Student Publications

Alaniz RC, Thomas SA, Perez-Melgosa M, Mueller K, Farr AG, Palmiter RD and CB Wilson. 1999. Dopamine b-hydroxylase deficiency impairs cellular immunity. Proc. Natl. Acad. Sci. USA, 96(5):2274-8.

Peckham D, Andersen-Nissen E, Finkelman FD, Stunz LL and RF Ashman. 2001. Difference in apoptosis induction between surface IgD and IgM. Int Immunol. (3):285-95.

Smith KD, Andersen-Nissen E, Hayashi F, Strobe K, Bergman MA, Barrett SL, Cookson BT and A Aderem. 2003. Toll-like receptor 5 recognizes a conserved site on flagellin required for protofilament formation and bacterial motility. Nature Immunol (12):1247-53.

Alaniz RC, Sandall S, Thomas EK and CB Wilson. 2004. Increased Dendritic Cell Numbers Impair Protective Immunity to Intracellular Bacteria Despite Augmenting Antigen-Specific CD8+ T Lymphocyte Responses. J Immunol, 172: 3725-3735.

Andersen-Nissen E, Smith KD, Bonneau R, Strong RK, Aderem A. 2007. A conserved surface on Toll-like receptor 5 recognizes bacterial flagelin. J Exp Med. 204(2):393-403.

Schillace RV, Andrews SF, Galligan SG, Burton KA, Starks HJ, Bouwer HG, McKnight GS, Davey MP, Carr DW.  2005.  The role of protein kinase A anchoring via the RII alpha regulatory subunit in the murine immune system.  J Immunol   174(11):6847-53

Meyer-Bahlburg A, Andrews SF, Yu KO, Porcelli SA, Rawlings DJ. 2008. Characterization of a late transitional
B cell population highly sensitive to BAFF-mediated homeostatic proliferation. J Exp Med.  205(1):155-68.

Yu PW, Tabuchi RS, Kato RM, Astrakhan A, Humblet-Baron S, Kipp K, Chae K, Ellmeier W, Witte ON,
Rawlings DJ 2004. Sustained correction of B-cell development and function in a murine model of X-linked agammaglobulinemia (XLA) using retroviral-mediated gene transfer. Blood 104(5):1281-90.

Astrakhan A, Omori M, Nguyen T, Becker-Herman S, Iseki M, Aye T, Hudkins K, Dooley J, Farr A, Alpers CE,
Ziegler SF, Rawlings DJ. 2007. Local increase in thymic stromal lymphopoietin induces systemic alterations in B cell development. Nature Immunol. 8(5):522-31.

Sommer K, Guo B, Pomerantz JL, Bandaranayake AD, Moreno-Garcia ME, Ovechkina YL, Rawlings DJ.  2005.  Phosphorylation of the CARMA1 linker controls NF-kappaB activation.  Immunity 23:561-574.

Moreno-Garcia ME, Sommer KM, Bandaranayake AD, Rawlings DJ.  2006.  Proximal signals controlling B-cell antigen receptor mediated NF-kappaB activation.  Adv Exp Med Biol 584:89-106.

Barton GM and AY Rudensky. 1998. An altered invariant chain protein with an antigenic peptide in place of CLIP forms SDS-stable complexes with class II ab dimers and facilitates highly efficient peptide loading. Intl. Immunol. 10:1159-1165.

Barton GM and AY Rudensky. 1999. Evaluating peptide repertoires within the context of thymocyte development. Seminars in Immunology, 11:417-422.

Barton, GM and AY Rudensky. 1999. Requirement for Diverse, Low-Abundance Peptides in Positive Selection of T Cells. Science 283:67-70.

Barton GM, Beers C, DeRoos P, Eastman SE, Gomez ME, Forbush KA and AY Rudensky. 2000. Positive selection of self-reactive T cells by specific peptide-MHC class II complexes. Proc Nat Acad Sci USA 99(10):6937-42.

Wong, P., Barton GM, Forbush KA and AY Rudensky. 2001. Tuning of T cell reactivity by self-peptide/MHC ligands. J.Exp. Med., 193:1179-1188.

Volna P, Jarjour J, Baxter S, Roffler SR, Monnat RJ Jr, Stoddard BL, Scharenberg AM. 2007. Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases. Nucleic Acids Res. Nucleic Acids Res. 35(8):2748-58.

He Y-W, Beers C, Deftos ML, Ojala EW and KA Forbush. 2000. Down-regulation of the orphan nuclear receptor RORy t is essential for T lymphocyte maturation. J Immunol 164 (11):5668-74.

Suzuki I, Martin S, Beers C, Boursalian TE and PJ Fink. 2000. Fas ligand costimulates the in vivo proliferation of CD8+ T cells. Proc Natl Acad Sci U S A. 97(4):1707-12.

Honey K, Duff M, Beers C, Maric M, Cresswell P and AY Rudensky. 2001. Cathepsin S regulates expression of cathepsin L and turnover of GILT in B lymphocytes. J. Biol. Chem. 276:22573-8.

Honey K, BenlaghaK, Beers C, Forbush K, Teyton L, Kleijmeer MJ, Rudensky AY, Bendelac A. 2002. Thymocyte expression of cathepsin L is essential for NKT cell development. Nat Immunol. 3(11): 1069-74.

Hsieh CS, deRoos P, Honey K, Beers C and AY Rudensky. 2002. A role for cathepsin L and cathepsin S in peptide generation for MHC class II presentation. J. Immunol. 168:2618-2625.

Barton GM, Beers C, deRoos P, Eastman SR, Gomez ME, Forbush KA and AY Rudensky. 2002. Positive selection of self-MHC-reactive T cells by individual peptide-MHC class II complexes. Proc. Natl. Acad. Sci. USA 99:6937-6942.

Eisenman J, Ahdieh M, Beers C, Brasel K, Kennedy MK, Le T, Bonnert TP, Paxton RJ, Park LS.  2002.  Interleukin-15 interactions with interleukin-15 receptor complexes:  characterization and species specificity.  Cytokine  20(3):121-9.

Erickson M, Morkowski S, Lehar S, Gillard G, Beers C, Dooley J, Rubin JS, Rudensky A, Farr AG.  2002.  Regulation of thymic epithelium by keratinocyte growth factor.  Blood  100(9):3269-78.

Beers C, Honey K, Finks, Fink S, Forbush K, Rudensky A. 2003. Differential regulation of cathepsin S and cathepsin L in interferon gamma-treated macrophages. J Exp Med. 197(2):169-79.

Beers C, Burich A, Kleijmeer MJ, Griffith JM, Wong P, Rudensky AY.  2005.  Cathepsin S controls HMC class II-mediated antigen presentation by epithelial cells in vivo.  J Immunol 174(3):1205-12.

Rudensky A, Beers C.  2006.  Lysosomal cysteine proteases and antigen presentation.  Ernst Schering Res Found Workshop  56:81-95.

Blish CA, Dillon SR, Farr AG and PJ Fink. 1999. Anergic CD8+ T cells can persist and function in vivo. J Immunol. 163(1):155-64.

Blish CA, Gallay BJ, Turk GL, Kline KM, Wheat W and PJ Fink. 1999. Chronic modulation of the TCR repertoire in the lymphoid periphery. J Immunol. 162(6):3131-40.

Buelow B, Scharenberg AM.  2008. Characterization of parameters required for effective use of tamoxifen-regulated recombination. PLoS ONE. 3(9):e3264.

Buelow B, Song Y, Scharenberg AM. 2008  The Poly(ADP-ribose) polymerase PARP-1 is required for oxidative stress-induced TRPM2 activation in lymphocytes. J Biol Chem. 283(36):24571-83.

Song Y, Buelow B, Perraud AL, Scharenberg AM.  2008.  Development and validation of a cell-based high-throughput screening assay for TRPM2 channel modulators. J Biomol Screen.  13(1):54-61.

Gantner BN, Simmons RM, Canavera SJ, Akira, S. and DM Underhill. 2003. Collaborative induction of inflammatory responses by dectin-1 and Toll-like receptor 2. J Exp Med. 197(9): 1107-17.

Troxell CL, Sweezy MA, West RR, Reed KD, Carson BD, Pidoux AL, Cande WZ, McIntosh JR.  2001.  pkl1(+)and klp2(+): Two kinesins of the Kar3 subfamily in fission yeast perform different functions in both mitosis and meiosis.  Mol Biol Cell  12(11):3476-88.

Ohlen C, Kalos M, Cheng LE, Shur AC, Hong DJ, Carson BD, Kokot NC, Lerner CG, Sather BD, Huseby ES, and PD Greenberg. 2002. CD8(+) T Cell Tolerance to a Tumor-associated Antigen Is Maintained at the Level of Expansion Rather than Effector Function. J Exp Med. 195(11):1407-18.

Polanczyk MJ, Carson BD, Subramanian S, Afentoulis M, Vandenbark AA, Ziegler SF and H Offner. 2004. Cutting edge: estrogen drives expansion of the CD4+CD25+ regulatory T cell compartment. J Immunol. 173(4):2227-30.

Walker MR, Carson BD, Nepom GT, Ziegler SF, Buckner JH.  2005.  De novo generation of antigen-specific CD4+CD25+ regulatory T cells from human CD4+CD25- cells.  Proc Natl Acad Sci USA 102(11):4103-8.

