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IFNγ-induced memory in human macrophages is sustained by the durability of cytokine signaling itself. J Exp Med. 2026 Apr 06; 223(4). Gorin A, Niu S, Harriott N, Koduvayur V, Cheng QJ, Hoffmann A. PMID: 41706052; PMCID: PMC12915527.
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Numeracy 2.0-From analyzing data to evaluating biological insight. Cell Syst. 2026 Feb 18; 17(2):101538. Hoffmann A. PMID: 41713396.
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Unleashing the power of non-toxic Zn-guanidine catalysts for sustainable lactide polymerization through smart modeling. Faraday Discuss. 2026 Jan 08; 262(0):248-274. Ke J, Conen N, Latz F, Neumann JN, Fuchs M, Hoffmann A, Jupke A, Herres-Pawlis S. PMID: 40985253.
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Open- and Closed-Loop Recycling of Polyesters and Post-Consumer Waste Under Industrially Relevant Conditions Using Bisguanidine Organocatalysts. ChemSusChem. 2026 Jan; 19(1):e202502062. Burkart L, Hahn A, Blum D, Kara Y, Hoffmann A, Herres-Pawlis S. PMID: 41527328; PMCID: PMC12796559.
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Clinical and molecular characterization of AXL in colorectal cancer, CALGB (Alliance)/SWOG 80405 and real-world data. J Immunother Cancer. 2025 Dec 21; 13(12). Ashouri K, Millstein J, Yang Y, Xiu J, Soni S, Mittal P, Algaze S, Torres-Gonzalez L, Jayachandran P, Zhang W, Mumenthaler S, Shields AF, Goldberg R, Lou E, Weinberg BA, Graeber TG, Marshall JL, Venook AP, Hoffmann A, Finley SD, Meyer AS, Battaglin F, Lenz HJ. PMID: 41423272; PMCID: PMC12719898.
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A data-driven model of macrophage polarization states reveals an IFN macrophage signature in active Crohn's disease. Front Immunol. 2025; 16:1707719. Lowe SC, Leitman M, Yan N, Hoffmann A. PMID: 41425579; PMCID: PMC12711780.
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All-Round Talent: Unique Zinc Guanidine Catalyst Performs Efficiently in Synthesis and Chemical Recycling of (Bio)Polyesters. Adv Sci (Weinh). 2026 Feb; 13(8):e11260. Becker T, Takeuchi K, Süßmuth C, Boekhoff F, Schäfer MA, Kato S, Hoffmann A, Hayashi T, Herres-Pawlis S. PMID: 41133800; PMCID: PMC12884724.
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Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations. PLoS Comput Biol. 2025 Sep; 21(9):e1013462. Zhang J, Li X, Guo X, You Z, Böttcher L, Mogilner A, Hoffmann A, Chou T, Xia M. PMID: 40961166; PMCID: PMC12513633.
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Tackling microbial iron homeostasis: novel antimicrobial strategies. Trends Pharmacol Sci. 2025 Oct; 46(10):1004-1017. Hoffmann A, Grubwieser P, Bumann D, Haschka D, Weiss G. PMID: 40914687.
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NF-κB: master regulator of cellular responses in health and disease. Immun Inflamm. 2025; 1(1):2. Hoffmann A, Cheng G, Baltimore D. PMID: 41669117; PMCID: PMC12883533.
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SARS-CoV-2 nucleocapsid induces hyperinflammation and vascular leakage through the Toll-like receptor signaling axis in macrophages. bioRxiv. 2025 Aug 28. Yao Z, Alvarez PA, Chavez C, Delgado Y, Kaushal P, Austin D, Li Q, Yu Y, Zaiss AK, Arumugaswami V, Ding Q, Hsu JJ, Damoiseaux R, Bouhaddou M, Hoffmann A, Li MMH. PMID: 40909558; PMCID: PMC12407974.
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Distinct roles for NF-κB in hematopoietic stem cells and the bone marrow milieu in promoting hematopoietic aging. Cell Rep. 2025 Sep 23; 44(9):116193. Chia JJ, Singh A, Lin YS, Popko N, Mastro D, Liu Y, Tran T, King JK, Rao DS, Hoffmann A. PMID: 40875292; PMCID: PMC12515102.
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A computational workflow for assessing drug effects on temporal signaling dynamics reveals robustness in stimulus-specific NFκB signaling. PLoS Comput Biol. 2025 Aug; 21(8):e1013344. Bozich ER, Guo X, Wilson JL, Hoffmann A. PMID: 40839679; PMCID: PMC12370059.
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Gene regulatory logic of the interferon-β enhancer is characterized by two selectively deployed modes of transcription factor synergy. Proc Natl Acad Sci U S A. 2025 Aug 19; 122(33):e2502800122. Schiffman A, Cheng Z, Ourthiague D, Hoffmann A. PMID: 40794834; PMCID: PMC12377728.
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Modeling heterogeneous signaling dynamics of macrophages reveals principles of information transmission in stimulus responses. Nat Commun. 2025 Jul 01; 16(1):5986. Guo X, Adelaja A, Singh A, Wollman R, Hoffmann A. PMID: 40593748; PMCID: PMC12218168.
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IFNγ-induced memory in human macrophages is not sustained by epigenetic changes but the durability of the cytokine itself. bioRxiv. 2025 Jul 01. Gorin A, Harriott N, Koduvayur V, Cheng QJ, Hoffmann A. PMID: 40599159; PMCID: PMC12212440.
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Phased epigenetic fragility and stability accelerate the genetic evolution of B-cells. bioRxiv. 2025 Jun 27. Xiang MY, Narayanan HV, Kesarwani V, Wang T, Hoffmann A. PMID: 40667038; PMCID: PMC12262553.
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Synergy and antagonism in the integration of BCR and CD40 signals that control B-cell population expansion. Mol Syst Biol. 2025 Aug; 21(8):1119-1146. Huang H, Vaidehi Narayanan H, Xiang MY, Kesarwani V, Hoffmann A. PMID: 40473841; PMCID: PMC12322056.
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Tensor-Based Integration of Time-Series Measurements Reveals Relationships Between Underlying Disease, Early Injury, and CD4+ Polarization in Liver Transplantation. bioRxiv. 2025 May 30. Chin JL, Tan ZC, Sosa RA, Zheng Y, Gjertson DW, Hoffmann A, Kaldas FM, Zhai Y, Kupiec-Weglinski JW, Reed EF, Meyer AS. PMID: 40501716; PMCID: PMC12154882.
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Protocol for the imputation of stimulus-induced single-cell gene expression trajectories from time-series scRNA-seq data. STAR Protoc. 2025 Jun 20; 6(2):103811. Sheu KM, Hoffmann A. PMID: 40343799; PMCID: PMC12135371.
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A computational workflow for assessing drug effects on temporal signaling dynamics reveals robustness in stimulus-specific NFκB signaling. bioRxiv. 2025 Apr 02. Bozich ER, Guo X, Wilson JL, Hoffmann A. PMID: 40236106; PMCID: PMC11996442.
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Macrophages maintain signaling fidelity in response to ligand mixtures. bioRxiv. 2025 Apr 01. Guo X, Sen S, Gonzalez J, Hoffmann A. PMID: 40236137; PMCID: PMC11996307.
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Population dynamics modeling reveals that myeloid bias involves both HSC differentiation and progenitor proliferation biases. Blood. 2025 Mar 20; 145(12):1293-1308. Singh A, Chia JJ, Rao DS, Hoffmann A. PMID: 39791596; PMCID: PMC11952015.
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The golden goal of entatic state model design: lowering the internal reorganization energy leads to exponential increase in electron transfer rate. Chem Commun (Camb). 2025 Feb 25; 61(18):3684-3687. Seitz T, Karabulut A, Suzuki RM, Hoffmann A, Heck J, Herres-Pawlis S. PMID: 39918444.
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Temporal dose inversion properties of adaptive biomolecular circuits. bioRxiv. 2025 Feb 11. Nakamura E, Blanchini F, Giordano G, Hoffmann A, Franco E. PMID: 39990486; PMCID: PMC11844413.
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Macrophage memory emerges from coordinated transcription factor and chromatin dynamics. Cell Syst. 2025 Feb 19; 16(2):101171. Wang AG, Son M, Gorin A, Kenna E, Padhi A, Keisham B, Schauer A, Hoffmann A, Tay S. PMID: 39938520; PMCID: PMC12147866.
