Systems Immunity Program Publications

Innate immunity and the new forward genetics.
Beutler B.
Best Pract Res Clin Haematol. 2016 Dec;29(4):379-387.

Insulin resistance and diabetes caused by genetic or diet-induced KBTBD2 deficiency in mice
Zhang Z, Turer E, Li X, Zhan X, Choi M, Tang M, Press A, Smith SR, Divoux A, Moresco EM, Beutler B.
Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):E6418-E6426.

MiR-155-regulated molecular network orchestrates cell fate in the innate and adaptive immune response to Mycobacterium tuberculosis.
Rothchild AC, Sissons JR, Shafiani S, Plaisier C, Min D, Mai D, Gilchrist M, Peschon J, Larson RP, Bergthaler A, Baliga NS, Urdahl KB, Aderem A.
Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):E6172-E6181.

Inhibiting TLR9 and other UNC93B1-dependent TLRs paradoxically increases accumulation of MYD88L265P plasmablasts in vivo
Wang JQ, Beutler B, Goodnow CC, Horikawa K.
Blood. 2016 Sep 22;128(12):1604-8.

A Novel Mutation in Nucleoporin 35 Causes Murine Degenerative Colonic Smooth Muscle Myopathy
Parish IA, Stamp LA, Lorenzo AM, Fowler SM, Sontani Y, Miosge LA, Howard DR, Goodnow CC, Young HM, Furness JB.
Am J Pathol. 2016 Sep;186(9):2254-61.

In Reply
Angst MS, Fragiadakis GK, Gaudillière B, Aghaeepour N, Nolan GP.
Anesthesiology. 2016 Jun;124(6):1414-5.

Automated mapping of phenotype space with single-cell data
Samusik N, Good Z, Spitzer MH, Davis KL, Nolan GP.
Nat Methods. 2016 Jun;13(6):493-6.

DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations
Andrews TD, Jeelall Y, Talaulikar D, Goodnow CC, Field MA.
PeerJ. 2016 May 24;4:e2074.

Heterogeneity of Human Neutrophil CD177 Expression Results from CD177P1 Pseudogene Conversion
Wu Z, Liang R, Ohnesorg T, Cho V, Lam W, Abhayaratna WP, Gatenby PA, Perera C, Zhang Y, Whittle B, Sinclair A, Goodnow CC, Field M, Andrews TD, Cook MC.
PLoS Genet. 2016 May 26;12(5):e1006067.

Highly multiplexed simultaneous detection of RNAs and proteins in single cells
Frei AP, Bava FA, Zunder ER, Hsieh EW, Chen SY, Nolan GP, Gherardini PF.
Nat Methods. 2016 Mar;13(3):269-75.

NLRP3 activation and mitosis are mutually exclusive events coordinated by NEK7, a new inflammasome component
Shi H, Wang Y, Li X, Zhan X, Tang M, Fina M, Su L, Pratt D, Bu CH, Hildebrand S, Lyon S, Scott L, Quan J, Sun Q, Russell J, Arnett S, Jurek P, Chen D, Kravchenko VV, Mathison JC, Moresco EM, Monson NL, Ulevitch RJ, Beutler B.
Nat Immunol. 2016 Mar;17(3):250-8.

TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS
Wang Y, Su L, Morin MD, Jones BT, Whitby LR, Surakattula MM, Huang H, Shi H, Choi JH, Wang KW, Moresco EM, Berger M, Zhan X, Zhang H, Boger DL, Beutler B.
Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):E884-93.

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes
Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR.
Cytometry A. 2016 Jan;89(1):16-21.

Patient-specific Immune States before Surgery Are Strong Correlates of Surgical Recovery
Fragiadakis GK, Gaudillière B, Ganio EA, Aghaeepour N, Tingle M, Nolan GP, Angst MS.
Anesthesiology. 2015 Dec;123(6):1241-55.

Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies
Field MA, Cho V, Andrews TD, Goodnow CC.
PLoS One. 2015 Nov 23;10(11):e0143199.

Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus
O'Gorman WE, Hsieh EW, Savig ES, Gherardini PF, Hernandez JD, Hansmann L, Balboni IM, Utz PJ, Bendall SC, Fantl WJ, Lewis DB, Nolan GP, Davis MM.
J Allergy Clin Immunol. 2015 Nov;136(5):1326-36.

Deletions in the cytoplasmic domain of iRhom1 and iRhom2 promote shedding of the TNF receptor by the protease ADAM17
Maney SK, McIlwain DR, Polz R, Pandyra AA, Sundaram B, Wolff D, Ohishi K, Maretzky T, Brooke MA, Evers A, Vasudevan AA, Aghaeepour N, Scheller J, Münk C, Häussinger D, Mak TW, Nolan GP, Kelsell DP, Blobel CP, Lang KS, Lang PA.
Sci Signal. 2015 Nov 3;8(401):ra109.

Mutation of the ER retention receptor KDELR1 leads to cell-intrinsic lymphopenia and a failure to control chronic viral infection
Siggs OM, Popkin DL, Krebs P, Li X, Tang M, Zhan X, Zeng M, Lin P, Xia Y, Oldstone MB, Cornall RJ, Beutler B.
Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):E5706-14.

Systems integration of innate and adaptive immunity.
Zak DE, Aderem A.
Vaccine. 2015 Sep 29;33(40):5241-8.

Comparison of predicted and actual consequences of missense mutations
Miosge LA, Field MA, Sontani Y, Cho V, Johnson S, Palkova A, Balakishnan B, Liang R, Zhang Y, Lyon S, Beutler B, Whittle B, Bertram EM, Enders A, Goodnow CC, Andrews TD.
Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):E5189-98.

Canonical Inflammasomes Drive IFN-γ to Prime Caspase-11 in Defense against a Cytosol-Invasive Bacterium.
Aachoui Y, Kajiwara Y, Leaf IA, Mao D, Ting JP, Coers J, Aderem A, Buxbaum JD, Miao EA.
Cell Host Microbe. 2015 Sep 9;18(3):320-32.

Extent of Systemic Spread Determines CD8+ T Cell Immunodominance for Laboratory Strains, Smallpox Vaccines, and Zoonotic Isolates of Vaccinia Virus
Flesch IE, Hollett NA, Wong YC, Quinan BR, Howard D, da Fonseca FG, Tscharke DC.
J Immunol. 2015 Sep 1;195(5):2263-72.

Implementing Mass Cytometry at the Bedside to Study the Immunological Basis of Human Diseases: Distinctive Immune Features in Patients with a History of Term or Preterm Birth
Gaudillière B, Ganio EA, Tingle M, Lancero HL, Fragiadakis GK, Baca QJ, Aghaeepour N, Wong RJ, Quaintance C, El-Sayed YY, Shaw GM, Lewis DB, Stevenson DK, Nolan GP, Angst MS.
Cytometry A. 2015 Sep;87(9):817-29.

Interleukin 27R regulates CD4+ T cell phenotype and impacts protective immunity during Mycobacterium tuberculosis infection.
Torrado E, Fountain JJ, Liao M, Tighe M, Reiley WW, Lai RP, Meintjes G, Pearl JE, Chen X, Zak DE, Thompson EG, Aderem A, Ghilardi N, Solache A, McKinstry KK, Strutt TM, Wilkinson RJ, Swain SL, Cooper AM.
J Exp Med. 2015 Aug 24;212(9):1449-63.

mir-181a-1/b-1 Modulates Tolerance through Opposing Activities in Selection and Peripheral T Cell Function
Schaffert SA, Loh C, Wang S, Arnold CP, Axtell RC, Newell EW, Nolan G, Ansel KM, Davis MM, Steinman L, Chen CZ.
J Immunol. 2015 Aug 15;195(4):1470-9.

Synthetically Modified Viral Capsids as Versatile Carriers for Use in Antibody-Based Cell Targeting
ElSohly AM, Netirojjanakul C, Aanei IL, Jager A, Bendall SC, Farkas ME, Nolan GP, Francis MB.
Bioconjug Chem. 2015 Aug 19;26(8):1590-6.

IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system
Spitzer MH, Gherardini PF, Fragiadakis GK, Bhattacharya N, Yuan RT, Hotson AN, Finck R, Carmi Y, Zunder ER, Fantl WJ, Bendall SC, Engleman EG, Nolan GP.
Science. 2015 Jul 10;349(6244):1259425.

Delayed control of herpes simplex virus infection and impaired CD4+ T-cell migration to the skin in mouse models of DOCK8 deficiency.
Flesch IE, Randall KL, Hollett NA, Di Law H, Miosge LA, Sontani Y, Goodnow CC, Tscharke DC.
Immunol Cell Biol. 2015 Jul;93(6):517-21.

IL-33 signaling contributes to the pathogenesis of myeloproliferative neoplasms
Mager LF, Riether C, Schürch CM, Banz Y, Wasmer MH, Stuber R, Theocharides AP, Li X, Xia Y, Saito H, Nakae S, Baerlocher GM, Manz MG, McCoy KD, Macpherson AJ, Ochsenbein AF, Beutler B, Krebs P.
J Clin Invest. 2015 Jul 1;125(7):2579-91.

Reducing the search space for causal genetic variants with VASP
Field MA, Cho V, Cook MC, Enders A, Vinuesa CG, Whittle B, Andrews TD, Goodnow CC.
Bioinformatics. 2015 Jul 15;31(14):2377-9.

Identification of phenotypically and functionally heterogeneous mouse mucosal-associated invariant T cells using MR1 tetramers
Rahimpour A, Koay HF, Enders A, Clanchy R, Eckle SB, Meehan B, Chen Z, Whittle B, Liu L, Fairlie DP, Goodnow CC, McCluskey J, Rossjohn J, Uldrich AP, Pellicci DG, Godfrey DI.
J Exp Med. 2015 Jun 29;212(7):1095-108.

Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome
Johar AS, Mastronardi C, Rojas-Villarraga A, Patel HR, Chuah A, Peng K, Higgins A, Milburn P, Palmer S, Silva-Lara MF, Velez JI, Andrews D, Field M, Huttley G, Goodnow C, Anaya JM, Arcos-Burgos M.
J Transl Med. 2015 Jun 2;13:173.

An LXR-NCOA5 gene regulatory complex directs inflammatory crosstalk-dependent repression of macrophage cholesterol efflux.
Gillespie MA, Gold ES, Ramsey SA, Podolsky I, Aderem A, Ranish JA.
EMBO J. 2015 May 5;34(9):1244-58.

Methyl-CpG Binding Protein 2 Regulates Microglia and Macrophage Gene Expression in Response to Inflammatory Stimuli.
Cronk JC, Derecki NC, Ji E, Xu Y, Lampano AE, Smirnov I, Baker W, Norris GT, Marin I, Coddington N, Wolf Y, Turner SD, Aderem A, Klibanov AL, Harris TH, Jung S, Litvak V, Kipnis J.
Immunity. 2015 Apr 21;42(4):679-91.

Quantitative Reduction of the TCR Adapter Protein SLP-76 Unbalances Immunity and Immune Regulation.
Siggs OM, Miosge LA, Daley SR, Asquith K, Foster PS, Liston A, Goodnow CC.
J Immunol. 2015 Mar 15;194(6):2587-95.

A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry.
Zunder ER, Lujan E, Goltsev Y, Wernig M, Nolan GP.
Cell Stem Cell. 2015 Mar 5;16(3):323-37.

Real-time resolution of point mutations that cause phenovariance in mice.
Wang T, Zhan X, Bu CH, Lyon S, Pratt D, Hildebrand S, Choi JH, Zhang Z, Zeng M, Wang KW, Turer E, Chen Z, Zhang D, Yue T, Wang Y, Shi H, Wang J, Sun L, SoRelle J, McAlpine W, Hutchins N, Zhan X, Fina M, Gobert R, Quan J, Kreutzer M, Arnett S, Hawkins K, Leach A, Tate C, Daniel C, Reyna C, Prince L, Davis S, Purrington J, Bearden R, Weatherly J, White D, Russell J, Sun Q, Tang M, Li X, Scott L, Moresco EM, McInerney GM, Karlsson Hedestam GB, Xie Y, Beutler B.
Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):E440-9.