Weber SE, Harbetson J. Godebu E, Mros GA, Padrick RC, Carson BD, Ziegler SF, Bradley LM.  2006.  Adaptive islet-specific regulatory CD4 T cells control autoimmune diabetes and mediate the disappearance of pathogenic Th1 cells in vivo.  J Immunol  176(8):4730-9.

Carson BD*, Lopes JE*, Soper DM*, Ziegler SF. 2006. Insights into transcriptional regulation by FOXP3. Front Biosci. 11:1607-19. * Authors contributed equally to this work.

Carson BD, Ziegler SF. 2007. Impaired T cell receptor signaling in Foxp3+ CD4 T cells. Ann NY Acad Sci. 1103:167-78.

Cheng LE, Ohlen C, Nelson BH and PD Greenberg. 2002. Enhanced signaling through the IL-2 receptor in CD8+ T cells regulated by antigen recognition results in preferential proliferation and expansion of responding CD8+ T cells rather than promotion of cell death. Proc Natl Acad Sci U S A. 99(5):3001-6.

Blattman JN, Cheng LE, Greenberg PD. 2002.  CD8⁺ T cell responses: it’s all downhill after their prime.  Nat Immunol 3:601–2.

Cheng LE, Greenberg PD. 2002.  Elective delivery of augmented IL–2 signals to responding CD8⁺ T cells increases the size of the acute antiviral response and of the resulting memory T cell pool.  J Immunol 169:4990–7.

Ohlen C, Kalos M, Cheng LE, Shur AC, Hong DJ, Carson BD, Kokot NC, Lerner CG, Sather BD, Huseby ES, and PD Greenberg. 2002. CD8(+) T Cell Tolerance to a Tumor-associated Antigen Is Maintained at the Level of Expansion Rather than Effector Function. J Exp Med. 195(11):1407-18.

Eastman S, Deftos M, DeRoos PC, Hsu DH, Teyton L, Braunstein NS, Hackett CJ and AY Rudensky. 1996. A study of complexes of class II invariant chain peptide: major histocompatibility complex class II molecules using a new complex-specific monoclonal antibody. Eur J Immunol. 26:385-93.

Deftos ML, He Y-W, Ojala EW and MJ Bevan. 1998. Correlating Notch signaling with thymocyte maturation. Immunity 9:777-786.

He YW, Deftos ML, Ojala EW and MJ Bevan. 1998. RORy t, a novel isoform of an orphan receptor, negatively regulates Fas ligand expression and IL-2 production in T cells. Immunity 9:797-806.

Deftos ML and MJ Bevan. 2000. Notch signaling in T cell development. Curr Opin Immunol. 12:166-72.

He Y-W, Beers C, Deftos ML, Ojala EW, Forbush KA and MJ Bevan. 2000. Down regulation of the orphan nuclear receptor ROR? t is essential for T lymphocyte maturation. J. Immunol. 164:5668-5674.

Deftos M.L., Huang E, Ojala EW, Forbush KA and MJ Bevan. 2000. Notch-1 signalling promotes the maturation of CD4 and CD8 thymocytes. Immunity 13:73-84.

Krebs LT, Deftos ML, Bevan MJ, Gridley T 2001. The Nrarp gene encodes an ankyrin-repeat protein that is transcriptionally regulated by the notch signaling pathway. Dev Biol 238(1): 110-19.

Dillon SR, Jameson SC and PJ Fink. 1994. V beta 5+ T cell receptors skew toward OVA+H-2Kb recognition. J. Immunol. 152:1790-1801.

Dillon SR, MacKay VL and PJ Fink. 1995. A functionally compromised intermediate in extrathymic CD8+ T cell deletion. Immunity. 3:321-333.

Dillon SR and PJ Fink. 1995. Thymic selection events mediated by the pre-TCR do not depend upon a limiting ligand. Intl. Immunol. 7:1363-1373.

Han S, Dillon SR, Zheng B, Shimoda M, Schlissel MS and G Kelsoe. 1997. V(D)J recombinase activity in a subset of germinal center B lymphocytes. Science. 278:301-5.

Blish CA, Dillon SR, Farr AG and PJ Fink. 1999. Anergic CD8+ T cells can persist and function in vivo. J Immunol. 163:155-64.

Dillon SR, Mancini M, Rosen A and MS Schlissel. 2000. Annexin V binds to viable B cells and colocalizes with a marker of lipid rafts upon B cell receptor activation. J Immunol. 164:1322-32.

Parrish-Novak J, Dillon SR, Nelson A, Hammond A, Sprecher C, Gross JA, et al. 2000. Interleukin 21 and its receptor are involved in NK cell expansion and regulation of lymphocyte function. Nature 408(6808):57-63

Gross JA, Johnston J, Mudri S, Enselman R, Dillon SR, Madden K, et al. TACI and BCMA are receptors for a TNF homologue implicated in B-cell autoimmune disease. 2000. Nature 404(6781):995-9.

Dillon SR, Constantinescu A and MS Schlissel. 2001. Annexin V binds to positively selected B cells. J Immunol 166(1):58-71.

Ho WY, Blattman JN, Dossett ML., Yee C, Greenberg PD.  2003.  Adoptive immunotherapy:  Engineering T cell responses as biologic weapons for tumor mass destruction.  Cancer Cell3:431-7.

Teague RM, Sather BD, Sacks JA, Huang^, MZ, Dossett ML, Morimoto J, Tan XX, Sutton SE, Cooke MP, Ohlen, C, Greenberg PD.  2006. Interleukin-15 rescues tolerant CD8⁺ T cells for use in adoptive immunotherapy of established tumors.  Nat Med.  12:335-41.

Richman SA, Healan SJ, Webert KS, Donermeyer DL, Dossett ML, Greenberg PD, Allen PM, Kranz DM.  2006.  Devleopment of a novel strategy for engineering high-affinity proteins by yeast display.  Prot Eng Des Sel 19:255-64.

Kuball J, Dossett ML, Wolfl M, Ho WY, Voss RH, Fowler C, Greenberg PD. 2007. Facilitating matched pairing and expression of TCR chains introduced into human T cells. Blood. 109(6):2331-8.

Teague RM, Greenberg PD, Fowler C, Huang MZ, Tan X, Morimoto J, Dossett ML, Huseby ES, Ohlén C.  2008.Peripheral CD8+ T cell tolerance to self-proteins is regulated proximally at the T cell receptor. Immunity. May;28(5):662-74.

Rice J, Dossett ML, Ohlén C, Buchan SL, Kendall TJ, Dunn SN, Stevenson FK, Greenberg PD.  2008. DNA fusion gene vaccination mobilizes effective anti-leukemic cytotoxic T lymphocytes from a tolerized repertoire. Eur J Immunol. 38(8):2118-30.

Richman SA, Aggen DH, Dossett ML, Donermeyer DL, Allen PM, Greenberg PD, Kranz DM.  2008. Structural features of T cell receptor variable regions that enhance domain stability and enable expression as single-chain ValphaVbeta fragments. Mol Immunol. 2008 Oct 27.[Epub ahead of print] PMID: 18962897.

Dossett ML, Teague RM, Schmitt TM, Tan X, Cooper LJ, Pinzon C, Greenberg PD. 2009. Adoptive Immunotherapy of Disseminated Leukemia With TCR-transduced, CD8(+) T Cells Expressing a Known Endogenous TCR.
Mol Ther. 2009 Feb 10. [Epub ahead of print]PMID: 19209146 [PubMed - as supplied by publisher]

Law CL, Aruffo A, Chandran KA, Doty RT and EA Clark. 1995. Ig domains 1 and 2 of murine CD22 constitute the ligand-binding domain and bind multiple sialylated Ligands expressed on B and T cells. J Immunol. 155:3368-76

Doty RT and EA Clark. 1996. Subcellular localization of CD80 receptors is dependent on an intact cytoplasmic tail and is required for CD28-dependent T cell costimulation. J. Immunol. 157:3270-3279.

Doty RT and EA Clark. 1998. Two regions in the CD80 cytoplasmic rail regulate CD80 redistribution and cell costimulation. J Immunol 161:2700-7.

Doty RT, Xia D, Nguyen SP, Hathaway TR and DM Willerford. 1999. Promoter element for transcription of unrearranged T-cell receptor beta-chain gene in pro-T cells. Blood 93:3017-25.

Pinchuk LM, Grouard-Vogel G, Magaletti DM, Doty RT, Andres RG and EA Clark. 1999. Isolation and characterization of macaque dendritic cells from CD34(+) bone marrow progenitors. Cell Immunol. 196:34-40.

Eddy J, Maizels N.  2006.  Gene function correlates with potential for G4 DNA formation in the human genome.  Nucleic Acids Research 34:3887-3896.

Eddy J, Maizels N. 2008. Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes. Nucleic Acids Res. 36(4):1321-33.

Fink PJ, Fang CA and GL Turk. 1994. The induction of peripheral tolerance by the chronic activation and deletion CD4+V beta 5+ cells. J Immunol 152:4270-81.

