James Ryan, MD
Professor
Medicine
School of Medicine

Education & Training

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• Post-Doc Fellow/Scholar Medicine University of California, San Francisco 1991
• Residency University of California, San Francisco

Grants and Projects

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• Bay Area Hepatitis C Cooperative Research Center, NIH, 2010-2016
• HCV resolution correlates with patterned KIR expressions on lymphocytes., NIH, 2010-2016
• Control of Allogenic Nk Cell Lysis by Lectin Receptors, NIH, 1999-2005
• Molecular Activation of Nk Cells through Nkr-p1, NIH, 1993-1998

Publications (85)

Top publication keywords:
Microarray AnalysisBottle-Nosed DolphinMembrane GlycoproteinsReceptors, NK Cell Lectin-LikeLectins, C-TypeCiguatoxinsAntigens, LyCytotoxicity, ImmunologicKiller Cells, NaturalReceptors, ImmunologicEnvironmental ExposureCiguatera PoisoningAnkle FracturesHistocompatibility Antigens Class IHistocompatibility Antigens

• Association of the patterns of use of medications with mortality of COVID-19 infection: a hospital-based observational study.
  BMJ open 2021 Wallace AW, Cirillo PM, Ryan JC, Krigbaum NY, Badathala A, Cohn BA
• Surgical Site Complications in Open Pronation-Abduction Ankle Fracture-Dislocations With Medial Tension Failure Wounds.
  Journal of orthopaedic trauma 2021 Martin CW, Ryan JC, Bullock TS, Cabot JH, Makhani AA, Griffin LP, Zelle BA
• Fate of the Uninsured Ankle Fracture: Significant Delays in Treatment Result in an Increased Risk of Surgical Site Infection.
  Journal of orthopaedic trauma 2021 Zelle BA, Johnson TR, Ryan JC, Martin CW, Cabot JH, Griffin LP, Bullock TS, Ahmad F, Brady CI, Shah K
• Skin closure with surgical staples in ankle fractures: a safe and reliable method.
  International orthopaedics 2020 Prabhakar G, Bullock TS, Martin CW, Ryan JC, Cabot JH, Makhani AA, Griffin LP, Shah K, Zelle BA
• SHIP1 Deficiency in Inflammatory Bowel Disease Is Associated With Severe Crohn's Disease and Peripheral T Cell Reduction.
  Frontiers in immunology 2018 Fernandes S, Srivastava N, Sudan R, Middleton FA, Shergill AK, Ryan JC, Kerr WG

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• Identification of MHC Class Ib Ligands for Stimulatory and Inhibitory Ly49 Receptors and Induction of Potent NK Cell Alloresponses in Rats.
  Journal of immunology (Baltimore, Md. : 1950) 2018 Dai KZ, Ryan JC, Naper C, Vaage JT
• Memory T Cell Proliferation before Hepatitis C Virus Therapy Predicts Antiviral Immune Responses and Treatment Success.
  Journal of immunology (Baltimore, Md. : 1950) 2017 Méndez-Lagares G, Lu D, Chen C, Terrault N, Segal MR, Khalili M, Monto A, Shen H, Manos MM, Lanier LL, Ryan JC, McCune JM, Hartigan-O'Connor DJ
• NKG2D ligand expression in Crohn's disease and NKG2D-dependent stimulation of CD8+ T cell migration.
  Experimental and molecular pathology 2017 Vadstrup K, Galsgaard ED, Jensen H, Lanier LL, Ryan JC, Chen SY, Nolan GP, Vester-Andersen MK, Pedersen JS, Gerwien J, Jensen T, Bendtsen F
• P-305 SHIP1 Deficiency in Adult Inflammatory Bowel Disease Is Associated with Severe Crohn's Disease and Peripheral T Cell Reduction.