T-cell STAT3 is required for the maintenance of humoral immunity to LCMV.
McIlwain DR, Grusdat M, Pozdeev VI, Xu HC, Shinde P, Reardon C, Hao Z, Beyer M, Bergthaler A, Hüssinger D, Nolan GP, Lang KS, Lang PA.
Eur J Immunol. 2015 Feb;45(2):418-27.

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.
Zunder ER, Finck R, Behbehani GK, Amir el-AD, Krishnaswamy S, Gonzalez VD, Lorang CG, Bjornson Z, Spitzer MH, Bodenmiller B, Fantl WJ, Pe’er D, Nolan GP.
Nat Protoc. 2015 Feb;10(2):316-33.

The methyltransferase Setdb2 mediates virus-induced susceptibility to bacterial superinfection.
Schliehe C, Flynn EK, Vilagos B, Richson U, Swaminathan S, Bosnjak B, Bauer L, Kandasamy RK, Griesshammer IM, Kosack L, Schmitz F, Litvak V, Sissons J, Lercher A, Bhattacharya A, Khamina K, Trivett AL, Tessarollo L, Mesteri I, Hladik A, Merkler D, Kubicek S, Knapp S, Epstein MM, Symer DE, Aderem A, Bergthaler A.
Nat Immunol. 2015 Jan;16(1):67-74.

MAVS, cGAS, and endogenous retroviruses in T-independent B cell responses.
Zeng M, Hu Z, Shi X, Li X, Zhan X, Li XD, Wang J, Choi JH, Wang KW, Purrington T, Tang M, Fina M, DeBerardinis RJ, Moresco EM, Pedersen G, McInerney GM, Karlsson Hedestam GB, Chen ZJ, Beutler B.
Science. 2014 Dec 19;346(6216):1486-92.

Epigenome-guided analysis of the transcriptome of plaque macrophages during atherosclerosis regression reveals activation of the Wnt signaling pathway.
Ramsey SA, Vengrenyuk Y, Menon P, Podolsky I, Feig JE, Aderem A, Fisher EA, Gold ES.
PLoS Genet. 2014 Dec 4;10(12):e1004828.

Systems biology. Conditional density-based analysis of T cell signaling in single-cell data.
Krishnaswamy S, Spitzer MH, Mingueneau M, Bendall SC, Litvin O, Stone E, Pe’er D, Nolan GP.
Science. 2014 Nov 28;346(6213):1250689.

Single-cell mass cytometry of TCR signaling: amplification of small initial differences results in low ERK activation in NOD mice.
Mingueneau M, Krishnaswamy S, Spitzer MH, Bendall SC, Stone EL, Hedrick SM, Pe’er D, Mathis D, Nolan GP, Benoist C.
Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16466-71.

Clinical recovery from surgery correlates with single-cell immune signatures.
Gaudillière B, Fragiadakis GK, Bruggner RV, Nicolau M, Finck R, Tingle M, Silva J, Ganio EA, Yeh CG, Maloney WJ, Huddleston JI, Goodman SB, Davis MM, Bendall SC, Fantl WJ, Angst MS, Nolan GP.
Sci Transl Med. 2014 Sep 24;6(255):255ra131.

25-Hydroxycholesterol acts as an amplifier of inflammatory signaling.
Gold ES, Diercks AH, Podolsky I, Podyminogin RL, Askovich PS, Treuting PM, Aderem A.
Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10666-71.

RNA and Imidazoquinolines Are Sensed by Distinct TLR7/8 Ectodomain Sites Resulting in Functionally Disparate Signaling Events.
Colak E, Leslie A, Zausmer K, Khatamzas E, Kubarenko AV, Pichulik T, Klimosch SN, Mayer A, Siggs O, Hector A, Fischer R, Klesser B, Rautanen A, Frank M, Hill AV, Manoury B, Beutler B, Hartl D, Simmons A, Weber AN.
J Immunol. 2014 Jun 15;192(12):5963-73.

