illness chronic ciguatera using markers of chronic systemic inflammatory disturbances: a case/control study. Neurotoxicol Teratol. 2010 Nov-Dec; 32(6):633-9. PMID: 20685390.
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      19. Li L, Fang CJ, Ryan JC, Niemi EC, Lebrón JA, Björkman PJ, Arase H, Torti FM, Torti SV, Nakamura MC, Seaman WE. Binding and uptake of H-ferritin are mediated by human transferrin receptor-1. Proc Natl Acad Sci U S A. 2010 Feb 23; 107(8):3505-10. PMID: 20133674; PMCID: PMC2840523.
      20. Shergill AK, Asundi KR, Barr A, Shah JN, Ryan JC, McQuaid KR, Rempel D. Pinch force and forearm-muscle load during routine colonoscopy: a pilot study. Gastrointest Endosc. 2009 Jan; 69(1):142-6. PMID: 19111694.
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      21. Maher JJ, Leon P, Ryan JC. Beyond insulin resistance: Innate immunity in nonalcoholic steatohepatitis. Hepatology. 2008 Aug; 48(2):670-8. PMID: 18666225; PMCID: PMC3592568.
      22. Morey JS, Ryan JC, Bottein Dechraoui MY, Rezvani AH, Levin ED, Gordon CJ, Ramsdell JS, Van Dolah FM. Liver genomic responses to ciguatoxin: evidence for activation of phase I and phase II detoxification pathways following an acute hypothermic response in mice. Toxicol Sci. 2008 Jun; 103(2):298-310. PMID: 18353800.
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      23. Twiner MJ, Ryan JC, Morey JS, Smith KJ, Hammad SM, Van Dolah FM, Hess P, McMahon T, Satake M, Yasumoto T, Doucette GJ. Transcriptional profiling and inhibition of cholesterol biosynthesis in human T lymphocyte cells by the marine toxin azaspiracid. Genomics. 2008 Mar; 91(3):289-300. PMID: 18191373.
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      24. Currie SL, Ryan JC, Tracy D, Wright TL, George S, McQuaid R, Kim M, Shen H, Monto A. A prospective study to examine persistent HCV reinfection in injection drug users who have previously cleared the virus. Drug Alcohol Depend. 2008 Jan 11; 93(1-2):148-54. PMID: 17977668.
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      25. Ryan JC, Bottein Dechraoui MY, Morey JS, Rezvani A, Levin ED, Gordon CJ, Ramsdell JS, Van Dolah FM. Transcriptional profiling of whole blood and serum protein analysis of mice exposed to the neurotoxin Pacific Ciguatoxin-1. Neurotoxicology. 2007 Nov; 28(6):1099-109. PMID: 17868886.
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      26. Morey JS, Ryan JC, Van Dolah FM. Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR. Biol Proced Online. 2006; 8:175-93. PMID: 17242735; PMCID: PMC1779618.
      27. Kveberg L, Dai KZ, Dissen E, Ryan JC, Rolstad B, Vaage JT, Naper C. Strain-dependent expression of four structurally related rat Ly49 receptors; correlation with NK gene complex haplotype and NK alloreactivity. Immunogenetics. 2006 Nov; 58(11):905-16. PMID: 17028855.
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      28. Kveberg L, Bäck CJ, Dai KZ, Inngjerdingen M, Rolstad B, Ryan JC, Vaage JT, Naper C. The novel inhibitory NKR-P1C receptor and Ly49s3 identify two complementary, functionally distinct NK cell subsets in rats. J Immunol. 2006 Apr 1; 176(7):4133-40. PMID: 16547249.
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      29. Ryan JC, Morey JS, Ramsdell JS, Van Dolah FM. Acute phase gene expression in mice exposed to the marine neurotoxin domoic acid. Neuroscience. 2005; 136(4):1121-32. PMID: 16216424.
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      30. Lidie KB, Ryan JC, Barbier M, Van Dolah FM. Gene expression in Florida red tide dinoflagellate Karenia brevis: analysis of an expressed sequence tag library and development of DNA microarray. Mar Biotechnol (NY). 2005 Sep-Oct; 7(5):481-93. PMID: 15976935.
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      31. Kveberg L, Ryan JC, Rolstad B, Inngjerdingen M. Expression of regulator of G protein signalling proteins in natural killer cells, and their modulation by Ly49A and Ly49D. Immunology. 2005 Jul; 115(3):358-65. PMID: 15946253; PMCID: PMC1782169.