Greenberg PD, Finch RJ, Gavin MA, Kalos M, Lewinsohn DA, Lonergan M, Lord JD, Nelson BH, Ohlen C, Sing AP, Warren EH, Yee C and SR Riddell. 1998. Genetic modification of T-cell clones for therapy of human viral and malignant diseases. Cander J Sci Am. Suppl 1:S100-5.

Finch RJ, Fields PE and PD Greenberg. 2001. A transcriptional block in the IL-2 promoter at the -150 AP-1 site in effector CD8+ T cells. J Immunol.166(11):6530-6.

Ozinsky A, Underhill DM, Fontenot JD, Hajjar AM, Smith KD, Wilson DB, Schroeder L and AA Aderem. 2000. The repertoire for pattern recognition of pathogens by the innate immune system is defined by cooperation between toll-like receptors. Proc Natl Acad Sci USA. 97 (25):13766-71.

Fontenot JD, Gavin MA and AY Rudensky. 2003. Foxp3 programs the development and function of CD4+CD25+ regulatory T cells. Nat Immunol. Apr;4(4):330-6.

Fontenot JD and AY Rudensky. 2004. Molecular aspects of regulatory T cell development. Semin Immunol. (2):73-80. Review.

Fontenot JD, Rasmussen JP, Williams LM, Dooley JL, Farr AG, Rudensky AY.  2005.  Regulatory T cell lineage specification by the forkhead transcription factor foxp3.  Immunity  22(3):329-41.

Fontenot JD, Rudensky AY.  2005.  A well adapted regulatory contrivance: regulatory T cell development and the forkhead family transcription factor Foxp3.  Nat Immunol  6(4):331-7.

Fontenot JD, Dooley JL, Farr AG, Rudensky AY.  2005.  Developmental regulation of Foxp3 expression during ontogeny.  J Exp Med   3;202(7):901-6.

Fontenot JD, Rasmussen JP, Gavin MA, Rudensky AY.  2005.  A function for interleukin 2 in Foxp3-expressing regulatory T cells.  Nat Immunol   6(11):1142-51.

Hsieh CS, Zheng Y, Liang Y, Fontenot JD, Rudensky AY.  2006.  An intersection between the self-reactive regulatory and nonregulatory T cell receptor repertoires.  Nat Immunol   7(4):401-10.

Kuball J, Dossett ML, Wolfl M, Ho WY, Voss RH, Fowler C, Greenberg PD. 2007. Facilitating matched pairing and expression of TCR chains introduced into human T cells. Blood. 109(6):2331-8.

Teague RM, Greenberg PD, Fowler C, Huang MZ, Tan X, Morimoto J, Dossett ML, Huseby ES, Ohlén C.  2008.  Peripheral CD8+ T cell tolerance to self-proteins is regulated proximally at the T cell receptor. Immunity 28(5):662-74.

Friend SL, Hosier S, Nelson A, Foxworthe D, Williams DE and A Farr. 1994. A thymic stromal cell line supports in vitro development of surface IgM+ B cells and produces a novel growth factor affecting B and T lineage cells. Exp. Hematol. 22:321-328.

Huang EY, Gallegos AM, Richards SM, Lehar SM, Bevan MJ.  2003.  Surface expression of Notch1 on thymocytes: correlation with the double-negative to double-positive transition.  J Immunol 171(5):2296-304.

Gallegos AM, Bevan MJ.  2004.  Driven to autoimmunity:  The NOD mouse.  Cell 117:149-51. 

Gallegos A, Bevan MJ.  2004. Central tolerance to tissue-specific antigens mediated by direct and indirect antigen presentation.  J. Exp. Med. 200:1039-1049. 

Gallegos AM, Bevan MJ.  2006.  Central tolerance:  good but imperfect.  Immunol Rev 209:290-296.

Norment AM, Bogatzki LY, Gantner BN and MJ Bevan. 2000. Murine CCR9, a chemokine receptor for thymus-expressed chemokine that is up-regulated following pre-TCR signaling. J Immunol. 164(2):639-48.

Gantner BN, Simmons RM, Canavera SJ, Akira, S. and DM Underhill. 2003. Collaborative induction of inflammatory responses by dectin-1 and Toll-like receptor 2. J Exp Med. 197(9): 1107-17.

Underhill DM, Gantner BN.  2004.  Integration of Toll-like receptor and phagocytic signaling for tailored immunity.  Microbes Infect 6(15):1368-1373.

Gantner BN, Simmons RM, Underhill DM. 2005. Dectin-1 mediates macrophage recognition of Candida albicans yeast but not filaments. EMBO J. Feb 24.

Gavin MA, Gilbert MJ, Riddell SR, Greenberg PD and MJ Bevan. 1993. Alkali hydrolysis of recombinant proteins allows for the rapid identification of class I MHC-restricted CTL epitopes. J. Immunol. 151:3971-3980.

Hogquist KA, Gavin MA and MJ Bevan. 1993. Positive selection of CD8+ T cells induced by major histocompatibility complex binging peptides in fetal thymic organ culture. J Exp Med. 177:1469-73.

Gavin MA, Dere B, Grandea III AG, Hogquist KA, and MJ Bevan. 1994. MHC class I allele specific for peptide libraries: Identification of peptides that mimic an H-Y T cell epitope. Eur. J. Immunol. 24:2124-2133.

Gavin MA and MJ Bevan. 1995. Increased peptide promiscuity provides a rationale for the lack of N-regions in the neonatal T cell repertoire. Immunity 3:793-800.

Gavin MA and MJ Bevan. 1998. Major histocompatibility complex allele-specific peptide libraries and identification of T-cell memotopes. Methods Mol Biol. 87:235-48.

Ehrmann IE, Ellis PS, Mazeyrat S, Duthie S, Brockdorff N, Mattei MG, Gavin MA, Affara NA, Brown GM, Simpson E, Mitchell MJ, Scott DM. 1998 Characterization of genes encoding translation initiation factor eIF-2gamma in mouse and human: sex chromosome localization, escape from X-inactivation and evolution. Hum Mol Genet 7:1725-37

Greenberg PD, Finch RJ, Gavin MA, Kalos M, Lewinsohn DA, Lonergan M, Lord JD, Nelson BH, Ohlen C, Sing AP, Warren EH, Yee C, and SR Riddell. 1998. Genetic modification of T-cell clones for therapy of human viral and malignant diseases. Cander J Sci Am. May; 4 Suppl 1:S100-5.

Warren EH, Gavin MA, Simpson E, Chandler P, Page DC, Disteche C, Stankey KA, Greenberg PD, Riddell SR. 2000. The human UTY gene encodes a novel HLA-B8-restricted H-Y antigen. J Immunol. 164:2807-14.

Gavin MA, Torgerson TR, Houston E, DeRoos P, Ho WY, Stray-Pedersen A, Ocheltree EL, Greenberg PD, Ochs HD, Rudensky AY. 2006. Single-cell analysis of normal and FOXP3-mutant human T cells: FOXP3 expression without regulatory T cell development. Proc Natl Acad Sci U S A. 103(17):6659-64.

Erickson M, Morkowski S, Lehar S, Gillard G, Beers C, Dooley J, Rubin JS, Rudensky AY and AG Farr. 2002. Regulation of thymic epithelium by keratinocyte growth factor. Blood 100:3269-78.

Nakayama T, Kasprowicz DJ, Yamashita M, Schubert LA, Gillard G, Kimura M, Didierlaurent A, Koseki H and SF Ziegler. 2002. The generation of mature, single-positive thymocytes in vivo is dysregulated by CD69 blockade or overexpression. J Immunol. Jan 1;168(1):87-94.

Gillard GO, Farr AG.  2005.  Contrasting models of promiscuous gene expression by thymic epithelium.  J Exp Med 202(1):15-9.

Gillard GO, Farr AG.  2006.  Features of medullary thymic epithelium implicate postnatal development in maintaining epithelial heterogeneity and tissue-restricted antigen expression.  J Immunol  176(10):5815-24.

Dooley J, Erickson M, Gillard GO, Far AG.  2006.  Cervical thymus in the mouse.  J Immunol  176(11):6484-90.

Gillard GO, Farr AG.  2006.   The thymus: a house dividing.  Blood December 108:3629-3630.

Gillard GO, Dooley J, Erickson M, Peltonen L, Farr AG. 2007. Aire-dependent alterations in medullary thymic epithelium indicate a role for aire in thymic epithelial differentation. J Immunol. Mar 1. 178(5):3007-15.

Dooley J, Erickson M, Larochelle WJ, Gillard GO, Farr, AG. 2007. FGF$2IIIb signaling regulates thymic epithelial differentiation. Dev. Dyn. 236(12):3459-71.

Hovav AH, Panas MW, Rahman S, Sircar P, Gillard G, Cayabyab MJ, Letvin NL. 2007. Duration of antigen expression in vivo following DNA immunization modifies the magnitude, contraction, and secondary responses of CD8+ T lymphocytes. J Immunol. 179(10):6725-33

Morkowski S, Goldrath AW, Eastman S, Ramachandra L, Freed DC, Whiteley P and AY Rudensky. 1995. T cell recognition of major histocompatibility complex class II complexes with invariant chain processing intermediates. J Exp Med. 182:1403-13.

Goldrath AW, Hogquist KA and MJ Bevan. 1997. CD8 lineage commitment in the absence of CD8. Immunity 6:663-642.