Multiscale representation of genomic signals.
Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I.
Nat Methods. 2014 Jun;11(6):689-94.

Mutation of mouse Samd4 causes leanness, myopathy, uncoupled mitochondrial respiration, and dysregulated mTORC1 signaling.
Chen Z, Holland W, Shelton JM, Ali A, Zhan X, Won S, Tomisato W, Liu C, Li X, Moresco EM, Beutler B.
Proc Natl Acad Sci U S A. 2014 May 20;111(20):7367-72.

Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.
Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Simonds EF, Chen TJ, Shenfeld DK, Nolan GP, Pe’er D.
Cell. 2014 Apr 24;157(3):714-25.

A ZAP-70 kinase domain variant prevents thymocyte-positive selection despite signalling CD69 induction.A ZAP-70 kinase domain variant prevents thymocyte-positive selection despite signalling CD69 induction.
Siggs OM, Yates AL, Schlenner S, Liston A, Lesage S, Goodnow CC.
Immunology. 2014 Apr;141(4):587-95.

Multiplexed ion beam imaging of human breast tumors.
Angelo M, Bendall SC, Finck R, Hale MB, Hitzman C, Borowsky AD, Levenson RM, Lowe JB, Liu SD, Zhao S, Natkunam Y, Nolan GP.
Nat Med. 2014 Apr;20(4):436-42.

Zinc-finger protein ZFP318 is essential for expression of IgD, the alternatively spliced Igh product made by mature B lymphocytes.
Enders A, Short A, Miosge LA, Bergmann H, Sontani Y, Bertram EM, Whittle B, Balakishnan B, Yoshida K, Sjollema G, Field MA, Andrews TD, Hagiwara H, Goodnow CC.
Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4513-8.

Consequences of the recurrent MYD88(L265P) somatic mutation for B cell tolerance.
Wang JQ, Jeelall YS, Beutler B, Horikawa K, Goodnow CC.
J Exp Med. 2014 Mar 10;211(3):413-26.

Antigen-dependent integration of opposing proximal TCR-signaling cascades determines the functional fate of T lymphocytes.
Wolchinsky R, Hod-Marco M, Oved K, Shen-Orr SS, Bendall SC, Nolan GP, Reiter Y.
J Immunol. 2014 Mar 1;192(5):2109-19.

Characterization of innate responses to influenza virus infection in a novel lung type I epithelial cell model.
Rosenberger CM, Podyminogin RL, Askovich PS, Navarro G, Kaiser SM, Sanders CJ, McClaren JL, Tam VC, Dash P, Noonan JG, Jones BG, Surman SL, Peschon JJ, Diercks AH, Hurwitz JL, Doherty PC, Thomas PG, Aderem A.
J Gen Virol. 2014 Feb;95(Pt 2):350-62.

A hydrolase of trehalose dimycolate induces nutrient influx and stress sensitivity to balance intracellular growth of Mycobacterium tuberculosis.
Yang Y, Kulka K, Montelaro RC, Reinhart TA, Sissons J, Aderem A, Ojha AK.
Cell Host Microbe. 2014 Feb 12;15(2):153-63.

Ndfip1 mediates peripheral tolerance to self and exogenous antigen by inducing cell cycle exit in responding CD4+ T cells.
Altin JA, Daley SR, Howitt J, Rickards HJ, Batkin AK, Horikawa K, Prasad SJ, Nelms KA, Kumar S, Wu LC, Tan SS, Cook MC, Goodnow CC.
Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2067-74.

The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA.
Cho V, Mei Y, Sanny A, Chan S, Enders A, Bertram EM, Tan A, Goodnow CC, Andrews TD.
Genome Biol. 2014 Jan 29;15(1):R26.

Systems-level analysis of innate immunity.
Zak DE, Tam VC, Aderem A.
Annu Rev Immunol. 2014;32:547-77.