      32. Naper C, Dai KZ, Kveberg L, Rolstad B, Niemi EC, Vaage JT, Ryan JC. Two structurally related rat Ly49 receptors with opposing functions (Ly49 stimulatory receptor 5 and Ly49 inhibitory receptor 5) recognize nonclassical MHC class Ib-encoded target ligands. J Immunol. 2005 Mar 1; 174(5):2702-11. PMID: 15728478.
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      33. Saether PC, Westgaard IH, Flornes LM, Hoelsbrekken SE, Ryan JC, Fossum S, Dissen E. Molecular cloning of KLRI1 and KLRI2, a novel pair of lectin-like natural killer-cell receptors with opposing signalling motifs. Immunogenetics. 2005 Feb; 56(11):833-9. PMID: 15650876.
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      34. Nylenna O, Naper C, Vaage JT, Woon PY, Gauguier D, Dissen E, Ryan JC, Fossum S. The genes and gene organization of the Ly49 region of the rat natural killer cell gene complex. Eur J Immunol. 2005 Jan; 35(1):261-72. PMID: 15593300.
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      35. Nylenna O, Flornes LM, Westgaard IH, Woon PY, Naper C, Vaage JT, Gauguier D, Ryan JC, Dissen E, Fossum S. Killer cell lectin-like receptors and the natural killer cell gene complex. Adv Exp Med Biol. 2005; 564:23-4. PMID: 16400803.
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      36. Inngjerdingen M, Rolstad B, Ryan JC. Activating and inhibitory Ly49 receptors modulate NK cell chemotaxis to CXC chemokine ligand (CXCL) 10 and CXCL12. J Immunol. 2003 Sep 15; 171(6):2889-95. PMID: 12960311.
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      37. Hoelsbrekken SE, Nylenna Ø, Saether PC, Slettedal IO, Ryan JC, Fossum S, Dissen E. Cutting edge: molecular cloning of a killer cell Ig-like receptor in the mouse and rat. J Immunol. 2003 Mar 1; 170(5):2259-63. PMID: 12594244.
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      38. Naper C, Hayashi S, Kveberg L, Niemi EC, Lanier LL, Vaage JT, Ryan JC. Ly-49s3 is a promiscuous activating rat NK cell receptor for nonclassical MHC class I-encoded target ligands. J Immunol. 2002 Jul 1; 169(1):22-30. PMID: 12077224.
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      39. Naper C, Hayashi S, Joly E, Butcher GW, Rolstad B, Vaage JT, Ryan JC. Ly49i2 is an inhibitory rat natural killer cell receptor for an MHC class Ia molecule (RT1-A1c). Eur J Immunol. 2002 Jul; 32(7):2031-6. PMID: 12115624.
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      40. Naper C, Hayashi S, Løvik G, Kveberg L, Niemi EC, Rolstad B, Dissen E, Ryan JC, Vaage JT. Characterization of a novel killer cell lectin-like receptor (KLRH1) expressed by alloreactive rat NK cells. J Immunol. 2002 May 15; 168(10):5147-54. PMID: 11994469.
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      41. Ma J, Znoiko S, Othersen KL, Ryan JC, Das J, Isayama T, Kono M, Oprian DD, Corson DW, Cornwall MC, Cameron DA, Harosi FI, Makino CL, Crouch RK. A visual pigment expressed in both rod and cone photoreceptors. Neuron. 2001 Nov 8; 32(3):451-61. PMID: 11709156.
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      42. Routes JM, Ryan JC, Ryan S, Nakamura M. MHC class I molecules on adenovirus E1A-expressing tumor cells inhibit NK cell killing but not NK cell-mediated tumor rejection. Int Immunol. 2001 Oct; 13(10):1301-7. PMID: 11581175.
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      43. Ryan JC, Crouch RK, Ma JX. Cloning and characterization of three salamander retinal G-protein beta subunits. Mol Vis. 2001 Oct 1; 7:222-7. PMID: 11590364.
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      44. Ryan JC, Naper C, Hayashi S, Daws MR. Physiologic functions of activating natural killer (NK) complex-encoded receptors on NK cells. Immunol Rev. 2001 Jun; 181:126-37. PMID: 11513134.
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      45. Rolstad B, Naper C, Løvik G, Vaage JT, Ryan JC, Bäckman-Petersson E, Kirsch RD, Butcher GW. Rat natural killer cell receptor systems and recognition of MHC class I molecules. Immunol Rev. 2001 Jun; 181:149-57. PMID: 11513136.