Brabb T, Goldrath AW, von Dassow P, Paez A, Liggitt HD and J Goverman. 1997. Triggers of auto-immune disease in a murine TCR-transgenic model for multiple sclerosis. J Immunol. 159:497-507.

Brossart P, Goldrath AW, Butz EA, Marin S and MJ Bevan. 1997. Virus-mediated delivery of antigenic epitopes into dendritic cells as a means to induce CTL. J Immunol. 158:3270-6.

Goldrath AW and MJ Bevan. 1999. Selecting and maintaining a diverse T-cell repertoire. Nature 402:255-62.

Goldrath AW, and MJ Bevan. 1999. Low-affinity ligands for the TCR drive proliferation of mature CD8+ T cells in lymphopenic hosts. Immunity 11(2):183-90.

Bevan MJ, Goldrath AW.  2000. T-cell memory: You must remember this ...  Curr Biol  4;10(9):R338-40.

Wong P, Goldrath AW and AY Rudensky. 2000. Competition for specific intrathymic ligands limits positive selection in a TCR transgenic model of CD4+ T cell development. J Immunol. 164(12):6252-9

Goldrath AW, Bogatzki LY and MJ Bevan. 2000. Naïve T cells transiently acquire a memory-like phenotype during homeostasis driven proliferation. J Exp Med 192:557-564.

Grubin CE, Kovats S, DeRoos P, and AY Rudensky. 1997. Deficient positive selection of CD4 T cells in mice displaying altered repertoires of MHC class II-bound self-peptides. Immunity 7:197-208.

Kovats S, Grubin CE, Eastman S, DeRoos P, Dongre A, Van Kaer L, and AY Rudensky. 1998. Invariant chain-independent function of H-2M in the formation of endogene peptide-major histo-compatibility complex class II complexes in vivo. J Exp Med 187:245-51.

Guo B, Kato RM, Garcia-Lloret M, Wahl MI and DJ Rawlings. 2000. Engagement of the human pre-B cell receptor generates a lipid raft-dependent calcium signaling complex. Immunity, 13:243-253

Su TT, Guo B, (Co-First Authors) Kawakami Y, Sommer K, Chae K, Humphries LA, Kato RM, Kang S, Patrone L, Wall R, Teitell M, Leitges M, Kawakami T and DJ Rawlings. 2002. PKC-beta controls I kappa B kinase lipid raft recruitment and activation in response to BCR signaling. Nat Immunol. Aug;3(8):780-6. Epub Jul 15.

Su TT, Guo B and DJ Rawlings. 2002. Emerging roles for PKC isoforms in immune cell function. Molecular Interventions 2:141.

Su TT, Guo B, Wei B, Braun J and DJ Rawlings. 2004. Signaling in transitional type 2 B cells is critical for peripheral B-cell development. Immunol Rev. Feb;197:161-78.

Hale JS, Boursalian TE, Turk GL, and PJ Fink. 2006. Thymic Output In Aged Mice. Proc Natl Acad Sci U S A. 103(22):8447-52.

Hale JS, Fink PJ. 2009. Back to the thymus: peripheral T cells come home. Innunol Cell Biol. 87(1): 58-64.

Hamilton N, Huber T.  2008.  An introduction to protein contact prediction. Methods Mol Biol. 453:87-104.

Hamerman JA, Page ST, and AM Pullen. 1997. Distinct methylation states of the CD8ß gene in peripheral T cells and intraepithelial lymphocytes. J. Immunol. 159:1240-1246.

Page ST, Bogatzki LY, Hamerman JA, Sweenie CH, Hogarth PJ, Malissen M, Perlmutter RM, and AM Pullen. 1998. Intestinal intracepithelial lymphocytes include precursors committed to the T cell receptor ab lineage. Proc. Natl. Acad. Sci. USA 95:9459-9464.

Morrissette, N. S., E. S. Gold, J. Guo, J. A. Hamerman, A. Ozinsky, V. Bedian, and A. A. Aderem. 1999. Isolation and characterization of monoclonal antibodies directed against novel components of macrophage phagosomes. J Cell Sci 112 ( Pt 24):4705-4713.

Page, S. T., L. Y. Bogatzki, J. A. Hamerman, M. Malissen, R. M. Perlmutter, and A. M. Pullen. 1999. Differential effects of manipulating signaling in early T cell development in intestinal intraepithelial lymphocytes and thymocytes. Int Immunol 11:169-177.

Hamerman JA and AA Aderem. 2001. Function transitions in macrophages during in vivo infection with Mycobacterium bovis bacillus Calmette-Guerin. J. Immunol.167:2227-2233.

Hamerman JA, Hayashi F, Schroeder LA, Gygi SP, Haas AL, Hampson L, Coughlin P, Aebersold R, Aderem A.  2002.   Serpin 2a is induced in activated macrophages and conjugates to a ubiquitin homolog.  J Immunol 1;168(5):2415-23.

Havenar-Daughton C, Kolumam GA, Murali-Krishna K. 2006. Cutting Edge: The direct action of type I IFN on CD4 T cells is critical for sustaining clonal expansion in response to a viral but not a bacterial infection. J Immunol, 176:3315-9.

Way SS, Havenar-Daughton C, Kolumam GA, Orgunn NN, Murali-Krishna, K. 2007. IL-12 and Type-1 IFN synergize for IFN-(gamma) production by CD4 T cells, whereas neither are required for IFN-(gamma) production by CD8 T cells after Listeria monocytogenes infection. J Immunol. 178(7):4498-505.

Hayashi F, Smith KD, Ozinsky A, Hawn TR, Yi EC, Golldlett DR, Eng JK, Akira S, Underhill DM and AA Aderem. 2001. The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature 410 (6832):1099-1103.

Werts C., Tapping RI, Mathison JC, Chuang TH, Kravechenko V, Saint Girons I, Hakke DA, Godowski PJ, Hayashi F, Ozinsky A, Underhill DM, Kirschning CJ, Wagner H, Aderem A, Tobias PS and Ulevitch RJ. 2001. Leptosprial lipopolysaccharide activates cells through a TLR2-dependent mechanism. Nature Immunol. 4:346-352.

Hamerman JA, Hayashi F, Schroeder LA, Gygi SP, Haas AL, Hampson L, Coughlin P, Aebersold R, Aderem A.  2002.   Serpin 2a is induced in activated macrophages and conjugates to a ubiquitin homolog.  J Immunol 1;168(5):2415-23.

Zhou B, Headley MB, Aye T, Tocker J, Comeau MR, Ziegler SF.  2008.  Reversal of thymic stromal lymphopoietin-induced airway inflammation through inhibition of Th2 responses. J Immunol. 181(9):6557-62.

Lee HC, Headley MB, Iseki M, Ikuta K, Ziegler SF.  2008.  Cutting edge: Inhibition of NF-kappaB-mediated TSLP expression by retinoid X receptor. J Immunol. 181(8):5189-93.

Headley MB, Zhou B, Shih WX, Aye T, Comeau MR, Ziegler SF. 2009. TSL P conditions the lung immune environment for the generation of pathogenic innate and antigen-specific adaptive immune responses. J Imkmunol. 182(3):1641-7.

Acosta-Rodriguez EV, Craxton A, Hendricks DW, Merino MC, Montes CL, Clark EA, Gruppi A. 2007. BAFF and LPS cooperate to induce B cells to become susceptible to CD95/Fas-mediated cell death. Eur J Immunol. 37(4):990-1000.

Hunder NN, Wallen H, Cao J, Hendricks DW, Reilly JZ, Rodmyre R, Jungbluth A, Gnjatic S, Thompson JA, Yee C.  2008.  Treatment of metastatic melanoma with autologous CD4+ T cells against NY-ESO-1.  N Engl J Med. 358(25):2698-703.

Hendricks DW and Fink PJ. 2009. Uneven colonization of the lymphoid periphery by T cells that undergo early TCRalpha rearrangements. J Immunol 182(7):4267-4274.

Makaroff LE, Hendricks DW, Niec RE and Fink PJ. 2009. Postthymic maturation influences the CD8 T cell response to antigen. Proc Natl Acad Sci USA 106(12):4799-4804.

Houston ED Jr., Nechanitzky R, Fink PJ. 2008. Cutting edge: Contact with secondary lymphoid organs drives postthymic T cell maturation. J Immunol. 181(8): 5213--7.

Nakagawa TY, Brissette WH, Lira PD, Griffiths RJ, Petrushova N, Stock J, McNeish JD, Eastman SE, Howard ED, Clarke SR, Rosloniec EF, Elliot EA and AY Rudensky. 1999. Impaired invariant chain degradation and antigen presentation and diminished collagen-induced arthritis in cathepsin S null mice. Immunity. 10:207-17.

Hsing LC, Rudensky AY. 2005. The lysosomal cysteine proteases in MHC class II antigen presentation. Immunol Rev., Oct 207:229-41.

Bulynko YA, Hsing LC, Mason RW, Grigoryev SA.  2006. Cathepsin L stabilizes the histone modification landscape on the Y chromosome and pericentromeric heterochromatin.  Mol. Cell. Biol. 26:4172-4184.

Goverman J, Brabb T, Huseby ES and AG Farr. 1997. TCR signaling regulates thymic organization: lessons from TCR-transgenic mice. Immunol Today. 18:204-8.