Rasgrp1 mutation increases naive T-cell CD44 expression and drives mTOR-dependent accumulation of Helios+ T cells and autoantibodies.
Daley SR, Coakley KM, Hu DY, Randall KL, Jenne CN, Limnander A, Myers DR, Polakos NK, Enders A, Roots C, Balakishnan B, Miosge LA, Sjollema G, Bertram EM, Field MA, Shao Y, Andrews TD, Whittle B, Barnes SW, Walker JR, Cyster JG, Goodnow CC, Roose JP.
Elife. 2013 Dec 12;2:e01020.

Snapin, positive regulator of stimulation- induced Ca2+ release through RyR, is necessary for HIV-1 replication in T cells.
Kinoshita SM, Kogure A, Taguchi S, Nolan GP.
PLoS One. 2013 Oct 10;8(10):e75297.

Differential host response, rather than early viral replication efficiency, correlates with pathogenicity caused by influenza viruses.
Askovich PS, Sanders CJ, Rosenberger CM, Diercks AH, Dash P, Navarro G, Vogel P, Doherty PC, Thomas PG, Aderem A.
PLoS One. 2013 Sep 20;8(9):e74863.

DOCK8 is critical for the survival and function of NKT cells.
Crawford G, Enders A, Gileadi U, Stankovic S, Zhang Q, Lambe T, Crockford TL, Lockstone HE, Freeman A, Arkwright PD, Smart JM, Ma CS, Tangye SG, Goodnow CC, Cerundolo V, Godfrey DI, Su HC, Randall KL, Cornall RJ.
Blood. 2013 Sep 19;122(12):2052-61.

Single-cell mass cytometry for analysis of immune system functional states.
Bjornson ZB, Nolan GP, Fantl WJ.
Curr Opin Immunol. 2013 Aug;25(4):484-94.

Lipidomic profiling of influenza infection identifies mediators that induce and resolve inflammation.
Tam VC, Quehenberger O, Oshansky CM, Suen R, Armando AM, Treuting PM, Thomas PG, Dennis EA, Aderem A.
Cell. 2013 Jul 3;154(1):213-27. doi: 10.1016/j.cell.2013.05.052.

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia.
Amir el-AD, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe’er D.
Nat Biotechnol. 2013 Jun;31(6):545-52.

Heterozygous mis-sense mutations in Prkcb as a critical determinant of anti-polysaccharide antibody formation.
Teh CE, Horikawa K, Arnold CN, Beutler B, Kucharska EM, Vinuesa CG, Bertram EM, Goodnow CC, Enders A.
Genes Immun. 2013 Jun;14(4):223-33.

Detection of pyroptosis by measuring released lactate dehydrogenase activity.
Rayamajhi M, Zhang Y, Miao EA.
Methods Mol Biol. 2013 Jun;1040:85-90.

Going forward with genetics: recent technological advances and forward genetics in mice.
Moresco EM, Li X, Beutler B.
Am J Pathol. 2013 May;182(5):1462-73.

Understanding the immunological impact of the human mutation explosion.
Andrews TD, Sjollema G, Goodnow CC.
Trends Immunol. 2013 Mar;34(3):99-106.

Caspase-11 protects against bacteria that escape the vacuole.
Aachoui Y, Leaf IA, Hagar JA, Fontana MF, Campos CG, Zak DE, Tan MH, Cotter PA, Vance RE, Aderem A, Miao EA.
Science. 2013 Feb 22;339(6122):975-8.

Essential requirement for IRF8 and SLC15A4 implicates plasmacytoid dendritic cells in the pathogenesis of lupus.
Baccala R, Gonzalez-Quintial R, Blasius AL, Rimann I, Ozato K, Kono DH, Beutler B, Theofilopoulos AN.
Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2940-5.

Involvement of Toso in activation of monocytes, macrophages, and granulocytes.
Lang KS, Lang PA, Meryk A, Pandyra AA, Boucher LM, Pozdeev VI, Tusche MW, Göthert JR, Haight J, Wakeham A, You-Ten AJ, McIlwain DR, Merches K, Khairnar V, Recher M, Nolan GP, Hitoshi Y, Funkner P, Navarini AA, Verschoor A, Shaabani N, Honke N, Penn LZ, Ohashi PS, Hüssinger D, Lee KH, Mak TW.
Proc Natl Acad Sci U S A. 2013 Feb 12;110(7):2593-8.