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NF-κB RelB suppresses the inflammatory gene expression programs of dendritic cells by competing with RelA for binding to target gene promoters. Cell Discov. 2025 Feb 11; 11(1):13. Navarro HI, Daly AE, Rodriguez B, Wu S, Ngo KA, Fraser A, Schiffman A, Liu Y, Smale ST, Chia JJ, Hoffmann A. PMID: 39929805; PMCID: PMC11811218.
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Gene regulatory logic of the interferon-β enhancer contains multiple selectively deployed modes of transcription factor synergy. bioRxiv. 2025 Feb 08. Schiffman A, Cheng Z, Ourthiague D, Hoffmann A. PMID: 39975349; PMCID: PMC11838565.
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Enhancing FAIRdata by providing digital workflows from data generation to the publication of data: an open source approach described for cyclic voltammetry. Chem Sci. 2025 Mar 05; 16(10):4430-4441. Herrmann D, Hodapp P, Starman M, Huang PC, Lin CL, Le LBQ, Fischer TG, Bizzarri C, Röse P, Oppel N, Klar J, Tremouilhac P, Holzhauer L, Herres-Pawlis S, Hoffmann A, Seitz T, Dorn A, Zeitler K, Jung N, Bräse S. PMID: 39916882; PMCID: PMC11796049.
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Systems biology-enabled targeting of NF-κΒ and BCL2 overcomes microenvironment-mediated BH3-mimetic resistance in DLBCL. bioRxiv. 2025 Feb 01. Vareli A, Narayanan HV, Clark H, Jayawant E, Zhou H, Liu Y, Stott L, Simoes F, Hoffmann A, Pepper A, Pepper C, Mitchell S. PMID: 39677808; PMCID: PMC11642794.
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The metabolic cofactor Coenzyme A enhances alternative macrophage activation via MyD88-linked signaling. bioRxiv. 2025 Jan 20. Jones AE, Rios A, Ibrahimovic N, Chavez C, Bayley NA, Ball AB, Hsieh WY, Sammarco A, Bianchi AR, Cortez AA, Graeber TG, Hoffmann A, Bensinger SJ, Divakaruni AS. PMID: 38585887; PMCID: PMC10996702.
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Distinct causes of three phenotypic hallmarks of hematopoietic aging. bioRxiv. 2025 Jan 19. Chia JJ, Singh A, Lin Y, Popko N, Mastro D, Liu Y, Tran T, King JK, Rao DS, Hoffmann A. PMID: 39868295; PMCID: PMC11761768.
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IRF1 cooperates with ISGF3 or GAF to form innate immune de novo enhancers in macrophages. Sci Signal. 2025 Jan 07; 18(868):eado8860. Chavez C, Lin K, Malveaux A, Gorin A, Brizuela S, Cheng QJ, Hoffmann A. PMID: 39772531; PMCID: PMC12052582.
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What unique insights can modeling approaches capture about the immune system? Cell Syst. 2024 Dec 18; 15(12):1148-1152. Yuan Kueh H, Handel A, Hoffmann A, Chowell D, Gottschalk RA, Singh H, Germain RN, Meier-Schellersheim M, Miller-Jensen K, Altan-Bonnet G. PMID: 39701031.
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Single-cell stimulus-response gene expression trajectories reveal the stimulus specificities of dynamic responses by single macrophages. Mol Cell. 2024 Nov 07; 84(21):4095-4110.e6. Sheu KM, Pimplaskar A, Hoffmann A. PMID: 39413794; PMCID: PMC11560543.
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Tracking of lineage mass via quantitative phase imaging and confinement in low refractive index microwells. Lab Chip. 2024 09 10; 24(18):4440-4449. Zhang J, Griffin J, Roy K, Hoffmann A, Zangle TA. PMID: 39190401; PMCID: PMC11412070.
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Examining NF-κB genomic interactions by ChIP-seq and CUT&Tag. bioRxiv. 2024 Aug 12. Daly AE, Schiffman A, Hoffmann A, Smale ST. PMID: 39185161; PMCID: PMC11343132.
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Synergy and antagonism in the integration of BCR and CD40 signals that control B-cell proliferation. bioRxiv. 2024 Jul 29. Huang H, Narayanan HV, Hoffmann A. PMID: 39131345; PMCID: PMC11312454.
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Intramolecularly O,N,O-Coordinated Tin(II) Salts: Syntheses, Structures, Cyclization, and Transition Metal Complexation. Chemistry. 2024 Aug 12; 30(45):e202400580. Alnasr H, Mroß D, Platzek A, Nayyar B, Ricica T, Schollmeyer D, Jambor R, Hoffmann A, Jurkschat K. PMID: 38838081.
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Direct observation correlates NFκB cRel in B cells with activating and terminating their proliferative program. Proc Natl Acad Sci U S A. 2024 Jul 23; 121(30):e2309686121. Vaidehi Narayanan H, Xiang MY, Chen Y, Huang H, Roy S, Makkar H, Hoffmann A, Roy K. PMID: 39024115; PMCID: PMC11287273.
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Dynamical and combinatorial coding by MAPK p38 and NFκB in the inflammatory response of macrophages. Mol Syst Biol. 2024 Aug; 20(8):898-932. Luecke S, Guo X, Sheu KM, Singh A, Lowe SC, Han M, Diaz J, Lopes F, Wollman R, Hoffmann A. PMID: 38872050; PMCID: PMC11297158.
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Stimulus-response signaling dynamics characterize macrophage polarization states. Cell Syst. 2024 Jun 19; 15(6):563-577.e6. Singh A, Sen S, Iter M, Adelaja A, Luecke S, Guo X, Hoffmann A. PMID: 38843840; PMCID: PMC11226196.
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Use of Transcriptional Signatures to Differentiate Pathogen-Specific and Treatment-Specific Host Responses in Patients With Bacterial Bloodstream Infections. J Infect Dis. 2024 May 15; 229(5):1535-1545. Thaden JT, Ahn R, Ruffin F, Gjertson DW, Hoffmann A, Fowler VG, Yeaman MR. PMID: 38001039; PMCID: PMC11095544.
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Tensor modeling of MRSA bacteremia cytokine and transcriptional patterns reveals coordinated, outcome-associated immunological programs. PNAS Nexus. 2024 May; 3(5):pgae185. Chin JL, Tan ZC, Chan LC, Ruffin F, Parmar R, Ahn R, Taylor SD, Bayer AS, Hoffmann A, Fowler VG, Reed EF, Yeaman MR, Meyer AS, with the MRSA Systems Immunobiology Group . PMID: 38779114; PMCID: PMC11109816.
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The noncanonical NFκB pathway: Regulatory mechanisms in health and disease. WIREs Mech Dis. 2024 Nov-Dec; 16(6):e1646. Rodriguez BN, Huang H, Chia JJ, Hoffmann A. PMID: 38634218; PMCID: PMC11486840.
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Co-imaging of RelA and c-Rel reveals features of NF-κB signaling for ligand discrimination. Cell Rep. 2024 03 26; 43(3):113940. Rahman SMT, Singh A, Lowe S, Aqdas M, Jiang K, Vaidehi Narayanan H, Hoffmann A, Sung MH. PMID: 38483906; PMCID: PMC11015162.
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TNFR1 mediates heterogeneity in single-cell NF-κB activation. iScience. 2024 Apr 19; 27(4):109486. Cheng CT, Hsiao JC, Hoffmann A, Tu HL. PMID: 38551009; PMCID: PMC10973173.
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Myeloid spatial and transcriptional molecular signature of ischemia-reperfusion injury in human liver transplantation. Hepatol Commun. 2024 01 01; 8(1). Sosa RA, Ahn R, Li F, Terry AQ, Qian Z, Bhat A, Sen S, Naini BV, Ito T, Kaldas FM, Hoffmann A, Busuttil RW, Kupiec-Weglinski JW, Gjertson DW, Reed EF. PMID: 38206205; PMCID: PMC10786592.