Huseby ES, Ohlen C, and J Goverman. 1999. Cutting edge: myelin basic protein-specific cytotoxic T cell tolerance is maintained in vivo by a single dominant epitope in H-2k mice. J Immunol Aug 1;163(3):1115-8.

Loftus C, Huseby E, Gopaul P, Beeson C and J Goverman. 1999. Highly cross-reactive T cell responses to myelin basic protein epitopes reveal a nonpredictable form of TCR degeneracy. J Immunol 162:6451-7.

Huseby ES and J Goverman. 2000. Tolerating the nervous system: a delicate balance. J Exp Med. 191:757-60.

Bernhard H, Huseby ES, Hand SL, Lohmann M, Batten WY, Disis ML, Gralow JR, Meyer zum Buschenfelde HK, Ohlen C, Cheever MA.  2000.  Dendritic cells lose abilaity to present protein antigen after stimulating antigen-specific T cell responses, despite upregulation of MHC class II expression.  Immunobiology 201:568-82.

Huseby, ES, Sather B, Huseby PG and J Goverman. 2001. Age dependent T cell tolerance and autoimmunity to myelin basic protein. Immunity 14:471-481.

Huseby ES, Liggitt D, Brabb T, Schnabel B, Ohlen C, Goverman J.  2001.  A pathogenic role for myelin-specific CD8(+) T cells in a model for multiple sclerosis.  J Exp Med 194:669-76.

Ohlen C, Kalos M, Cheng LE, Shur AC, Hong DJ, Carson BD, Kokot NC, Lerner CG, Sather BD, Huseby ES and PD Greenberg. 2002. CD8(+) T cell tolerance to a tumor-associated antigen is maintained at the level of expansion rather than effector function. J Exp Med. Jun 3;195(11):1407-18.

Iritani BM, Forbush KA, Farrar MA, and RM Perlmutter. 1997. Control of B cell development by Ras-mediated activation of Raf. EMBO J. 16:7019-7031.

Iritani BM, Alberola-Ila J, Forbush KA and RM Perlmutter. 1999. Distinct signals mediate maturation and allelic exclusion in lymphocyte progenitors. Immunity. Jun;10(6):713-22.

Volna P, Jarjour J, Baxter S, Roffler SR, Monnat RJ Jr, Stoddard BL, Scharenberg AM. 2007. Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases. Nucleic Acids Res. Nucleic Acids Res. 35(8):2748-58.

Kerner JD, Appleby MW, Mohr RN, Chien S, Rawlings DJ, Maliszewski CR, Witte ON, and RM Perlmutter. 1995. Impaired expansion of mouse B cell progenitors lacking Btk. Immunity 3:301-312.

Dahlman I, Eaves IA, Kosoy R, Morrison VA, Heward J, Gough SC, Allahabadia A, Franklyn JA, Tuomilehto J, Tuomilehot-Wolf E., Cucca F, Guja C, Ionexcu-Tirgoviste C, Stevens H, Carr P, Nutland S, McKinney P, Shiield JP, Wang W, Cordell HJ, Walkerm N, Todd JA and P Concannon. 2002. Parameters for reliable results in genetic association studies in common disease. Nature Genet 30(2):149-150.

Kosoy R, Yokoi N, Seino S and P Concannon. 2004. Polymorphic variation in the CBLB gene in human type 1 diabetes. Genes Immun. May;5(3):232-5.

Kosoy R and P Concannon. 2005. Functional variants in SUMO4, TAB2, and NFkappaB and the risk of type 1 diabetes. Genes Immun. (3):231-5.

den Haan JM, Lehar SM and MJ Bevan. 2000. CD8(+) but not CD8(-) dendritic cells cross-prime cytotoxic T cells in vivo. J Exp Med. 192(12):1685-96.

Lee PP, Fitzpatrick DR, Beard C, Jessup HK, Lehar SM, Makar KW, Perez-Melgosa M, Sweetser, MT, Schlissel MS, Nguyen S, Cherry SR, Tsai JH, Tucker S, Weaver WM, Kelso A, Jaenisch R and CB Wilson. 2001. A critical role for Dnmt1 and DNA methylation in T cell development, function and survival. Immunity 15:763-774.

Erickson M, Morkowski S, Lehar S, Gillard G, Beers C, Dooley J, Rubin JS, Rudensky A, Farr AG.  2002.  Regulation of thymic epithelium by keratinocyte growth factor.  Blood  100(9):3269-78.

Lehar SM, Bevan MJ.  2002.  T cell development in culture.  Immunity  17:689-92.

Huang EY, Gallegos AM, Richards SM, Lehar SM, Bevan MJ.  2003.   Surface expression of Notch1 on thymocytes: correlation with the double-negative to double-positive transition.  J Immunol 171(5):2296-304.

Lehar SM, Bevan MJ. 2004. Immunology: polarizing a T-cell response. Nature. Jul 8;430(6996):150-1.

Lehar SM, Dooley J, Farr AG and MJ Bevan. 2005. Notch ligands Delta 1 and Jagged1 transmit distinct signals to T-cell precursors. Blood 105(4):1440-7.

Lehar SM, Bevan MJ.  2006.  T cells develop normally in the absence of both Deltex1 and Deltex2.  Mol Cell Biol  26(20):7358-71.

Sun JC, Lehar SM, Bevan MJ.  2006.   Augmented IL-7 signaling during viral infection drives greater expansion of effector T cells but does not enhance memory.  J Immunol  177(7):4458-63.

Lenz LL, Dere B and MJ Bevan. 1996. Identification of an H2-M3-restricted Listeria epitope: implications for antigen presentation by M3. Immunity 5-63-72.

Lenz LL and MJ Bevan. 1996. H2-M3-restricted presentation of Listeria monocytogenes antigens. Immunol. Rev. 151:107-121.

Lenz LL and MJ Bevan. 1997. CTL responses to H2-M3-restricted Listeria epitopes. Immunol. Rev. 158:115-121.
Harty JT, Lenz LL and MJ Bevan. Primary and secondary immune responses to Listeria monocytogenes. Curr Opin Immunol 8:526-30.

Princiota MF, Lenz LL, Bevan MJ and UD Staerz. 1998. H2-M3 restricted presentation of a Listeria-derived leader peptide. J Exp Med 187:1711-9.

Lenz LL, Butz EA and MJ Bevan. 2000. Requirements for bone marrow-derived antigen presenting cells in priming cytotoxic T cell responses to intracellular pathogens. J. Exp. Med. 192:1135-1142.

Marshall AJ, Niiro H, Lerner CG, Yun TJ, Thomas S, Disteche CM and EA Clark. 2000. A novel B lymphocyte-associated adaptor protein, bam32, regulates antigen receptor signaling downstream of phosphatidylinositol 3-kinase. J Exp Med. 191:1319-32.

Ohlen C, Kalos M, Cheng LE, Shur AC, Hong DJ, Carson BD, Kokot NC, Lerner CG, Sather BD, Huseby ES, and PD Greenberg. 2002. CD8(+) T Cell Tolerance to a Tumor-associated Antigen Is Maintained at the Level of Expansion Rather than Effector Function. J Exp Med. 195(11):1407-18.

Way SS, Thompson L, Lopes J, Hajjar AM, Kollmann TR, Freitag,NE, and CB Wilson. 2004. Characterization of flagellin expression and its role in Listeria monocytogenes infection and immunity. Cell Microbio. 6:235-242.

Lopes JE, Soper DM, Ziegler SF. 2007. Foxp3 is required throughout the life of a regulatory T cell. Sci STKE. (393):36

Nelson BH, Lord JD and PD Greenberg. 1994. Cytoplasmic domains of the interleukin-2 receptor beta and gamma chains mediate the signal for T-cell proliferation. Nature 369:333-6.

Nelson BH, Lord JD and PD Greenberg. 1996. A membrane-proximal region of the interleukin-2 receptor gamma chain sufficient for Jak kinases activation and induction of proliferation in T cells. Mol Cell Biol. 16:309-17.

Lord JD, McIntosh BC, Greenberg, PD, and BH Nelson. 1998. The IL-2 receptor promotes proliferation bcl-2 and bcl-x induction, but not cell viability through the adaptor molecule Shc. J. Immunol. 161:4627-4633.

Greenberg PD, Finch RJ, Gavin MA, Kalos M, Lewinsohn DA, Lonergan M, Lord JD, Nelson BH, Ohlen C, Sing AP, Warren EH, Yee C and SR Riddell. 1998. Genetic modification of T-cell clones for therapy of human viral and malignant diseases. Cander J Sci Am. May; 4 Suppl 1:S100-5.

Van Parijs L, Refaeli Y, Lord JD, Nelson BH, Abbas AK and D Baltimore. 1999. Uncoupling IL-2 signals that regulate T cell proliferation, survival, and Fas-mediated activation-induced cell death. Immunity 11:281-8.

Hunt AE, Lali FV, Lord JD, Nelson BH, Miyazaki T, Tracey KJ and BM Foxwell. 1999. Role of interleukin (IL)-2 receptor beta-chain subdomains and Shc in p38 mitogen-activated protein (MAP) kinase and p54 MAP kinase (stress-activated protein Kinase/c-Jun N-terminal Kinase) activation. IL-2-driven proliferation is independent of p38 and p54 MAP kinase activation. J Biol Chem. 2;74:7591-7.