  Inflammatory Bowel Diseases 2017 Sandra Fernandes Denney, Neetu Srivastava, Frank Middleton, James Ryan, William Kerr
• IL-33 promotes growth and liver metastasis of colorectal cancer in mice by remodeling the tumor microenvironment and inducing angiogenesis.
  Molecular carcinogenesis 2016 Zhang Y, Davis C, Shah S, Hughes D, Ryan JC, Altomare D, Peña MM
• Improved Survival Among all Interferon-α-Treated Patients in HCV-002, a Veterans Affairs Hepatitis C Cohort of 2211 Patients, Despite Increased Cirrhosis Among Nonresponders.
  Digestive diseases and sciences 2016 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
• P-176 SHIP1 Deficiency in Human IBD.
  Inflammatory Bowel Diseases 2016 William Kerr, Sandra Fernandes, Frank Middleton, John Chisholm, James Ryan
• P-177 Altered SHIP1-Protein Degradation in a Subset of IBD Patients.
  Inflammatory Bowel Diseases 2016 Sandra Fernandes, James Ryan, Frank Middleton, John Chisholm, William Kerr
• Protective association of colonoscopy against proximal and distal colon cancer and patterns in interval cancer.
  Gastrointestinal endoscopy 2015 Shergill AK, Conners EE, McQuaid KR, Epstein S, Ryan JC, Shah JN, Inadomi J, Somsouk M
• Transcriptomic signatures in whole blood of patients who acquire a chronic inflammatory response syndrome (CIRS) following an exposure to the marine toxin ciguatoxin.
  BMC medical genomics 2015 Ryan JC, Wu Q, Shoemaker RC
• Microarray applications to understand the impact of exposure to environmental contaminants in wild dolphins (Tursiops truncatus).
  Marine genomics 2014 Mancia A, Abelli L, Kucklick JR, Rowles TK, Wells RS, Balmer BC, Hohn AA, Baatz JE, Ryan JC
• Structural brain abnormalities in patients with inflammatory illness acquired following exposure to water-damaged buildings: a volumetric MRI study using NeuroQuant®.
  Neurotoxicology and teratology 2014 Shoemaker RC, House D, Ryan JC
• Machine learning approaches to investigate the impact of PCBs on the transcriptome of the common bottlenose dolphin (Tursiops truncatus).
  Marine environmental research 2014 Mancia A, Ryan JC, Van Dolah FM, Kucklick JR, Rowles TK, Wells RS, Rosel PE, Hohn AA, Schwacke LH
• Expanded use of aggressive therapies improves survival in early and intermediate hepatocellular carcinoma.
  HPB : the official journal of the International Hepato Pancreato Biliary Association 2014 Ho EY, Cozen ML, Shen H, Lerrigo R, Trimble E, Ryan JC, Corvera CU, Monto A, HOVAS Group (Hepatocellular Carcinoma Treatment Outcome at VA San Francisco)
• Monocyte activation by interferon α is associated with failure to achieve a sustained virologic response after treatment for hepatitis C virus infection.
  The Journal of infectious diseases 2013 Hartigan-O'Connor DJ, Lin D, Ryan JC, Shvachko VA, Cozen ML, Segal MR, Terrault NA, Lanier LL, Manos MM, McCune JM
• O-018 SHIP1-deficiency in a Subset of IBD Patients.
  Inflammatory Bowel Diseases 2013 Sandra Fernandes, James Ryan, William Kerr
• Transcriptomic responses of juvenile Pacific whiteleg shrimp, Litopenaeus vannamei, to hypoxia and hypercapnic hypoxia.
  Physiological genomics 2013 Rathburn CK, Sharp NJ, Ryan JC, Neely MG, Cook M, Chapman RW, Burnett LE, Burnett KG
• Nonresponse to interferon-α based treatment for chronic hepatitis C infection is associated with increased hazard of cirrhosis.