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A systematic approach to managing complications after proximal tibial osteotomies of the knee. J Exp Orthop. 2023 Dec 06; 10(1):131. Valcarenghi J, Vittone G, Mouton C, Coelho Leal A, Ibañez M, Hoffmann A, Pape D, Ollivier M, Seil R. PMID: 38055158; PMCID: PMC10700288.
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RelB-deficient autoinflammatory pathology presents as interferonopathy, but in mice is interferon-independent. J Allergy Clin Immunol. 2023 11; 152(5):1261-1272. Navarro HI, Liu Y, Fraser A, Lefaudeux D, Chia JJ, Vong L, Roifman CM, Hoffmann A. PMID: 37460023; PMCID: PMC10858800.
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Virtually the Same? Evaluating the Effectiveness of Remote Undergraduate Research Experiences. CBE Life Sci Educ. 2023 06; 22(2):ar25. Hess RA, Erickson OA, Cole RB, Isaacs JM, Alvarez-Clare S, Arnold J, Augustus-Wallace A, Ayoob JC, Berkowitz A, Branchaw J, Burgio KR, Cannon CH, Ceballos RM, Cohen CS, Coller H, Disney J, Doze VA, Eggers MJ, Ferguson EL, Gray JJ, Greenberg JT, Hoffmann A, Jensen-Ryan D, Kao RM, Keene AC, Kowalko JE, Lopez SA, Mathis C, Minkara M, Murren CJ, Ondrechen MJ, Ordoñez P, Osano A, Padilla-Crespo E, Palchoudhury S, Qin H, Ramírez-Lugo J, Reithel J, Shaw CA, Smith A, Smith RJ, Tsien F, Dolan EL. PMID: 37058442; PMCID: PMC10228262.
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Tonic TNF conditioning of macrophages safeguards stimulus-specific inflammatory responses. EMBO Rep. 2023 07 05; 24(7):e55986. Luecke S, Adelaja A, Guo X, Sen S, Spreafico R, Singh A, Liu Y, Taylor B, Diaz J, Cheng Q, Hoffmann A. PMID: 37212045; PMCID: PMC10328066.
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Designer genes courtesy of artificial intelligence. Genes Dev. 2023 05 01; 37(9-10):351-353. Hoffmann A. PMID: 37253615; PMCID: PMC10270197.
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Rethinking global digital health and AI-for-health innovation challenges. PLOS Glob Public Health. 2023; 3(4):e0001844. Farlow A, Hoffmann A, Tadesse GA, Mzurikwao D, Beyer R, Akogo D, Weicken E, Matika T, Nweje MI, Wamae W, Arts S, Wiegand T, Bennett C, Farhat MR, Gröschel MI. PMID: 37115743; PMCID: PMC10146484.
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A stimulus-contingent positive feedback loop enables IFN-β dose-dependent activation of pro-inflammatory genes. Mol Syst Biol. 2023 05 09; 19(5):e11294. Wilder CL, Lefaudeux D, Mathenge R, Kishimoto K, Zuniga Munoz A, Nguyen MA, Meyer AS, Cheng QJ, Hoffmann A. PMID: 36929731; PMCID: PMC10167482.
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The NF-κB multidimer system model: A knowledge base to explore diverse biological contexts. Sci Signal. 2023 03 14; 16(776):eabo2838. Mitchell S, Tsui R, Tan ZC, Pack A, Hoffmann A. PMID: 36917644; PMCID: PMC10195159.
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A biochemical necroptosis model explains cell-type-specific responses to cell death cues. Biophys J. 2023 03 07; 122(5):817-834. Ildefonso GV, Oliver Metzig M, Hoffmann A, Harris LA, Lopez CF. PMID: 36710493; PMCID: PMC10027451.
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Quantifying stimulus-response specificity to probe the functional state of macrophages. Cell Syst. 2023 03 15; 14(3):180-195.e5. Sheu KM, Guru AA, Hoffmann A. PMID: 36657439; PMCID: PMC10023480.
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Kinetics of mRNA nuclear export regulate innate immune response gene expression. Nat Commun. 2022 11 23; 13(1):7197. Lefaudeux D, Sen S, Jiang K, Hoffmann A, UCLA Ribonomics Group. PMID: 36424375; PMCID: PMC9691726.
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NFκB pathway dysregulation due to reduced RelB expression leads to severe autoimmune disorders and declining immunity. J Autoimmun. 2023 May; 137:102946. Sharfe N, Dalal I, Naghdi Z, Lefaudeux D, Vong L, Dadi H, Navarro H, Tasher D, Ovadia A, Zangen T, Ater D, Ngan B, Hoffmann A, Roifman CM. PMID: 36402602; PMCID: PMC10861023.
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Author Correction: IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells. NPJ Syst Biol Appl. 2022 Aug 04; 8(1):26. Ando M, Magi S, Seki M, Suzuki Y, Kasukawa T, Lefaudeux D, Hoffmann A, Okada M. PMID: 35927293; PMCID: PMC9352786.
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Quantifying information of intracellular signaling: progress with machine learning. Rep Prog Phys. 2022 07 12; 85(8). Tang Y, Hoffmann A. PMID: 35724636; PMCID: PMC9507437.
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Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling. Cell Rep. 2022 07 12; 40(2):111076. Kim J, Sheu KM, Cheng QJ, Hoffmann A, Enciso G. PMID: 35830792; PMCID: PMC10074953.
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Manipulating electron transfer - the influence of substituents on novel copper guanidine quinolinyl complexes. Chem Sci. 2022 Jul 20; 13(28):8274-8288. Heck J, Metz F, Buchenau S, Teubner M, Grimm-Lebsanft B, Spaniol TP, Hoffmann A, Rübhausen MA, Herres-Pawlis S. PMID: 35919707; PMCID: PMC9297705.
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Bruins-in-Genomics: Evaluation of the impact of a UCLA undergraduate summer program in computational biology on participating students. PLoS One. 2022; 17(5):e0268861. Coller HA, Beggs S, Andrews S, Maloy J, Chiu A, Sankararaman S, Pellegrini M, Freimer N, Johnson T, Papp J, Eskin E, Hoffmann A. PMID: 35622842; PMCID: PMC9140266.
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From Antibody Repertoires to Cell-Cell Interactions to Molecular Networks: Bridging Scales in the Germinal Center. Front Immunol. 2022; 13:898078. Vaidehi Narayanan H, Hoffmann A. PMID: 35603162; PMCID: PMC9114758.
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Functional Hallmarks of Healthy Macrophage Responses: Their Regulatory Basis and Disease Relevance. Annu Rev Immunol. 2022 04 26; 40:295-321. Sheu KM, Hoffmann A. PMID: 35471841; PMCID: PMC10074967.
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Controlling Cancer Cell Death Types to Optimize Anti-Tumor Immunity. Biomedicines. 2022 Apr 22; 10(5). Oliver Metzig M, Hoffmann A. PMID: 35625711; PMCID: PMC9138898.
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"How Do We Do This at a Distance?!" A Descriptive Study of Remote Undergraduate Research Programs during COVID-19. CBE Life Sci Educ. 2022 03; 21(1):ar1. Erickson OA, Cole RB, Isaacs JM, Alvarez-Clare S, Arnold J, Augustus-Wallace A, Ayoob JC, Berkowitz A, Branchaw J, Burgio KR, Cannon CH, Ceballos RM, Cohen CS, Coller H, Disney J, Doze VA, Eggers MJ, Farina S, Ferguson EL, Gray JJ, Greenberg JT, Hoffmann A, Jensen-Ryan D, Kao RM, Keene AC, Kowalko JE, Lopez SA, Mathis C, Minkara M, Murren CJ, Ondrechen MJ, Ordoñez P, Osano A, Padilla-Crespo E, Palchoudhury S, Qin H, Ramírez-Lugo J, Reithel J, Shaw CA, Smith A, Smith R, Summers AP, Tsien F, Dolan EL. PMID: 34978923; PMCID: PMC9250374.
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Pathogenic TNF-α drives peripheral nerve inflammation in an Aire-deficient model of autoimmunity. Proc Natl Acad Sci U S A. 2022 01 25; 119(4). Wang Y, Guo L, Yin X, McCarthy EC, Cheng MI, Hoang AT, Chen HC, Patel AY, Allard Trout D, Xu E, Yakobian N, Hugo W, Howard JF, Sheu KM, Hoffmann A, Lechner MG, Su MA. PMID: 35058362; PMCID: PMC8795502.