Gu H, Maeda H, Moon JJ, Lord JD, Yoakim M, Nelson BH and BG Neel. 2000. A new role for Shc in activation of the PI-3K/Akt pathway. Mol Cell Biol. 20:7109-20.

Lord JD, McIntosh BC, Greenberg PD and BH Nelson. 2000. The IL-2 receptor promotes lymphocyte proliferation and induction of the cmyc, bcl-2, and bcl-x genes through the trans-activation domain of Stat5. J Immunol. 164:2533-41.

Martino A, Holmes JH, Lord JD, Moon JJ and BH Nelson. 2001. Stat5 and SP1 regulate transcription of the cyclin D2 gene in response to Interleukin-2. J. Immunol. 166:1723-1729.

Mathis M, Schoenborn J, Wilson C.  2007.  Stability of memory CD4 and CD8 T cell effector lineage commitment in the presence or absence of innate signals.  Abstract, Immunological Memory Keystone Symposium, Santa Fe, NM, March 3-8, 2007.

Orr MT, Mathis M, Lagunoff M, Sacks J, Wilson CB. 2007. CD8 T Cell Control of HSV Reactivation from Latency is Abrogated by Viral Inhibition of MHC Class I. Cell Host and Microbe, 2(3):172-80.

Orgun NN, Mathis MA, Wilson CB, Way SS. 2008. Deviation from a strong Th1-dominated to a modest Th17-dominated CD4 T cell response in the absence of IL-12p40 and type I IFNs sustains protective CD8 T cells. J Immunol. 180(6):4109-15.

Coles MC, McMahon CW, Takizawa H and DH Raulet. 2000. Memory CD8 T lymphocytes express inhibitory MHC-specific Ly49 receptors. Eur J Immunol. 30:236-44.

McMahon CW, Bogatski LY and AM Pullen. 1997. Mouse mammary tumor virus superantigens require N-linked glycosylation for effective presentation to T cells. Virology 228:161-170.

McMahon CW, Traxler B, Grigg MD and AM Pullen. 1998. Transposon-mediated random insertions and site-directed mutagenesis prevent the trafficking of a mouse mammary tumor virus superantigen. Virology 243:354-65.

Grigg ME, McMahon CW, Morkowski S, Rudensky AY and AM Pullen. 1998. Mtv-1 superantigen trafficks independently of major histocompatibility complex class II directly to the B-cell surface by the exocytic pathway. J Virol 72:2577-88.

Hanke T, Takizawa H, McMahon CW, Busch DH, Pamer EG, Miller JD, Altman JD, Liu Y, Cado D, Lemonnier FA, Bjorkman PJ and DH Raulet. 1999. Direct assessment of MHC class I binding by seven Ly49 inhibitory NK cell receptors. Immunity. 11:67-77.

Hanke T, Takizawa H, McMahon CW, Busch DH, Pamer EG, Miller JD, Altman JD, Liu Y, Cado D, Lemonnier FA, Bjorkman PJ and DH Raulet. 1999. Direct assessment of MHC class I binding by seven Ly49 inhibitory NK cell receptors. Immunity. 11:67-77.

Beima KM, Miazgowicz MM, Lewis MD, Yan PS, Huang TH, Weinmann AS. 2006. T-bet binding to newly identified target gene promoters is cell type-independent but results in variable context-dependent functional effects. J Biol Chem. 281(17):11992-2000.

Lewis MD, Miller SA, Miazgowicz MM, Beima KM, Weinmann AS.  2007.  T-bet's ability to regulate individual target genes requires the conserved T-box domain to recruit histone methyltransferase activity and a separate family member-specific transactivation domain. Mol Cell Biol.  27(24):8510-21.

Sather BD, Treuting P, Perdue N, Miazgowicz M, Fontenot JD, Rudensky AY, Campbell DJ.  2007.  Altering the distribution of Foxp3(+) regulatory T cells results in tissue-specific inflammatory disease. J Exp Med. 204(6):1335-47.

Miller SA, Huang AC, Miazgowicz MM, Brassil MM, Weinmann AS.  2008. Coordinated but physically separable interaction with H3K27-demethylase and H3K4-methyltransferase activities are required for T-box protein-mediated activation of developmental gene expression. Genes Dev. 22(21):2980-93.

Gu H, Maeda H, Moon JJ, Lord JD, Yoakim M, Nelson BH and Neel BG. 2000. New role for Shc in activation of the phosphatidylinositol 3-kinase/Akt pathway. Mol Cell Biol 20:7109-7120.

Yun TJ, Tallquist MD, Aicher A, Rafferty KL, Marshall AJ, Moon JJ, Ewings MK, Mauhaupt M, Herring SW and EA Clark. 2001. Osteoprotegerin, a crucial regulator of bone metabolism, also regulates B cell development and function. Immunity. J Immunol 166:1482-1491.

Martino A, Holmes IV JH, Lord JD, Moon JJ and BH Nelson. 2001. Stat5 and Sp1 regulate transcription of the cyclin D2 gene in response to IL-2. J Immunol 166:1723-1729.

Moon, JJ and BH Nelson. 2001. Phosphatidylinositol 3-kinase potentiates, but does not trigger, T cell proliferation mediated by the IL-2 receptor. J. Immunol. 167:2714-2723.

Nelson BH, Martyak TP, Thompson LJ, Moon JJ, Wang T.  2003.  Uncoupling of promitogenic and antiapoptotic functions of IL-2 by Smad-dependent TGF-beta signaling.  J Immunol  170(11):5563-70.

Moon JJ, Rubio ED, Martino A, Krumm A, Nelson BH.  2004.  A permissive role for phosphatidylinositol 3-kinase in the Stat5-mediated expression of cyclin D2 by the interleukin-2 receptor.  J Biol Chem.  279(7):5520-7.

Farris SD, Rubio ED, Moon JJ, Gombert WM, Nelson BH, Krumm A.  2005.  Transcription-induced chromatin remodeling at the c-myc gene involves the local exchange of histone H2A.Z.  J Biol Chem  280(26):25298-303.

Cooper CJ, MT Orr, CJ McMahan, PJ Fink.  2003.  T cell receptor revision does not solely target recent thymic emigrants.  J. Immunol. 171:226-233.

Orr MT, Edelmann KH, Vieira J, Corey L, Raulet DH, Wilson CB.  2005.  Inhibition of MHC class I is a virulence factor in herpes simplex virus infection of mice. PLoS Pathogens 1:62-71.

Orr MT, Orgun NN, Wilson CB, Way SS. 2007. Cutting Edge: Recombinant Listeria monocytogenes expressing a single immune-dominant peptide confers protective immunity to Herpes Simplex Virus-1 infection. J Immunol, 178:4731-4735.

Orr MT, Mathis M, Lagunoff M, Sacks J, Wilson CB. 2007. CD8 T Cell Control of HSV Reactivation from Latency is Abrogated by Viral Inhibition of MHC Class I. Cell Host and Microbe, Sep 13;2(3):172-80.

Otipoby KL, Andersson KB, Draves KE, Klaus SJ, Farr AG, Kerner JD, Perlmutter RM, Law CL and EA Clark. 1996. CD22 regulates thymus-independent responses and the lifespan of B cells. Nature 384:634-637.

Otipoby KL, Draves KE and Clark EA. 2001. CD22 regulates BCR-mediated signals via two domains that independently recruit Grb2 and SHP-1. J. Biol. Chem. 276:44315-44322.

Page ST, Bogatzki LY, Hamerman JA, Malissen M, Perlmutter RM and AM Pullen. 1999. Differential effects of manipulating signaling in early T cell development in intestinal intraepithelial lymphocytes and thymocytes. Int Immunol (2): 69-77.

Seamons A, Perchellet A, Goverman J. 2003.  Immune tolerance to myelin proteins.  Immunol Res. 28(3):201-21.

Perchellet A, Stromnes I, Pang JM, Goverman J. 2004. CD8+ T cells maintain tolerance to myelin basic protein by 'epitope theft'. Nat Immunol. (6):606-14.

Goverman J, Perchellet A, Huseby E.  2005.  The role of CD8⁺ T cells in Multiple Sclerosis and its animal models. Curr Drug Targets Inflamm Allergy. 4(2):239-45. Review.

Seamons A, Perchellet A, Goverman J. 2006. Endogenous myelin basic protein is presented in the periphery by both dendritic cells and resting B cells with different functional consequences. J Immunol. 177(4):2097-106.

Perchellet A, Brabb T, Goverman JM. 2008. Crosspresentation by nonhematopoietic and direct presentation by hematopoietic cells induce central tolerance to myelin basic protein. Proc Natl Acad Sci U S A. 105(37):14040-5.

Prasad DVR, Richards S, Mai X M, Dong C.  2003.  B7S1, a novel B7 family member that inhibits T cell activation.  Immunity 18:863-873.

Huang EY, Gallegos AM, Richards SM, Lehar SM, Bevan MJ.  2003.  Surface expression of Notch1 on thymocytes: correlation with the double-negative to double-positive transition.  J Immunol 171(5):2296-304.