  PloS one 2013 Cozen ML, Ryan JC, Shen H, Lerrigo R, Yee RM, Sheen E, Wu R, Monto A
• Impaired lymphocyte reactivity measured by immune function testing in untransplanted patients with cirrhosis.
  Clinical and vaccine immunology : CVI 2013 Yee RM, Lehil MS, Rongey C, Shen H, Cozen ML, Monto A, Ryan JC
• Health status, infection and disease in California sea lions (Zalophus californianus) studied using a canine microarray platform and machine-learning approaches.
  Developmental and comparative immunology 2011 Mancia A, Ryan JC, Chapman RW, Wu Q, Warr GW, Gulland FM, Van Dolah FM
• Transcriptome remodeling associated with chronological aging in the dinoflagellate, Karenia brevis.
  Marine genomics 2011 Johnson JG, Morey JS, Neely MG, Ryan JC, Van Dolah FM
• Development of a measure of work motivation for a meta-theory of motivation.
  Psychological reports 2011 Ryan JC
• The rat NK cell receptors Ly49s4 and Ly49i4 recognize nonclassical MHC-I molecules on Listeria monocytogenes-infected macrophages.
  Journal of leukocyte biology 2011 Shegarfi H, Dai KZ, Daws MR, 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.
  European journal of immunology 2010 Shegarfi H, Dai KZ, Inngjerdingen M, Ryan JC, Vaage JT, Rolstad B, Naper C
• Effects of COX inhibitors on neurodegeneration and survival in mice exposed to the marine neurotoxin domoic acid.
  Neuroscience letters 2010 Ryan JC, Cross CA, Van Dolah FM
• Gene expression profiling in brain of mice exposed to the marine neurotoxin ciguatoxin reveals an acute anti-inflammatory, neuroprotective response.
  BMC neuroscience 2010 Ryan JC, Morey JS, Bottein MY, Ramsdell JS, Van Dolah FM
• Defining the neurotoxin derived illness chronic ciguatera using markers of chronic systemic inflammatory disturbances: a case/control study.
  Neurotoxicology and teratology 2010 Shoemaker RC, House D, Ryan JC
• Binding and uptake of H-ferritin are mediated by human transferrin receptor-1.
  Proceedings of the National Academy of Sciences of the United States of America 2010 Li L, Fang CJ, Ryan JC, Niemi EC, Lebrón JA, Björkman PJ, Arase H, Torti FM, Torti SV, Nakamura MC, Seaman WE
• Response.
  Gastrointestinal Endoscopy 2009 Amandeep K. Shergill, Krishna R. Asundi, Alan Barr, Janak N. Shah, James C. Ryan, Kenneth R. McQuaid, David Rempel
• Pinch force and forearm-muscle load during routine colonoscopy: a pilot study.
  Gastrointestinal endoscopy 2009 Shergill AK, Asundi KR, Barr A, Shah JN, Ryan JC, McQuaid KR, Rempel D
• Beyond insulin resistance: Innate immunity in nonalcoholic steatohepatitis.
  Hepatology (Baltimore, Md.) 2008 Maher JJ, Leon P, Ryan JC
• Corrigendum to “A prospective study to examine persistent HCV reinfection in injection drug users who have previously cleared the virus” [Drug Alcohol Depend. 93(1–2) (2008) 148–154].
  Drug and Alcohol Dependence 2008 Sue L. Currie, James C. Ryan, Daniel Tracy, Teresa L. Wright, Sally George, Rosemary McQuaid, Michael Kim, Hui Shen, Alexander Monto
• Endoscopic Evaluation and Management of Colonic Postpolypectomy Hemorrhage.
  Gastrointestinal Endoscopy 2008 Joseph Chen, Amandeep K. Shergill, Kenneth R. Mcquaid, James C. Ryan, Janak N. Shah
• Liver genomic responses to ciguatoxin: evidence for activation of phase I and phase II detoxification pathways following an acute hypothermic response in mice.