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IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells. NPJ Syst Biol Appl. 2021 12 01; 7(1):42. Ando M, Magi S, Seki M, Suzuki Y, Kasukawa T, Lefaudeux D, Hoffmann A, Okada M. PMID: 34853340; PMCID: PMC8636565.
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Acute and Chronic Changes in Gene Expression After CMV DNAemia in Kidney Transplant Recipients. Front Immunol. 2021; 12:750659. Ahn R, Schaenman J, Qian Z, Pickering H, Groysberg V, Rossetti M, Llamas M, Hoffmann A, Gjertson D, Deng M, Bunnapradist S, Reed EF, CMV Systems Immunobiology Group. PMID: 34867983; PMCID: PMC8634678.
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NK and CD8+ T cell phenotypes predict onset and control of CMV viremia after kidney transplant. JCI Insight. 2021 11 08; 6(21). Pickering H, Sen S, Arakawa-Hoyt J, Ishiyama K, Sun Y, Parmar R, Ahn RS, Sunga G, Llamas M, Hoffmann A, Deng M, Bunnapradist S, Schaenman JM, Gjertson DW, Rossetti M, Lanier LL, Reed EF, CMV Systems Immunobiology Group. PMID: 34609965; PMCID: PMC8663544.
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Stimulus-specific responses in innate immunity: Multilayered regulatory circuits. Immunity. 2021 09 14; 54(9):1915-1932. Luecke S, Sheu KM, Hoffmann A. PMID: 34525335; PMCID: PMC8452151.
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Identifying the combinatorial control of signal-dependent transcription factors. PLoS Comput Biol. 2021 06; 17(6):e1009095. Wang N, Lefaudeux D, Mazumder A, Li JJ, Hoffmann A. PMID: 34166361; PMCID: PMC8263068.
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NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages. Science. 2021 06 18; 372(6548):1349-1353. Cheng QJ, Ohta S, Sheu KM, Spreafico R, Adelaja A, Taylor B, Hoffmann A. PMID: 34140389; PMCID: PMC8489855.
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Melanoma dedifferentiation induced by IFN-γ epigenetic remodeling in response to anti-PD-1 therapy. J Clin Invest. 2021 06 15; 131(12). Kim YJ, Sheu KM, Tsoi J, Abril-Rodriguez G, Medina E, Grasso CS, Torrejon DY, Champhekar AS, Litchfield K, Swanton C, Speiser DE, Scumpia PO, Hoffmann A, Graeber TG, Puig-Saus C, Ribas A. PMID: 33914706; PMCID: PMC8203459.
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Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses. Immunity. 2021 05 11; 54(5):916-930.e7. Adelaja A, Taylor B, Sheu KM, Liu Y, Luecke S, Hoffmann A. PMID: 33979588; PMCID: PMC8184127.
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High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial Cells. Front Immunol. 2021; 12:651254. Kishimoto K, Wilder CL, Buchanan J, Nguyen M, Okeke C, Hoffmann A, Cheng QJ. PMID: 33897699; PMCID: PMC8062733.
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Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremia. Proc Natl Acad Sci U S A. 2021 03 09; 118(10). Chang YL, Rossetti M, Gjertson DW, Rubbi L, Thompson M, Montoya DJ, Morselli M, Ruffin F, Hoffmann A, Pellegrini M, Fowler VG, Yeaman MR, Reed EF, with the MRSA Systems Immunology Group. PMID: 33649198; PMCID: PMC7958259.
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Quantifying information accumulation encoded in the dynamics of biochemical signaling. Nat Commun. 2021 02 24; 12(1):1272. Tang Y, Adelaja A, Ye FX, Deeds E, Wollman R, Hoffmann A. PMID: 33627672; PMCID: PMC7904837.
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NF-κB responds to absolute differences in cytokine concentrations. Sci Signal. 2021 01 19; 14(666). Son M, Wang AG, Tu HL, Metzig MO, Patel P, Husain K, Lin J, Murugan A, Hoffmann A, Tay S. PMID: 34211635; PMCID: PMC8244746.
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An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF-induced necroptosis decisions. Mol Syst Biol. 2020 12; 16(12):e9677. Oliver Metzig M, Tang Y, Mitchell S, Taylor B, Foreman R, Wollman R, Hoffmann A. PMID: 33314666; PMCID: PMC7734648.
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IκBα Nuclear Export Enables 4-1BB-Induced cRel Activation and IL-2 Production to Promote CD8 T Cell Immunity. J Immunol. 2020 09 15; 205(6):1540-1553. Lisiero DN, Cheng Z, Tejera MM, Neldner BT, Warrick JW, Wuerzberger-Davis SM, Hoffmann A, Suresh M, Miyamoto S. PMID: 32817348; PMCID: PMC7484350.
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Reduced Arene Complexes of Scandium. Chemistry. 2020 Aug 12; 26(45):10290-10296. Ghana P, Hoffmann A, Spaniol TP, Okuda J. PMID: 32160350; PMCID: PMC7496515.
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Dissecting the Regulatory Strategies of NF-κB RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation Logics. Cell Rep. 2020 02 25; 30(8):2758-2775.e6. Ngo KA, Kishimoto K, Davis-Turak J, Pimplaskar A, Cheng Z, Spreafico R, Chen EY, Tam A, Ghosh G, Mitchell S, Hoffmann A. PMID: 32101750; PMCID: PMC7061728.
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Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene Expression. Cell Syst. 2020 02 26; 10(2):169-182.e5. Sen S, Cheng Z, Sheu KM, Chen YH, Hoffmann A. PMID: 31972132; PMCID: PMC7047529.
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Stimulus-specificity in the Responses of Immune Sentinel Cells. Curr Opin Syst Biol. 2019 Dec; 18:53-61. Sheu K, Luecke S, Hoffmann A. PMID: 32864512; PMCID: PMC7450653.
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Identifying determinants of persistent MRSA bacteremia using mathematical modeling. PLoS Comput Biol. 2019 07; 15(7):e1007087. Mikkaichi T, Yeaman MR, Hoffmann A, MRSA Systems Immunobiology Group. PMID: 31295255; PMCID: PMC6622483.
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Signaling Crosstalk Mechanisms That May Fine-Tune Pathogen-Responsive NFκB. Front Immunol. 2019; 10:433. Adelaja A, Hoffmann A. PMID: 31312197; PMCID: PMC6614373.
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An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct Mechanisms. Front Immunol. 2019; 10:1425. Mitchell S, Mercado EL, Adelaja A, Ho JQ, Cheng QJ, Ghosh G, Hoffmann A. PMID: 31293585; PMCID: PMC6604663.
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Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB. Proc Natl Acad Sci U S A. 2019 05 21; 116(21):10592-10597. Mitchell S, Hoffmann A. PMID: 31048505; PMCID: PMC6535030.
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Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions. Sci Rep. 2019 03 27; 9(1):5288. Cheng Q, Behzadi F, Sen S, Ohta S, Spreafico R, Teles R, Modlin RL, Hoffmann A. PMID: 30918279; PMCID: PMC6437173.
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A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation. Immunity. 2019 03 19; 50(3):616-628.e6. Roy K, Mitchell S, Liu Y, Ohta S, Lin YS, Metzig MO, Nutt SL, Hoffmann A. PMID: 30850343; PMCID: PMC6955201.
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Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing. Nucleic Acids Res. 2019 Feb 20; 47(3):1602-1603. Davis-Turak J, Johnson TL, Hoffmann A. PMID: 30649426; PMCID: PMC6379712.
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Dopamine Is a Siderophore-Like Iron Chelator That Promotes Salmonella enterica Serovar Typhimurium Virulence in Mice. mBio. 2019 02 05; 10(1). Dichtl S, Demetz E, Haschka D, Tymoszuk P, Petzer V, Nairz M, Seifert M, Hoffmann A, Brigo N, Würzner R, Theurl I, Karlinsey JE, Fang FC, Weiss G. PMID: 30723125; PMCID: PMC6428752.
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A Masked Cuprous Hydride as a Catalyst for Carbonyl Hydrosilylation in Aqueous Solutions. Angew Chem Int Ed Engl. 2019 Feb 04; 58(6):1818-1822. Ritter F, Mukherjee D, Spaniol TP, Hoffmann A, Okuda J. PMID: 30536497.