Richards S, Watanabe C, Santos L, Craxton A, Clark EA. 2008. Regulation of B-cell entry into the cell cycle. Immunol Rev. 224(1):183-200.

Roach JC, Boysen C, Wang K and L Hood. 1995. Pairwise end sequencing: a unified approach to genomic mapping and sequencing. Genomics 26:345-353.

Roach JC, Wang K, Gan L, and L Hood. 1997. The molecular evolution of the vertebrate trypsinogens. J. Mol. Evol. 45:640-652.

Teague RM, Sather BD, Sacks JA, Huang MZ, Dossett M, Morimoto J, Tan X, Sutton S, Cooke M, Ohlen C, Greenberg PD. 2006. Interleukin-15 rescues tolerant CD8+ T cells for use in adoptive immunotherapy of established tumors. Nature Medicine 12:335-341.

Orr MT, Mathis M, Lagunoff M, Sacks J, Wilson CB. 2007. CD8 T Cell Control of HSV Reactivation from Latency is Abrogated by Viral Inhibition of MHC Class I. Cell Host and Microbe, 2(3): 172-80.

Sacks JA, Bevan MJ.  2008.  TRAIL deficiency does not rescue impaired CD8+ T cell memory generated in the absence of CD4+ T cell help. J Immunol. 180(7):4570-6.

Schoenborn JR, Dorschner M, Sekimata M, Santer D, Shnyreva M, Fitzpatrick DR, Stamatoyonnapoulos JA, Wilson CB. 2007. Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing Ifng transcription. Nature Immunology. Jul;8(7):732-42

Kim D, Peck A, Santer D, Patole P, Schwartz SM, Molitor JA, Arnett FC, Elkon KB. 2008. Induction of interferon-alpha by scleroderma sera containing autoantibodies to topoisomerase I: association of higher interferon-alpha activity with lung fibrosis. Arthritis Rheum. 2008 Jul;58(7):2163-73.

Santer DM, Yoshio T, Minota S, Möller T, Elkon KB. 2009.  Potent Induction of IFN-alpha and chemokines by autoantibodies in the cerebrospinal fluid of patients with neuropsychiatric lupus. J Immunol. Jan 15;182(2):1192-201.

Brabb T, von Dassow P, Ordonez N, Schnabel B, Duke (Sather) B and J. Goverman. 2000. In Situ tolerance within the central nervous system as a mechanism for preventing autoimmunity. J. Exp Med. 192:871-880.

Huseby ES, Sather BD, Huseby PG and J. Goverman. 2001. Age-dependant T cell tolerance and autoimmunity to myelin basic protein. Immunity. 14:471-481.

Ohlen C, Kalos M, Cheng LE, Shur AC, Hong DJ, Carson BD, Kokot NC, Lerner CG, Sather BD, Huseby ES, and PD Greenberg. 2002. CD8(+) T Cell Tolerance to a Tumor-associated Antigen Is Maintained at the Level of Expansion Rather than Effector Function. J Exp Med. 195(11):1407-18

Teague RM, Sather BD, Sacks JA, Huang MZ, Dossett M, Morimoto J, Tan X, Sutton S, Cooke M, Ohlen C, Greenberg PD. 2006. Interleukin-15 rescues tolerant CD8+ T cells for use in adoptive immunotherapy of established tumors. Nature Medicine 12:335-341.

Cabbage SE, Huseby ES, Sather BD, Brabb T, Liggitt D, and Joan Goverman. 2007. Regulatory T Cells Maintain Long-Term Tolerance to Myelin Basic Protein by Inducing a Novel, Dynamic State of T Cell Tolerance. J. Immunol. Jan 15. Vol.178, No.2

Humblet-Baron S*, Sather BD*, Anover S, Becker-Herman S, Kasprowicz DJ, Khim S, Nguyen T, Hudkins-Loya K, Alpers CE, Ziegler S, Ochs H, Torgerson T, Campbell DJ, and DJ Rawlings. 2007. Wiskott Aldrich Syndrome Protein is Required for Regulatory T Cell Homeostasis.J Clin Invest, 117:407-18 (*Authors contributed equally to this work.)

BD Sather, Treuting P, Perdue N, Miazgowicz M, Fontenot J, Rudensky A and DJ Campbell.  2007.  Altering the distribution of FoxP3⁺ regulatory T cells results in tissue-specific inflammatory disease.  J Exp Med. 204(6):1335-47.

Wilson CB, Schoenborn J. BACing up the interferon-gamma locus. Immunity. 2006. Nov;25(5):691-3.

Schoenborn JR, Dorschner M, Sekimata M, Santer D, Fitzpatrick DR, Stamatoyannopoulos JA, Wilson CB.  2007. Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing Ifng transcription. Nature Immunol. Jul;8(7):732-42.

Schoenborn JR, Wilson CB.  2007. Regulation of IFN-gamma during innate and adaptive immune responses. Adv Immunol. 96:41-101.

Schubert LA, King G, Cron RQ, Lewis DB, Aruffo A, and D. Hollenbaugh. 1995. The human gp39 promoter. Two distinct nuclear factors of activated T cell protein-binding elements contribute independently to transcriptional activation. J. Biol. Chem. 270(50):29624-7.

Dolganov G, Bort S, Lovett M, Burr J, Schubert L, Short D, McGurn M, Gibson C and DB Lewis. 1996. Coexpression of the interleukin-13 and interleukin-4 genes correlates with their physical linkage in the cytokine gene cluster on human chromosome 5q23-31. Blood 87(8):3316-26.

Cron RQ, Schubert LA, Lewis DB, and CC Hughes. 1997. Consistent transient transfection of DNA into non-transformed human and murine T-lymphocytes. J Immunol Methods. 205(2):145-50.

Kollmann TR, Reikie B, Blimkie D, Way SS, Hajjar AM, Arispe K, Shaulov A, Wilson CB. 2007. Induction of protective immunity to Listeria monocytogenes in neonates. J Immunol. 178(6):3695-701.

Shaulov A, Murali-Krishna K. 2008. CD8 T cell expansion and memory differentiation are facilitated by simultaneous and sustained exposure to antigenic and inflammatory milieu. J Immunol. 180(2):1131-8.

Hashimoto K, Sohn SJ, Levin SD, Tada T, Perlmutter RM and T Nakayama. 1996. Requirement for p561ck tyrosine kinase activation in T cell receptor-mediated thymic selection. J Exp Med. 184:931-43.

Sohn SJ, Forbush KA, Nguyen N, Whitthuhn B, Nosaka T, Ihle JN and RM Perlmutter. 1998. Requirement for Jak3 in mature T cells: its role in regulation of T cell homeostasis. J. Immunol. 160:2130-2138.

Hernandez-Hoyos G, Sohn SJ, Rothenberg EV and J Alberola-Ila. 2000. Lck activity controls CD4/Cd8 T cell lineage commitment. Immunity 12:313-22.

Boursalian TE, Golob J, Soper DM, Cooper CJ, Fink PJ. 2004. Continued maturation of thymic emigrants in the periphery. Nature Immunology (4):418-25.

Kasprowicz DJ, Droin N, Soper DM, Ramsdell F, Green D, Ziegler SF. 2005. Dynamic regulation of Foxp3 expression regulates the balance between CD4+ T cell activation and cell death. Eur J Immunol. 35(12):3424-32.

Carson BD*, Lopes JE*, Soper DM*, Ziegler SF. 2006. Insights into transcriptional regulation by FOXP3. Front Biosci. 11:1607-19. * Authors contributed equally to this work.

Liu W, Putnam AL, Xu-Yu Z, Szot GL, Lee MR, Zhu S, Gottlieb PA, Kapranov P, Gingeras TR, Fazekas de St Groth B, Clayberger C, Soper DM, Ziegler SF, Bluestone JA. 2006. CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells. J Exp Med. 203(7):1701-11.

Soper DM, Kasprowicz DJ, Ziegler SF. 2007. IL-2R links IL-2R signaling with Foxp3 Expression. Eur J Immunol. 37(7):1817-26.

Lopes JE, Soper DM, Ziegler SF. 2007. Foxp3 is required throughout the life of a regulatory T cell. Sci STKE. (393):pe36.

Perchellet A., Stromnes I., and Goverman J. 2004.  CD8+ T Cells Maintain Tolerance to Myelin Basic Protein by Epitope Theft.  Nature Immunology 5:505-14.

Dittmer U, He H, Messer RJ, Schimmer S, Olbrich AR, Ohlen C, Greenberg PD, Stromnes IM, Iwashiro M, Sakaguchi S, Evans LH, Peterson KE, Yang G, Hasenkrug KJ .  2004.  Functional impairment of CD8(+) T cells by regulatory T cells during persistent retroviral infection.  Immunity 20(3):293-303.

Stromnes I, Goverman J. 2006. Active induction of experimental allergic encephalomyelitis. Nature Protocols 1810-1819.

Stromnes IM, Goverman J. 2006. Passive induction of experimental allergic encephalomyelitis. Nature Protocols 1952-1960.

Stromnes IM, Goverman JM. 2008. Osteopontin-induced survival of T cells. Nat Immunol. 8(1):19-20.

Stromnes IM, Cerretti LM, Liggitt D, Harris RA, Goverman JM.  2008.  Differential regulation of central nervous system autoimmunity by T(H)1 and T(H)17 cells.Nat Med. Mar;14(3):337-42.