  Toxicological sciences : an official journal of the Society of Toxicology 2008 Morey JS, Ryan JC, Bottein Dechraoui MY, Rezvani AH, Levin ED, Gordon CJ, Ramsdell JS, Van Dolah FM
• Transcriptional profiling and inhibition of cholesterol biosynthesis in human T lymphocyte cells by the marine toxin azaspiracid.
  Genomics 2008 Twiner MJ, Ryan JC, Morey JS, Smith KJ, Hammad SM, Van Dolah FM, Hess P, McMahon T, Satake M, Yasumoto T, Doucette GJ
• A prospective study to examine persistent HCV reinfection in injection drug users who have previously cleared the virus.
  Drug and alcohol dependence 2007 Currie SL, Ryan JC, Tracy D, Wright TL, George S, McQuaid R, Kim M, Shen H, Monto A
• Transcriptional profiling of whole blood and serum protein analysis of mice exposed to the neurotoxin Pacific Ciguatoxin-1.
  Neurotoxicology 2007 Ryan JC, Bottein Dechraoui MY, Morey JS, Rezvani A, Levin ED, Gordon CJ, Ramsdell JS, Van Dolah FM
• Evaluation of Distal Upper Extremity Musculoskeletal Load During Routine Colonoscopy.
  Gastrointestinal Endoscopy 2007 Amandeep K. Shergill, Krishna R. Asundi, Alan Barr, Janak N. Shah, James C. Ryan, Kenneth R. Mcquaid, David Rempel
• Prospective Randomized Trial of Standard Versus Magnetic Endoscope Imaging Colonoscopes On Patient Tolerance of Unsedated Colonoscopy.
  Gastrointestinal Endoscopy 2007 Amandeep K. Shergill, Arnel Deleon, James C. Ryan, Kenneth R. Mcquaid, Janak N. Shah
• Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR.
  Biological procedures online 2006 Morey JS, Ryan JC, Van Dolah FM
• Strain-dependent expression of four structurally related rat Ly49 receptors; correlation with NK gene complex haplotype and NK alloreactivity.
  Immunogenetics 2006 Kveberg L, Dai KZ, Dissen E, Ryan JC, Rolstad B, Vaage JT, Naper C
• The novel inhibitory NKR-P1C receptor and Ly49s3 identify two complementary, functionally distinct NK cell subsets in rats.
  Journal of immunology (Baltimore, Md. : 1950) 2006 Kveberg L, Bäck CJ, Dai KZ, Inngjerdingen M, Rolstad B, Ryan JC, Vaage JT, Naper C
• Acute phase gene expression in mice exposed to the marine neurotoxin domoic acid.
  Neuroscience 2005 Ryan JC, Morey JS, Ramsdell JS, Van Dolah FM
• Gene expression in Florida red tide dinoflagellate Karenia brevis: analysis of an expressed sequence tag library and development of DNA microarray.
  Marine biotechnology (New York, N.Y.) 2005 Lidie KB, Ryan JC, Barbier M, Van Dolah FM
• Expression of regulator of G protein signalling proteins in natural killer cells, and their modulation by Ly49A and Ly49D.
  Immunology 2005 Kveberg L, Ryan JC, Rolstad B, Inngjerdingen M
• 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.
  Journal of immunology (Baltimore, Md. : 1950) 2005 Naper C, Dai KZ, Kveberg L, Rolstad B, Niemi EC, Vaage JT, Ryan JC
• Molecular cloning of KLRI1 and KLRI2, a novel pair of lectin-like natural killer-cell receptors with opposing signalling motifs.
  Immunogenetics 2005 Saether PC, Westgaard IH, Flornes LM, Hoelsbrekken SE, Ryan JC, Fossum S, Dissen E
• Killer cell lectin-like receptors and the natural killer cell gene complex.
  Advances in experimental medicine and biology 2005 Nylenna O, Flornes LM, Westgaard IH, Woon PY, Naper C, Vaage JT, Gauguier D, Ryan JC, Dissen E, Fossum S
• The genes and gene organization of the Ly49 region of the rat natural killer cell gene complex.