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Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing. Nucleic Acids Res. 2018 11 16; 46(20):10598-10607. Davis-Turak J, Johnson TL, Hoffmann A. PMID: 30272246; PMCID: PMC6237756.
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Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. Proc Natl Acad Sci U S A. 2018 11 20; 115(47):E11061-E11070. Yeom KH, Mitchell S, Linares AJ, Zheng S, Lin CH, Wang XJ, Hoffmann A, Black DL. PMID: 30401736; PMCID: PMC6255174.
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Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation. Proc Natl Acad Sci U S A. 2018 03 20; 115(12):E2888-E2897. Mitchell S, Roy K, Zangle TA, Hoffmann A. PMID: 29514960; PMCID: PMC5866559.
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Deriving Quantitative Cell Biological Information from Dye-Dilution Lymphocyte Proliferation Experiments. Methods Mol Biol. 2018; 1707:81-94. Roy K, Shokhirev MN, Mitchell S, Hoffmann A. PMID: 29388101; PMCID: PMC8363314.
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Identifying Noise Sources governing cell-to-cell variability. Curr Opin Syst Biol. 2018 Apr; 8:39-45. Mitchell S, Hoffmann A. PMID: 29623300; PMCID: PMC5879788.
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Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX. Trends Biotechnol. 2017 10; 35(10):901-903. Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E. PMID: 28720283.
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Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells. Proc Natl Acad Sci U S A. 2017 03 28; 114(13):E2776-E2785. Mognol GP, Spreafico R, Wong V, Scott-Browne JP, Togher S, Hoffmann A, Hogan PG, Rao A, Trifari S. PMID: 28283662; PMCID: PMC5380094.
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Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms. Cell Syst. 2017 03 22; 4(3):330-343.e5. Cheng CS, Behar MS, Suryawanshi GW, Feldman KE, Spreafico R, Hoffmann A. PMID: 28237795; PMCID: PMC5434763.
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Functional importance of stripping in NFκB signaling revealed by a stripping-impaired IκBα mutant. Proc Natl Acad Sci U S A. 2017 02 21; 114(8):1916-1921. Dembinski HE, Wismer K, Vargas JD, Suryawanshi GW, Kern N, Kroon G, Dyson HJ, Hoffmann A, Komives EA. PMID: 28167786; PMCID: PMC5338396.
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Early cytokine signatures of ischemia/reperfusion injury in human orthotopic liver transplantation. JCI Insight. 2016 12 08; 1(20):e89679. Sosa RA, Zarrinpar A, Rossetti M, Lassman CR, Naini BV, Datta N, Rao P, Harre N, Zheng Y, Spreafico R, Hoffmann A, Busuttil RW, Gjertson DW, Zhai Y, Kupiec-Weglinski JW, Reed EF. PMID: 27942590; PMCID: PMC5135282.
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Oscillation dynamics underlie functional switching of NF-κB for B-cell activation. NPJ Syst Biol Appl. 2016; 2:16024. Inoue K, Shinohara H, Behar M, Yumoto N, Tanaka G, Hoffmann A, Aihara K, Okada-Hatakeyama M. PMID: 28725478; PMCID: PMC5516862.
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A miR-155-Peli1-c-Rel pathway controls the generation and function of T follicular helper cells. J Exp Med. 2016 08 22; 213(9):1901-19. Liu WH, Kang SG, Huang Z, Wu CJ, Jin HY, Maine CJ, Liu Y, Shepherd J, Sabouri-Ghomi M, Gonzalez-Martin A, Xu S, Hoffmann A, Zheng Y, Lu LF, Xiao N, Fu G, Xiao C. PMID: 27481129; PMCID: PMC4995083.
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Immune Response Signaling: Combinatorial and Dynamic Control. Trends Immunol. 2016 09; 37(9):570-572. Hoffmann A. PMID: 27461000; PMCID: PMC5003693.
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Surgical anatomy of medial open-wedge high tibial osteotomy: crucial steps and pitfalls. Knee Surg Sports Traumatol Arthrosc. 2017 Dec; 25(12):3661-3669. Madry H, Goebel L, Hoffmann A, Dück K, Gerich T, Seil R, Tschernig T, Pape D. PMID: 27236541.
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High-Content Quantification of Single-Cell Immune Dynamics. Cell Rep. 2016 Apr 12; 15(2):411-22. Junkin M, Kaestli AJ, Cheng Z, Jordi C, Albayrak C, Hoffmann A, Tay S. PMID: 27050527; PMCID: PMC4835544.
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Signaling via the NFκB system. Wiley Interdiscip Rev Syst Biol Med. 2016 05; 8(3):227-41. Mitchell S, Vargas J, Hoffmann A. PMID: 26990581; PMCID: PMC8363188.
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The REGγ-proteasome forms a regulatory circuit with IκBɛ and NFκB in experimental colitis. Nat Commun. 2016 Feb 22; 7:10761. Xu J, Zhou L, Ji L, Chen F, Fortmann K, Zhang K, Liu Q, Li K, Wang W, Wang H, Xie W, Wang Q, Liu J, Zheng B, Zhang P, Huang S, Shi T, Zhang B, Dang Y, Chen J, O'Malley BW, Moses RE, Wang P, Li L, Xiao J, Hoffmann A, Li X. PMID: 26899380; PMCID: PMC4764899.
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A stochastic spatio-temporal (SST) model to study cell-to-cell variability in HIV-1 infection. J Theor Biol. 2016 Apr 21; 395:87-96. Cheng Z, Hoffmann A. PMID: 26860658.
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B-cell survival and development controlled by the coordination of NF-κB family members RelB and cRel. Blood. 2016 Mar 10; 127(10):1276-86. Almaden JV, Liu YC, Yang E, Otero DC, Birnbaum H, Davis-Turak J, Asagiri M, David M, Goldrath AW, Hoffmann A. PMID: 26773039; PMCID: PMC4786837.
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A multi-scale mathematical modeling framework to investigate anti-viral therapeutic opportunities in targeting HIV-1 accessory proteins. J Theor Biol. 2015 Dec 07; 386:89-104. Suryawanshi GW, Hoffmann A. PMID: 26385832; PMCID: PMC4685255.
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Anatomy of a negative feedback loop: the case of IκBα. J R Soc Interface. 2015 Sep 06; 12(110):0262. Fagerlund R, Behar M, Fortmann KT, Lin YE, Vargas JD, Hoffmann A. PMID: 26311312; PMCID: PMC4614452.
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A Regulated, Ubiquitin-Independent Degron in IκBα. J Mol Biol. 2015 Aug 28; 427(17):2748-56. Fortmann KT, Lewis RD, Ngo KA, Fagerlund R, Hoffmann A. PMID: 26191773; PMCID: PMC4685248.
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Distinct single-cell signaling characteristics are conferred by the MyD88 and TRIF pathways during TLR4 activation. Sci Signal. 2015 Jul 14; 8(385):ra69. Cheng Z, Taylor B, Ourthiague DR, Hoffmann A. PMID: 26175492; PMCID: PMC6764925.
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IκBβ enhances the generation of the low-affinity NFκB/RelA homodimer. Nat Commun. 2015 May 07; 6:7068. Tsui R, Kearns JD, Lynch C, Vu D, Ngo KA, Basak S, Ghosh G, Hoffmann A. PMID: 25946967; PMCID: PMC4425231.
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Training the 21st Century Immunologist. Trends Immunol. 2015 May; 36(5):283-5. Spreafico R, Mitchell S, Hoffmann A. PMID: 25911462.
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Limited specificity of IRF3 and ISGF3 in the transcriptional innate-immune response to double-stranded RNA. J Leukoc Biol. 2015 Jul; 98(1):119-28. Ourthiague DR, Birnbaum H, Ortenlöf N, Vargas JD, Wollman R, Hoffmann A. PMID: 25896227; PMCID: PMC4467169.
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Regulation and Function of the Caspase-1 in an Inflammatory Microenvironment. J Invest Dermatol. 2015 Aug; 135(8):2012-2020. Lee DJ, Du F, Chen SW, Nakasaki M, Rana I, Shih VFS, Hoffmann A, Jamora C. PMID: 25815426; PMCID: PMC4504759.