Sukiennicki TL, Shewey LM and GT Nepom. 1993. Locus- and allele-specific DNA-protein interactions in the HLA-DQB1 X box. Immunol Res 12(4):317-29.

Beaty JS, Sukiennicki TL and GT Nepom. 1999. Allelic variation in transcription modulated MHC class II expression and function. Microbes Infect. 1:919-27.

Urdahl KB, Sun JC and MJ Bevan. 2002. Positive selection of MHC class Ib-restricted CD8+ T cells on hematopoietic cells. Nat Immunol. 3:772-9.

Sun JC and MJ Bevan. 2003. Defective CD8 T cell memory following acute infection without CD4 T cell help. Science. 300:339-42.

Sun JC, Williams MA and MJ Bevan. 2004. CD4+ T cells are required for the maintenance, not programming, of memory CD8+ T cells after acute infection. Nat Immunol. 5:927-33.

Sun JC and MJ Bevan. 2004. Cutting edge: long-lived CD8 memory and protective immunity in the absence of CD40 expression on CD8 T cells. J Immunol. 172:3385-9.

Tyznik AJ, Sun JC and MJ Bevan. 2004. The CD8 population in CD4-deficient mice is heavily contaminated with MHC class II-restricted T cells. J Exp Med. 199:559-65.

Williams MA, Holmes BJ, Sun JC, Bevan MJ.  2006.  Developing and maintaining protective CD8+ memory T cells.  Immunol Rev   211:146-53.

Sun JC, Lehar SM, Bevan MJ.  2006.  Augmented IL-7 signaling during viral infection drives greater expansion of effector T cells but does not enhance memory.  J Immunol  177(7):4458-63.

Sun, M., Richards, S., Prasad, D.V.R., Mai, X.M., Rudensky, A., and Dong, C. 2002. Characterization of Mouse and Human B7-H3 Genes. J. Immunol. 168: 6294

Cooper, C.J., Turk, G.L., Sun, M., Farr, A.G., and Fink, P.J. 2004. TCR Reversion Occurs in Germinal Centers. J. Immunol. 173: 6532

Sun, M., Ames, K.T., Suzuki, I., and Fink, P.J. 2006. The Cytoplasmic Domain of Fas Ligand Costimulates TCR Signals. J. Immunol. 177: 1481.

Suzuki I and PJ Fink. 1998. Maximal proliferation of cytotoxic T lymphocytes requires reverse signaling through Fas ligand. J. Exp. Med. 187:123-128.

Maggio-Price L, Nicholson KL, Kline KM, Birkebak T, Suzuki I, Wilson DL, Schauer D, Fink PJ.  1998.  Diminished reproduction, failure to thrive, and altered immunologic function in a colony of T-cell receptor transgenic mice: possible role of Citrobacter rodentium.  Lab Anim Sci   48(2):145-55.

Suzuki I and PJ Fink. 2000. The dual functions of Fas ligand in the regulation of peripheral CD8+ and CD4+ T cells. Proc Natl Acad Sci USA 97(4):1707-12.

Swan KA, Alberola-Ila, J, Gross JA, Appleby MW, Thomas JF and RM Perlmutter. 1995. Involvement of p21ras distinguishes positive and negative selection in thymocytes. EMBO J. 14:276-285.

Alberola-Ila J, Hogquist KA, Swan KA, Bevan MJ and RM Perlmutter. 1996. Positive and negative selection invoke distinct signaling pathways. J Exp Med 184:9-18.

Swan KA, Severson AF, Carter JC, Martin PR, Schnabel H, Schnabel R and B Bowerman. 1998. cyk-1: a C. elegans FH gene required for a late step in embryonic cytokines. J Cell Sci. 111:2017-27.

Stone B, Schummer M, Paley PJ, Thompson L, Stewart J, Ford M, Crawford M, Urban N, O'Briant K, Nelson BH. 2003. Serologic analysis of ovarian tumor antigens reveals a bias toward antigens encoded on 17q. Int J Cancer. 104(1):73-84.

Nelson BH, Martyak TP, Thompson LJ, Moon JJ, Wang T. 2003. Uncoupling of promitogenic and antiapoptotic functions of IL-2 by Smad-dependent TGF-beta signaling. J Immunol. 170(11):5563-70.

Matthews SA, Dayalu R, Thompson LJ, Scharenberg AM. 2003. Regulation of protein kinase Cnu by the B-cell antigen receptor. J Biol Chem. 278(11):9086-91.

Way SS, Thompson L, Lopes J, Hajjar AM, Kollmann TR, Freitag NE, and CB Wilson. 2004. Characterization of flagellin expression and its role in Listeria monocytogenes infection and immunity. Cell Microbio. 6:235-242.

Kolumam GA, Thomas S, Thompson LJ, Sprent J, Murali-Krishna K. 2005. Type I interferons act directly on CD8 T cells to allow clonal expansion and memory formation in response to viral infection. J Exp Med. 202(5):637-50.

Thompson LJ, Kolumam GA, Thomas S, Murali-Krishna K. J .2006. Innate inflammatory signals induced by various pathogens differentially dictate the IFN-I dependence of CD8 T cells for clonal expansion and memory formation. Immunol. 177(3):1746-54.

Lee PP, Fitzpatrick DR, Beard C, Jessup HK, Lehar S, Makar KW, Perez-Melgosa M, Sweetser, MT, Schlissel MS, Nguyen S, Cherry SR, Tsai JH, Tucker S, Weaver WM, Kelso A, Jaenisch R and CB Wilson. 2001. A critical role for Dnmt1 and DNA methylation in T cell development, function and survival. Immunity 15:763-774.

Tucker SN, Jessup HK, Fujii H and CB Wilson. 2002. Enforced Expression of the Ikaros Isoform IK5 Decreases the Numbers of Extrathymic IEL and NK1.1+ T Cells. Blood 99:513-9.

Kasprowicz DJ, Smallwood PS, Tyznik AJ, Ziegler SF. 2003. Scurfin (FoxP3) controls T-dependent immune responses in vivo through regulation of CD4+ T cell effector function. J Immunol. 171(3):1216-23.

Hsieh CS, Liang Y, Tyznik AJ, Self SG, Liggitt D and AY Rudensky. 2004. Recognition of the peripheral self by naturally arising CD25+ CD4+ T cell receptors. Immunity (2):267-77.

Tyznik AJ, Sun JC and MJ Bevan. 2004. The CD8 population in CD4-deficient mice is heavily contaminated with MHC class II-restricted T cells. J Exp Med. 199:559-65.

Williams MA, Tyznik AJ, Bevan MJ. 2006. Interleukin-2 signals during priming are required for secondary expansion of CD8+ memory T cells. Nature 441(7095):890-3.

Tyznik AJ, Bevan MJ. 2007. The surprising kinetics of the T cell response to live antigenic cells. J Immunol. 179(8):4988-95.

Miao EA, Andersen-Nissen E, Warren SE, Aderem A.  2007.  TLR5 and Ipaf: dual sensors of bacterial flagellin in the innate immune system. Semin Immunopathol. 29(3):275-88. 

Warren SE, Mao DP, Rodriguez AE, Miao EA, Aderem A.  2008.  Multiple Nod-like receptors activate caspase 1 during Listeria monocytogenes infection. J Immunol. 180(11):7558-64.

Wipke BT, Jameson SC, Bevan MJ, and EG Pamer. 1993. Variable binding affinities of listeriolysin O peptides for the H-2Kd class I molecule. Eur J Immunol (8):2005-10.

Buckner FS, Wipke BT and WC Van Voorhis. 1997. Trypanosoma cruzi infection does not impair major histocompatibility complex class I presentation of antigen to cytotoxic T lymphocytes. Eur J Immunol. 27:2541-8.

Wong P and AY Rudensky. 1996. Phenotype and function of CD4+ T cells in mice lacking invariant chain. J. Immunol. 156:2133-2142.

Nakagawa, T., W. Roth, P. Wong, Nelson A, Farr A, Deussing J, Villadangos JA, Ploegh H, Peters HC and AY Rudensky. 1998. Cathepsin L: critical role in Ii degradation and CD4 T cell selection in the thymus. Science, 280: 450-453.

Liljedahl, M., Winqvist O, Surh CD, Wong P, Ngo K, Teyton L, Peterson PA, Brunmark A, AY Rudensky, Fung-Leung W-P and L Karlsson. 1998. Altered antigen presentation in mice lacking H2-0. Immunity, 8: 233-243.

Wong P, Goldrath AW and AY Rudensky. 2000. Competition for specific intrathymic ligands limits positive selection in a TCR transgenic model of CD4+ T cell development. J Immunol. 164(12):6252-9

Wong P, Barton GM, Forbush KA and AY Rudensky. 2001. Dynamic tuning of T cell reactivity by self-peptide-major histocompatibility complex ligands. J Exp Med. May 21;193(10):1179-87.

Beers C, Burich A, Kleijmeer MJ, Griffith JM, Wong P and AY Rudensky. 2005. Cathepsin S controls MHC class II-mediated antigen presentation by epithelial cells in vivo. J Immunol. 2005 Feb 1;174(3):1205-12.

Updated 3/09