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      46. Ma JX, Kono M, Xu L, Das J, Ryan JC, Hazard ES, Oprian DD, Crouch RK. Salamander UV cone pigment: sequence, expression, and spectral properties. Vis Neurosci. 2001 May-Jun; 18(3):393-9. PMID: 11497415.
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      47. Daws MR, Lanier LL, Seaman WE, Ryan JC. Cloning and characterization of a novel mouse myeloid DAP12-associated receptor family. Eur J Immunol. 2001 Mar; 31(3):783-91. PMID: 11241283.
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      48. Zheng YM, Liu C, Chen H, Locke D, Ryan JC, Kahn ML. Expression of the platelet receptor GPVI confers signaling via the Fc receptor gamma -chain in response to the snake venom convulxin but not to collagen. J Biol Chem. 2001 Apr 20; 276(16):12999-3006. PMID: 11152687.
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      49. Løvik G, Vaage JT, Dissen E, Szpirer C, Ryan JC, Rolstad B. Characterization and molecular cloning of rat C1qRp, a receptor on NK cells. Eur J Immunol. 2000 Dec; 30(12):3355-62. PMID: 11093152.
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      50. Ryan JC, Znoiko S, Xu L, Crouch RK, Ma JX. Salamander rods and cones contain distinct transducin alpha subunits. Vis Neurosci. 2000 Nov-Dec; 17(6):847-54. PMID: 11193101.
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      51. Nakamura MC, Hayashi S, Niemi EC, Ryan JC, Seaman WE. Activating Ly-49D and inhibitory Ly-49A natural killer cell receptors demonstrate distinct requirements for interaction with H2-D(d). J Exp Med. 2000 Aug 7; 192(3):447-54. PMID: 10934233; PMCID: PMC2193226.
      52. Kumaresan PR, Stepp SE, Verrett PC, Chuang SS, Boles KS, Lai WC, Ryan JC, Bennett M, Kumar V, Mathew PA. Molecular characterization of the rat NK cell receptor 2B4. Mol Immunol. 2000 Aug-Sep; 37(12-13):735-44. PMID: 11275258.
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      53. Ryan JC, Niemi EC, Nakamura MC. Functional analysis of natural killer cell receptors in the RNK-16 rat leukemic cell line. Methods Mol Biol. 2000; 121:283-95. PMID: 10818734.
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      54. Nakamura MC, Naper C, Niemi EC, Spusta SC, Rolstad B, Butcher GW, Seaman WE, Ryan JC. Natural killing of xenogeneic cells mediated by the mouse Ly-49D receptor. J Immunol. 1999 Nov 1; 163(9):4694-700. PMID: 10528166.
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      55. Eriksson M, Leitz G, Fällman E, Axner O, Ryan JC, Nakamura MC, Sentman CL. Inhibitory receptors alter natural killer cell interactions with target cells yet allow simultaneous killing of susceptible targets. J Exp Med. 1999 Oct 4; 190(7):1005-12. PMID: 10510090; PMCID: PMC2195645.
      56. Eriksson M, Ryan JC, Nakamura MC, Sentman CL. Ly49A inhibitory receptors redistribute on natural killer cells during target cell interaction. Immunology. 1999 Jun; 97(2):341-7. PMID: 10447751; PMCID: PMC2326823.
      57. Naper C, Ryan JC, Kirsch R, Butcher GW, Rolstad B, Vaage JT. Genes in two major histocompatibility complex class I regions control selection, phenotype, and function of a rat Ly-49 natural killer cell subset. Eur J Immunol. 1999 Jun; 29(6):2046-53. PMID: 10382768.
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      58. Nakamura MC, Linnemeyer PA, Niemi EC, Mason LH, Ortaldo JR, Ryan JC, Seaman WE. Mouse Ly-49D recognizes H-2Dd and activates natural killer cell cytotoxicity. J Exp Med. 1999 Feb 1; 189(3):493-500. PMID: 9927511; PMCID: PMC2192910.
      59. Johansson MH, Höglund E, Nakamura MC, Ryan JC, Höglund P. Alpha1/alpha2 domains of H-2D(d), but not H-2L(d), induce "missing self" reactivity in vivo--no effect of H-2L(d) on protection against NK cells expressing the inhibitory receptor Ly49G2. Eur J Immunol. 1998 Dec; 28(12):4198-206. PMID: 9862356.