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A multi-scale approach reveals that NF-κB cRel enforces a B-cell decision to divide. Mol Syst Biol. 2015 Feb 13; 11(1):783. Shokhirev MN, Almaden J, Davis-Turak J, Birnbaum HA, Russell TM, Vargas JA, Hoffmann A. PMID: 25680807; PMCID: PMC4358656.
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Studying NF-κB signaling with mathematical models. Methods Mol Biol. 2015; 1280:647-61. Mitchell S, Tsui R, Hoffmann A. PMID: 25736777.
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Synthesis and characterization of 1,2,3,4,5-pentafluoroferrocene. J Am Chem Soc. 2015 Jan 14; 137(1):126-9. Sünkel K, Weigand S, Hoffmann A, Blomeyer S, Reuter CG, Vishnevskiy YV, Mitzel NW. PMID: 25531826.
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Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing. Nucleic Acids Res. 2015 Jan; 43(2):699-707. Davis-Turak JC, Allison K, Shokhirev MN, Ponomarenko P, Tsimring LS, Glass CK, Johnson TL, Hoffmann A. PMID: 25541195; PMCID: PMC4333389.
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Systems biology. Accurate information transmission through dynamic biochemical signaling networks. Science. 2014 Dec 12; 346(6215):1370-3. Selimkhanov J, Taylor B, Yao J, Pilko A, Albeck J, Hoffmann A, Tsimring L, Wollman R. PMID: 25504722; PMCID: PMC4813785.
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A pathway switch directs BAFF signaling to distinct NFκB transcription factors in maturing and proliferating B cells. Cell Rep. 2014 Dec 24; 9(6):2098-111. Almaden JV, Tsui R, Liu YC, Birnbaum H, Shokhirev MN, Ngo KA, Davis-Turak JC, Otero D, Basak S, Rickert RC, Hoffmann A. PMID: 25497099; PMCID: PMC4889572.
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MAP kinase p38α regulates type III interferon (IFN-λ1) gene expression in human monocyte-derived dendritic cells in response to RNA stimulation. J Leukoc Biol. 2015 Feb; 97(2):307-20. Jiang M, Österlund P, Fagerlund R, Rios DN, Hoffmann A, Poranen MM, Bamford DH, Julkunen I. PMID: 25473098.
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Network dynamics determine the autocrine and paracrine signaling functions of TNF. Genes Dev. 2014 Oct 01; 28(19):2120-33. Caldwell AB, Cheng Z, Vargas JD, Birnbaum HA, Hoffmann A. PMID: 25274725; PMCID: PMC4180974.
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Performance studies on distributed virtual screening. Biomed Res Int. 2014; 2014:624024. Krüger J, Grunzke R, Herres-Pawlis S, Hoffmann A, de la Garza L, Kohlbacher O, Nagel WE, Gesing S. PMID: 25032219; PMCID: PMC4083208.
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Positive feedback within a kinase signaling complex functions as a switch mechanism for NF-κB activation. Science. 2014 May 16; 344(6185):760-4. Shinohara H, Behar M, Inoue K, Hiroshima M, Yasuda T, Nagashima T, Kimura S, Sanjo H, Maeda S, Yumoto N, Ki S, Akira S, Sako Y, Hoffmann A, Kurosaki T, Okada-Hatakeyama M. PMID: 24833394.
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IκBε is a key regulator of B cell expansion by providing negative feedback on cRel and RelA in a stimulus-specific manner. J Immunol. 2014 Apr 01; 192(7):3121-32. Alves BN, Tsui R, Almaden J, Shokhirev MN, Davis-Turak J, Fujimoto J, Birnbaum H, Ponomarenko J, Hoffmann A. PMID: 24591377; PMCID: PMC3965642.
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Cross-talk between aryl hydrocarbon receptor and the inflammatory response: a role for nuclear factor-κB. J Biol Chem. 2014 Jan 17; 289(3):1866-75. Vogel CF, Khan EM, Leung PS, Gershwin ME, Chang WL, Wu D, Haarmann-Stemmann T, Hoffmann A, Denison MS. PMID: 24302727; PMCID: PMC3894361.
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The dynamics of signaling as a pharmacological target. Cell. 2013 Oct 10; 155(2):448-61. Behar M, Barken D, Werner SL, Hoffmann A. PMID: 24120141; PMCID: PMC3856316.
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Ex vivo innate immune cytokine signature of enhanced risk of relapsing brucellosis. PLoS Negl Trop Dis. 2013; 7(9):e2424. Feldman KE, Loriaux PM, Saito M, Tuero I, Villaverde H, Siva T, Gotuzzo E, Gilman RH, Hoffmann A, Vinetz JM. PMID: 24040434; PMCID: PMC3764229.
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Analysis of the RelA:CBP/p300 interaction reveals its involvement in NF-κB-driven transcription. PLoS Biol. 2013 Sep; 11(9):e1001647. Mukherjee SP, Behar M, Birnbaum HA, Hoffmann A, Wright PE, Ghosh G. PMID: 24019758; PMCID: PMC3760798.
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Chromatin-bound IκBα regulates a subset of polycomb target genes in differentiation and cancer. Cancer Cell. 2013 Aug 12; 24(2):151-66. Mulero MC, Ferres-Marco D, Islam A, Margalef P, Pecoraro M, Toll A, Drechsel N, Charneco C, Davis S, Bellora N, Gallardo F, López-Arribillaga E, Asensio-Juan E, Rodilla V, González J, Iglesias M, Shih V, Mar Albà M, Di Croce L, Hoffmann A, Miyamoto S, Villà-Freixa J, López-Bigas N, Keyes WM, Domínguez M, Bigas A, Espinosa L. PMID: 23850221; PMCID: PMC3962677.
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Tunable signal processing through a kinase control cycle: the IKK signaling node. Biophys J. 2013 Jul 02; 105(1):231-41. Behar M, Hoffmann A. PMID: 23823243; PMCID: PMC3699752.
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FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses. PLoS One. 2013; 8(6):e67620. Shokhirev MN, Hoffmann A. PMID: 23826329; PMCID: PMC3694893.
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Dual delayed feedback provides sensitivity and robustness to the NF-κB signaling module. PLoS Comput Biol. 2013; 9(6):e1003112. Longo DM, Selimkhanov J, Kearns JD, Hasty J, Hoffmann A, Tsimring LS. PMID: 23825938; PMCID: PMC3694842.
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A structural basis for IκB kinase 2 activation via oligomerization-dependent trans auto-phosphorylation. PLoS Biol. 2013; 11(6):e1001581. Polley S, Huang DB, Hauenstein AV, Fusco AJ, Zhong X, Vu D, Schröfelbauer B, Kim Y, Hoffmann A, Verma IM, Ghosh G, Huxford T. PMID: 23776406; PMCID: PMC3678999.
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Characterizing the relationship between steady state and response using analytical expressions for the steady states of mass action models. PLoS Comput Biol. 2013; 9(2):e1002901. Loriaux PM, Tesler G, Hoffmann A. PMID: 23509437; PMCID: PMC3585464.
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A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways. PLoS Comput Biol. 2013; 9(2):e1002932. Loriaux PM, Hoffmann A. PMID: 23468615; PMCID: PMC3585401.
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ER stress activates NF-κB by integrating functions of basal IKK activity, IRE1 and PERK. PLoS One. 2012; 7(10):e45078. Tam AB, Mercado EL, Hoffmann A, Niwa M. PMID: 23110043; PMCID: PMC3482226.
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Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways. Nat Immunol. 2012 Dec; 13(12):1162-70. Shih VF, Davis-Turak J, Macal M, Huang JQ, Ponomarenko J, Kearns JD, Yu T, Fagerlund R, Asagiri M, Zuniga EI, Hoffmann A. PMID: 23086447; PMCID: PMC3634611.
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The transcriptional specificity of NF-κB dimers is coded within the κB DNA response elements. Cell Rep. 2012 Oct 25; 2(4):824-39. Wang VY, Huang W, Asagiri M, Spann N, Hoffmann A, Glass C, Ghosh G. PMID: 23063365; PMCID: PMC4167904.