Helios marks strongly autoreactive CD4+ T cells in two major waves of thymic deletion distinguished by induction of PD-1 or NF-κB.
Daley SR, Hu DY, Goodnow CC.
J Exp Med. 2013 Feb 11;210(2):269-85.

B cell survival, surface BCR and BAFFR expression, CD74 metabolism, and CD8- dendritic cells require the intramembrane endopeptidase SPPL2A.
Bergmann H, Yabas M, Short A, Miosge L, Barthel N, Teh CE, Roots CM, Bull KR, Jeelall Y, Horikawa K, Whittle B, Balakishnan B, Sjollema G, Bertram EM, Mackay F, Rimmer AJ, Cornall RJ, Field MA, Andrews TD, Goodnow CC, Enders A.
J Exp Med. 2013 Jan 14;210(1):31-40.

miR-451 regulates dendritic cell cytokine responses to influenza infection.
Rosenberger CM, Podyminogin RL, Navarro G, Zhao GW, Askovich PS, Weiss MJ, Aderem A.
J Immunol. 2012 Dec 15;189(12):5965-75. doi: 10.4049/jimmunol.1201437.

Creating diseases to understand what prevents them: genetic analysis of inflammation in the gastrointestinal tract.
Brandl K, Beutler B.
Curr Opin Immunol. 2012 Dec;24(6):678-85.

ZBTB7B (Th-POK) regulates the development of IL-17-producing CD1d-restricted mouse NKT cells.
Enders A, Stankovic S, Teh C, Uldrich AP, Yabas M, Juelich T, Altin JA, Frankenreiter S, Bergmann H, Roots CM, Kyparissoudis K, Goodnow CC, Godfrey DI.
J Immunol. 2012 Dec 1;189(11):5240-9.

ENU-induced phenovariance in mice: inferences from 587 mutations.
Arnold CN, Barnes MJ, Berger M, Blasius AL, Brandl K, Croker B, Crozat K, Du X, Eidenschenk C, Georgel P, Hoebe K, Huang H, Jiang Z, Krebs P, La Vine D, Li X, Lyon S, Moresco EM, Murray AR, Popkin DL, Rutschmann S, Siggs OM, Smart NG, Sun L, Tabeta K, Webster V, Tomisato W, Won S, Xia Y, Xiao N, Beutler B.
BMC Res Notes. 2012 Oct 24;5:577.
LabArchives Notebook

A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses.
Litvak V, Ratushny AV, Lampano AE, Schmitz F, Huang AC, Raman A, Rust AG, Bergthaler A, Aitchison JD, Aderem A.
Nature. 2012 Oct 18;490(7420):421-5.

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators.
Bodenmiller B, Zunder ER, Finck R, Chen TJ, Savig ES, Bruggner RV, Simonds EF, Bendall SC, Sachs K, Krutzik PO, Nolan GP.
Nat Biotechnol. 2012 Sep;30(9):858-67.

A deep profiler’s guide to cytometry.
Bendall SC, Nolan GP, Roederer M, Chattopadhyay PK.
Trends Immunol. 2012 Jul;33(7):323-32.

From single cells to deep phenotypes in cancer.
Bendall SC, Nolan GP.
Nat Biotechnol. 2012 Jul 10;30(7):639-47.

A platinum-based covalent viability reagent for single-cell mass cytometry.
Fienberg HG, Simonds EF, Fantl WJ, Nolan GP, Bodenmiller B.
Cytometry A. 2012 Jun;81(6):467-75.

Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models.
Andrews TD, Whittle B, Field MA, Balakishnan B, Zhang Y, Shao Y, Cho V, Kirk M, Singh M, Xia Y, Hager J, Winslade S, Sjollema G, Beutler B, Enders A, Goodnow CC.
Open Biol. 2012 May;2(5):120061.