  European journal of immunology 2005 Nylenna O, Naper C, Vaage JT, Woon PY, Gauguier D, Dissen E, Ryan JC, Fossum S
• Activating and inhibitory Ly49 receptors modulate NK cell chemotaxis to CXC chemokine ligand (CXCL) 10 and CXCL12.
  Journal of immunology (Baltimore, Md. : 1950) 2003 Inngjerdingen M, Rolstad B, Ryan JC
• Cutting edge: molecular cloning of a killer cell Ig-like receptor in the mouse and rat.
  Journal of immunology (Baltimore, Md. : 1950) 2003 Hoelsbrekken SE, Nylenna Ø, Saether PC, Slettedal IO, Ryan JC, Fossum S, Dissen E
• Ly-49s3 is a promiscuous activating rat NK cell receptor for nonclassical MHC class I-encoded target ligands.
  Journal of immunology (Baltimore, Md. : 1950) 2002 Naper C, Hayashi S, Kveberg L, Niemi EC, Lanier LL, Vaage JT, Ryan JC
• Ly49i2 is an inhibitory rat natural killer cell receptor for an MHC class Ia molecule (RT1-A1c).
  European journal of immunology 2002 Naper C, Hayashi S, Joly E, Butcher GW, Rolstad B, Vaage JT, Ryan JC
• Characterization of a novel killer cell lectin-like receptor (KLRH1) expressed by alloreactive rat NK cells.
  Journal of immunology (Baltimore, Md. : 1950) 2002 Naper C, Hayashi S, Løvik G, Kveberg L, Niemi EC, Rolstad B, Dissen E, Ryan JC, Vaage JT
• A visual pigment expressed in both rod and cone photoreceptors.
  Neuron 2001 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
• Cloning and characterization of a novel mouse myeloid DAP12-associated receptor family.
  European journal of immunology 2001 Daws MR, Lanier LL, Seaman WE, Ryan JC
• 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.
  The Journal of biological chemistry 2001 Zheng YM, Liu C, Chen H, Locke D, Ryan JC, Kahn ML
• Characterization and molecular cloning of rat C1qRp, a receptor on NK cells.
  European journal of immunology 2000 Løvik G, Vaage JT, Dissen E, Szpirer C, Ryan JC, Rolstad B
• Activating Ly-49D and inhibitory Ly-49A natural killer cell receptors demonstrate distinct requirements for interaction with H2-D(d).
  The Journal of experimental medicine 2000 Nakamura MC, Hayashi S, Niemi EC, Ryan JC, Seaman WE
• Molecular characterization of the rat NK cell receptor 2B4.
  Molecular immunology 2000 Kumaresan PR, Stepp SE, Verrett PC, Chuang SS, Boles KS, Lai WC, Ryan JC, Bennett M, Kumar V, Mathew PA
• Functional analysis of natural killer cell receptors in the RNK-16 rat leukemic cell line.
  Methods in molecular biology (Clifton, N.J.) 2000 Ryan JC, Niemi EC, Nakamura MC
• Natural killing of xenogeneic cells mediated by the mouse Ly-49D receptor.
  Journal of immunology (Baltimore, Md. : 1950) 1999 Nakamura MC, Naper C, Niemi EC, Spusta SC, Rolstad B, Butcher GW, Seaman WE, Ryan JC
• Inhibitory receptors alter natural killer cell interactions with target cells yet allow simultaneous killing of susceptible targets.
  The Journal of experimental medicine 1999 Eriksson M, Leitz G, Fällman E, Axner O, Ryan JC, Nakamura MC, Sentman CL
• Genes in two major histocompatibility complex class I regions control selection, phenotype, and function of a rat Ly-49 natural killer cell subset.