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NEMO ensures signaling specificity of the pleiotropic IKKβ by directing its kinase activity toward IκBα. Mol Cell. 2012 Jul 13; 47(1):111-21. Schröfelbauer B, Polley S, Behar M, Ghosh G, Hoffmann A. PMID: 22633953; PMCID: PMC3398199.
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Paternal RLIM/Rnf12 is a survival factor for milk-producing alveolar cells. Cell. 2012 Apr 27; 149(3):630-41. Jiao B, Ma H, Shokhirev MN, Drung A, Yang Q, Shin J, Lu S, Byron M, Kalantry S, Mercurio AM, Lawrence JB, Hoffmann A, Bach I. PMID: 22541433; PMCID: PMC3342660.
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Lessons from mathematically modeling the NF-κB pathway. Immunol Rev. 2012 Mar; 246(1):221-38. Basak S, Behar M, Hoffmann A. PMID: 22435558; PMCID: PMC3343698.
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A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness. Methods Cell Biol. 2012; 110:81-109. Loriaux PM, Hoffmann A. PMID: 22482946; PMCID: PMC5763568.
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Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS Genet. 2011 Dec; 7(12):e1002401. Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, Heinz S, Spann NJ, Crotti A, Stender J, Ghisletti S, Reichart D, Cheng CS, Luna R, Ludka C, Sasik R, Garcia-Bassets I, Hoffmann A, Subramaniam S, Hardiman G, Rosenfeld MG, Glass CK. PMID: 22174696; PMCID: PMC3234212.
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NF-κB–inducing kinase plays an essential T cell–intrinsic role in graft-versus-host disease and lethal autoimmunity in mice. J Clin Invest. 2011 Dec; 121(12):4775-86. Murray SE, Polesso F, Rowe AM, Basak S, Koguchi Y, Toren KG, Hoffmann A, Parker DC. PMID: 22045568; PMCID: PMC3223068.
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How do pleiotropic kinase hubs mediate specific signaling by TNFR superfamily members? Immunol Rev. 2011 Nov; 244(1):29-43. Schröfelbauer B, Hoffmann A. PMID: 22017429; PMCID: PMC3357464.
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The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50. Sci Signal. 2011 Feb 22; 4(161):ra11. Cheng CS, Feldman KE, Lee J, Verma S, Huang DB, Huynh K, Chang M, Ponomarenko JV, Sun SC, Benedict CA, Ghosh G, Hoffmann A. PMID: 21343618; PMCID: PMC3096068.
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Nuclear export of the NF-κB inhibitor IκBα is required for proper B cell and secondary lymphoid tissue formation. Immunity. 2011 Feb 25; 34(2):188-200. Wuerzberger-Davis SM, Chen Y, Yang DT, Kearns JD, Bates PW, Lynch C, Ladell NC, Yu M, Podd A, Zeng H, Huang TT, Wen R, Hoffmann A, Wang D, Miyamoto S. PMID: 21333553; PMCID: PMC3111750.
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NF-κB potentiates caspase independent hydrogen peroxide induced cell death. PLoS One. 2011 Feb 15; 6(2):e16815. Ho JQ, Asagiri M, Hoffmann A, Ghosh G. PMID: 21347231; PMCID: PMC3039651.
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Understanding the logic of IκB:NF-κB regulation in structural terms. Curr Top Microbiol Immunol. 2011; 349:1-24. Huxford T, Hoffmann A, Ghosh G. PMID: 20845107.
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A single NFκB system for both canonical and non-canonical signaling. Cell Res. 2011 Jan; 21(1):86-102. Shih VF, Tsui R, Caldwell A, Hoffmann A. PMID: 21102550; PMCID: PMC3193412.
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Systems biology of cellular rhythms: from cacophony to symphony. Curr Opin Genet Dev. 2010 Dec; 20(6):571-3. Hasty J, Hoffmann A, Golden S. PMID: 21036033; PMCID: PMC4734115.
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Understanding the temporal codes of intra-cellular signals. Curr Opin Genet Dev. 2010 Dec; 20(6):684-93. Behar M, Hoffmann A. PMID: 20956081; PMCID: PMC2982931.
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IkappaBbeta acts to inhibit and activate gene expression during the inflammatory response. Nature. 2010 Aug 26; 466(7310):1115-9. Rao P, Hayden MS, Long M, Scott ML, West AP, Zhang D, Oeckinghaus A, Lynch C, Hoffmann A, Baltimore D, Ghosh S. PMID: 20740013; PMCID: PMC2946371.
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Defective regulation of CXCR2 facilitates neutrophil release from bone marrow causing spontaneous inflammation in severely NF-kappa B-deficient mice. J Immunol. 2010 Jul 01; 185(1):670-8. von Vietinghoff S, Asagiri M, Azar D, Hoffmann A, Ley K. PMID: 20519647; PMCID: PMC2891140.
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Differential activation and antagonistic function of HIF-{alpha} isoforms in macrophages are essential for NO homeostasis. Genes Dev. 2010 Mar 01; 24(5):491-501. Takeda N, O'Dea EL, Doedens A, Kim JW, Weidemann A, Stockmann C, Asagiri M, Simon MC, Hoffmann A, Johnson RS. PMID: 20194441; PMCID: PMC2827844.
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The regulatory logic of the NF-kappaB signaling system. Cold Spring Harb Perspect Biol. 2010 Jan; 2(1):a000216. O'Dea E, Hoffmann A. PMID: 20182598; PMCID: PMC2827908.
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Kinetic enhancement of NF-kappaBxDNA dissociation by IkappaBalpha. Proc Natl Acad Sci U S A. 2009 Nov 17; 106(46):19328-33. Bergqvist S, Alverdi V, Mengel B, Hoffmann A, Ghosh G, Komives EA. PMID: 19887633; PMCID: PMC2780789.
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Coherent activation of a synthetic mammalian gene network. Syst Synth Biol. 2010 Mar; 4(1):15-23. Longo DM, Hoffmann A, Tsimring LS, Hasty J. PMID: 19757189; PMCID: PMC2816225.
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A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell. 2009 Jul 10; 138(1):114-28. Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST. PMID: 19596239; PMCID: PMC2712736.
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NF-κB signaling. Wiley Interdiscip Rev Syst Biol Med. 2009 Jul-Aug; 1(1):107-115. O'Dea E, Hoffmann A. PMID: 20151024; PMCID: PMC2819170.
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The Nfkb1 and Nfkb2 proteins p105 and p100 function as the core of high-molecular-weight heterogeneous complexes. Mol Cell. 2009 Jun 12; 34(5):591-602. Savinova OV, Hoffmann A, Ghosh G. PMID: 19524538; PMCID: PMC4167889.
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Kinetic control of negative feedback regulators of NF-kappaB/RelA determines their pathogen- and cytokine-receptor signaling specificity. Proc Natl Acad Sci U S A. 2009 Jun 16; 106(24):9619-24. Shih VF, Kearns JD, Basak S, Savinova OV, Ghosh G, Hoffmann A. PMID: 19487661; PMCID: PMC2701028.
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Of elections and cell-death decisions. Mol Cell. 2009 May 15; 34(3):257-8. Loriaux P, Hoffmann A. PMID: 19450524; PMCID: PMC3703440.
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Antigen-mediated T cell expansion regulated by parallel pathways of death. Proc Natl Acad Sci U S A. 2008 Nov 11; 105(45):17463-8. Ch'en IL, Beisner DR, Degterev A, Lynch C, Yuan J, Hoffmann A, Hedrick SM. PMID: 18981423; PMCID: PMC2582294.
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Integrating computational and biochemical studies to explore mechanisms in NF-{kappa}B signaling. J Biol Chem. 2009 Feb 27; 284(9):5439-43. Kearns JD, Hoffmann A. PMID: 18940809; PMCID: PMC2645808.
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Encoding NF-kappaB temporal control in response to TNF: distinct roles for the negative regulators IkappaBalpha and A20. Genes Dev. 2008 Aug 01; 22(15):2093-101. Werner SL, Kearns JD, Zadorozhnaya V, Lynch C, O'Dea E, Boldin MP, Ma A, Baltimore D, Hoffmann A. PMID: 18676814; PMCID: PMC2492747.
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UV as an amplifier rather than inducer of NF-kappaB activity. Mol Cell. 2008 Jun 06; 30(5):632-41. O'Dea EL, Kearns JD, Hoffmann A. PMID: 18538661; PMCID: PMC2682114.