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      60. Wakil AE, Wang ZE, Ryan JC, Fowell DJ, Locksley RM. Interferon gamma derived from CD4(+) T cells is sufficient to mediate T helper cell type 1 development. J Exp Med. 1998 Nov 2; 188(9):1651-6. PMID: 9802977; PMCID: PMC2212510.
      61. Sundbäck J, Nakamura MC, Waldenström M, Niemi EC, Seaman WE, Ryan JC, Kärre K. The alpha2 domain of H-2Dd restricts the allelic specificity of the murine NK cell inhibitory receptor Ly-49A. J Immunol. 1998 Jun 15; 160(12):5971-8. PMID: 9637511.
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      62. Weber JR, Orstavik S, Torgersen KM, Danbolt NC, Berg SF, Ryan JC, Taskén K, Imboden JB, Vaage JT. Molecular cloning of the cDNA encoding pp36, a tyrosine-phosphorylated adaptor protein selectively expressed by T cells and natural killer cells. J Exp Med. 1998 Apr 6; 187(7):1157-61. PMID: 9529333; PMCID: PMC2212210.
      63. Naper C, Ryan JC, Nakamura MC, Lambracht D, Rolstad B, Vaage JT. Identification of an inhibitory MHC receptor on alloreactive rat natural killer cells. J Immunol. 1998 Jan 1; 160(1):219-24. PMID: 9551974.
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      64. Houchins JP, Lanier LL, Niemi EC, Phillips JH, Ryan JC. Natural killer cell cytolytic activity is inhibited by NKG2-A and activated by NKG2-C. J Immunol. 1997 Apr 15; 158(8):3603-9. PMID: 9103421.
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      65. Nakamura MC, Niemi EC, Fisher MJ, Shultz LD, Seaman WE, Ryan JC. Mouse Ly-49A interrupts early signaling events in natural killer cell cytotoxicity and functionally associates with the SHP-1 tyrosine phosphatase. J Exp Med. 1997 Feb 17; 185(4):673-84. PMID: 9034146; PMCID: PMC2196152.
      66. Ryan JC, Seaman WE. Divergent functions of lectin-like receptors on NK cells. Immunol Rev. 1997 Feb; 155:79-89. PMID: 9059884.
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      67. Dissen E, Ryan JC, Seaman WE, Fossum S. An autosomal dominant locus, Nka, mapping to the Ly-49 region of a rat natural killer (NK) gene complex, controls NK cell lysis of allogeneic lymphocytes. J Exp Med. 1996 May 1; 183(5):2197-207. PMID: 8642329; PMCID: PMC2192580.
      68. Ryan JC. Premalignant conditions of the small intestine. Semin Gastrointest Dis. 1996 Apr; 7(2):88-93. PMID: 8705262.
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      69. Ryan JC, Niemi EC, Nakamura MC, Seaman WE. NKR-P1A is a target-specific receptor that activates natural killer cell cytotoxicity. J Exp Med. 1995 May 1; 181(5):1911-5. PMID: 7722466; PMCID: PMC2191987.
      70. Chan AC, van Oers NS, Tran A, Turka L, Law CL, Ryan JC, Clark EA, Weiss A. Differential expression of ZAP-70 and Syk protein tyrosine kinases, and the role of this family of protein tyrosine kinases in TCR signaling. J Immunol. 1994 May 15; 152(10):4758-66. PMID: 8176201.
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      71. Ryan JC, Turck J, Niemi EC, Yokoyama WM, Seaman WE. Molecular cloning of the NK1.1 antigen, a member of the NKR-P1 family of natural killer cell activation molecules. J Immunol. 1992 Sep 1; 149(5):1631-5. PMID: 1506685.
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      72. Yokoyama WM, Ryan JC, Hunter JJ, Smith HR, Stark M, Seaman WE. cDNA cloning of mouse NKR-P1 and genetic linkage with LY-49. Identification of a natural killer cell gene complex on mouse chromosome 6. J Immunol. 1991 Nov 1; 147(9):3229-36. PMID: 1680927.
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      73. Ryan JC, Niemi EC, Goldfien RD, Hiserodt JC, Seaman WE. NKR-P1, an activating molecule on rat natural killer cells, stimulates phosphoinositide turnover and a rise in intracellular calcium. J Immunol. 1991 Nov 1; 147(9):3244-50. PMID: 1919012.
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