  European journal of immunology 1999 Naper C, Ryan JC, Kirsch R, Butcher GW, Rolstad B, Vaage JT
• Ly49A inhibitory receptors redistribute on natural killer cells during target cell interaction.
  Immunology 1999 Eriksson M, Ryan JC, Nakamura MC, Sentman CL
• Mouse Ly-49D recognizes H-2Dd and activates natural killer cell cytotoxicity.
  The Journal of experimental medicine 1999 Nakamura MC, Linnemeyer PA, Niemi EC, Mason LH, Ortaldo JR, Ryan JC, Seaman WE
• 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.
  European journal of immunology 1998 Johansson MH, Höglund E, Nakamura MC, Ryan JC, Höglund P
• Interferon gamma derived from CD4(+) T cells is sufficient to mediate T helper cell type 1 development.
  The Journal of experimental medicine 1998 Wakil AE, Wang ZE, Ryan JC, Fowell DJ, Locksley RM
• The alpha2 domain of H-2Dd restricts the allelic specificity of the murine NK cell inhibitory receptor Ly-49A.
  Journal of immunology (Baltimore, Md. : 1950) 1998 Sundbäck J, Nakamura MC, Waldenström M, Niemi EC, Seaman WE, Ryan JC, Kärre K
• Molecular cloning of the cDNA encoding pp36, a tyrosine-phosphorylated adaptor protein selectively expressed by T cells and natural killer cells.
  The Journal of experimental medicine 1998 Weber JR, Orstavik S, Torgersen KM, Danbolt NC, Berg SF, Ryan JC, Taskén K, Imboden JB, Vaage JT
• Identification of an inhibitory MHC receptor on alloreactive rat natural killer cells.
  Journal of immunology (Baltimore, Md. : 1950) 1998 Naper C, Ryan JC, Nakamura MC, Lambracht D, Rolstad B, Vaage JT
• Natural killer cell cytolytic activity is inhibited by NKG2-A and activated by NKG2-C.
  Journal of immunology (Baltimore, Md. : 1950) 1997 Houchins JP, Lanier LL, Niemi EC, Phillips JH, Ryan JC
• Mouse Ly-49A interrupts early signaling events in natural killer cell cytotoxicity and functionally associates with the SHP-1 tyrosine phosphatase.
  The Journal of experimental medicine 1997 Nakamura MC, Niemi EC, Fisher MJ, Shultz LD, Seaman WE, Ryan JC
• Divergent functions of lectin-like receptors on NK cells.
  Immunological reviews 1997 Ryan JC, Seaman WE
• 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.
  The Journal of experimental medicine 1996 Dissen E, Ryan JC, Seaman WE, Fossum S
• NKR-P1A is a target-specific receptor that activates natural killer cell cytotoxicity.
  The Journal of experimental medicine 1995 Ryan JC, Niemi EC, Nakamura MC, Seaman WE
• Differential expression of ZAP-70 and Syk protein tyrosine kinases, and the role of this family of protein tyrosine kinases in TCR signaling.
  Journal of immunology (Baltimore, Md. : 1950) 1994 Chan AC, van Oers NS, Tran A, Turka L, Law CL, Ryan JC, Clark EA, Weiss A
• Molecular cloning of the NK1.1 antigen, a member of the NKR-P1 family of natural killer cell activation molecules.
  Journal of immunology (Baltimore, Md. : 1950) 1992 Ryan JC, Turck J, Niemi EC, Yokoyama WM, Seaman WE
• NKR-P1, an activating molecule on rat natural killer cells, stimulates phosphoinositide turnover and a rise in intracellular calcium.
  Journal of immunology (Baltimore, Md. : 1950) 1991 Ryan JC, Niemi EC, Goldfien RD, Hiserodt JC, 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.
  Journal of immunology (Baltimore, Md. : 1950) 1991 Yokoyama WM, Ryan JC, Hunter JJ, Smith HR, Stark M, Seaman WE