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Crosstalk via the NF-kappaB signaling system. Cytokine Growth Factor Rev. 2008 Jun-Aug; 19(3-4):187-97. Basak S, Hoffmann A. PMID: 18515173; PMCID: PMC2675004.
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Understanding NF-kappaB signaling via mathematical modeling. Mol Syst Biol. 2008; 4:192. Cheong R, Hoffmann A, Levchenko A. PMID: 18463616; PMCID: PMC2424295.
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Negative regulation of constitutive NF-kappaB and JNK signaling by PKN1-mediated phosphorylation of TRAF1. Genes Cells. 2008 May; 13(5):509-20. Kato T, Gotoh Y, Hoffmann A, Ono Y. PMID: 18429822.
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Epigenetic control: slow and global, nimble and local. Genes Dev. 2008 May 01; 22(9):1110-4. Cheng CS, Johnson TL, Hoffmann A. PMID: 18451102; PMCID: PMC2732403.
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NF-kappaB dictates the degradation pathway of IkappaBalpha. EMBO J. 2008 May 07; 27(9):1357-67. Mathes E, O'Dea EL, Hoffmann A, Ghosh G. PMID: 18401342; PMCID: PMC2374849.
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Stabilization of RelB requires multidomain interactions with p100/p52. J Biol Chem. 2008 May 02; 283(18):12324-32. Fusco AJ, Savinova OV, Talwar R, Kearns JD, Hoffmann A, Ghosh G. PMID: 18321863; PMCID: PMC2431000.
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Generation and activation of multiple dimeric transcription factors within the NF-kappaB signaling system. Mol Cell Biol. 2008 May; 28(10):3139-50. Basak S, Shih VF, Hoffmann A. PMID: 18299388; PMCID: PMC2423155.
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NF-kappaB as a determinant of distinct cell death pathways. Methods Enzymol. 2008; 446:175-87. Ch'en IL, Hedrick SM, Hoffmann A. PMID: 18603122.
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A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity. Mol Syst Biol. 2007; 3:111. O'Dea EL, Barken D, Peralta RQ, Tran KT, Werner SL, Kearns JD, Levchenko A, Hoffmann A. PMID: 17486138; PMCID: PMC2673708.
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Inflammatory tales of liver cancer. Cancer Cell. 2007 Feb; 11(2):99-101. Hoffmann A, Xia Y, Verma IM. PMID: 17292819.
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A fourth IkappaB protein within the NF-kappaB signaling module. Cell. 2007 Jan 26; 128(2):369-81. Basak S, Kim H, Kearns JD, Tergaonkar V, O'Dea E, Werner SL, Benedict CA, Ware CF, Ghosh G, Verma IM, Hoffmann A. PMID: 17254973; PMCID: PMC1831796.
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IkappaBepsilon provides negative feedback to control NF-kappaB oscillations, signaling dynamics, and inflammatory gene expression. J Cell Biol. 2006 Jun 05; 173(5):659-64. Kearns JD, Basak S, Werner SL, Huang CS, Hoffmann A. PMID: 16735576; PMCID: PMC2063883.
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Circuitry of nuclear factor kappaB signaling. Immunol Rev. 2006 Apr; 210:171-86. Hoffmann A, Baltimore D. PMID: 16623771.
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Transient IkappaB kinase activity mediates temporal NF-kappaB dynamics in response to a wide range of tumor necrosis factor-alpha doses. J Biol Chem. 2006 Feb 03; 281(5):2945-50. Cheong R, Bergmann A, Werner SL, Regal J, Hoffmann A, Levchenko A. PMID: 16321974.
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Coordination between NF-kappaB family members p50 and p52 is essential for mediating LTbetaR signals in the development and organization of secondary lymphoid tissues. Blood. 2006 Feb 01; 107(3):1048-55. Lo JC, Basak S, James ES, Quiambo RS, Kinsella MC, Alegre ML, Weih F, Franzoso G, Hoffmann A, Fu YX. PMID: 16195333; PMCID: PMC1895903.
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Immortalized fibroblasts from NF-kappaB RelA knockout mice show phenotypic heterogeneity and maintain increased sensitivity to tumor necrosis factor alpha after transformation by v-Ras. Oncogene. 2005 Sep 29; 24(43):6574-83. Gapuzan ME, Schmah O, Pollock AD, Hoffmann A, Gilmore TD. PMID: 16027734.
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Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science. 2005 Sep 16; 309(5742):1857-61. Werner SL, Barken D, Hoffmann A. PMID: 16166517.
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A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activation. Genes Dev. 2005 Sep 15; 19(18):2138-51. Sanjabi S, Williams KJ, Saccani S, Zhou L, Hoffmann A, Ghosh G, Gerondakis S, Natoli G, Smale ST. PMID: 16166378; PMCID: PMC1221885.
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Cutting edge: innate immunity conferred by B cells is regulated by caspase-8. J Immunol. 2005 Sep 15; 175(6):3469-73. Beisner DR, Ch'en IL, Kolla RV, Hoffmann A, Hedrick SM. PMID: 16148088.
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Molecular determinants of crosstalk between nuclear receptors and toll-like receptors. Cell. 2005 Sep 09; 122(5):707-21. Ogawa S, Lozach J, Benner C, Pascual G, Tangirala RK, Westin S, Hoffmann A, Subramaniam S, David M, Rosenfeld MG, Glass CK. PMID: 16143103; PMCID: PMC1430687.
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Signaling pathways and genes that inhibit pathogen-induced macrophage apoptosis--CREB and NF-kappaB as key regulators. Immunity. 2005 Sep; 23(3):319-29. Park JM, Greten FR, Wong A, Westrick RJ, Arthur JS, Otsu K, Hoffmann A, Montminy M, Karin M. PMID: 16169504.
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Initiation and termination of NF-kappaB signaling by the intracellular protozoan parasite Toxoplasma gondii. J Cell Sci. 2005 Aug 01; 118(Pt 15):3501-8. Shapira S, Harb OS, Margarit J, Matrajt M, Han J, Hoffmann A, Freedman B, May MJ, Roos DS, Hunter CA. PMID: 16079291.
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Induction of NR4A orphan nuclear receptor expression in macrophages in response to inflammatory stimuli. J Biol Chem. 2005 Aug 12; 280(32):29256-62. Pei L, Castrillo A, Chen M, Hoffmann A, Tontonoz P. PMID: 15964844.
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Comment on "Oscillations in NF-kappaB signaling control the dynamics of gene expression". Science. 2005 Apr 01; 308(5718):52; author reply 52. Barken D, Wang CJ, Kearns J, Cheong R, Hoffmann A, Levchenko A. PMID: 15802586; PMCID: PMC2821939.
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One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers. Cell. 2004 Aug 20; 118(4):453-64. Leung TH, Hoffmann A, Baltimore D. PMID: 15315758.
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Unique CD40-mediated biological program in B cell activation requires both type 1 and type 2 NF-kappaB activation pathways. Proc Natl Acad Sci U S A. 2004 May 25; 101(21):8108-13. Zarnegar B, He JQ, Oganesyan G, Hoffmann A, Baltimore D, Cheng G. PMID: 15148378; PMCID: PMC419565.
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Genetic analysis of NF-kappaB/Rel transcription factors defines functional specificities. EMBO J. 2003 Oct 15; 22(20):5530-9. Hoffmann A, Leung TH, Baltimore D. PMID: 14532125; PMCID: PMC213788.
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CK2 Is a C-Terminal IkappaB Kinase Responsible for NF-kappaB Activation during the UV Response. Mol Cell. 2003 Oct; 12(4):829-39. Kato T, Delhase M, Hoffmann A, Karin M. PMID: 14580335.
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The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science. 2002 Nov 08; 298(5596):1241-5. Hoffmann A, Levchenko A, Scott ML, Baltimore D. PMID: 12424381.
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Cooperation of multiple signaling pathways in CD40-regulated gene expression in B lymphocytes. Proc Natl Acad Sci U S A. 2002 Feb 05; 99(3):1497-502. Dadgostar H, Zarnegar B, Hoffmann A, Qin XF, Truong U, Rao G, Baltimore D, Cheng G. PMID: 11830667; PMCID: PMC122219.
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