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NFkB Signaling - fundamentals

Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responsesAdelaja, A., Taylor, B., Sheu, K.M., Liu, Y., Luecke, S., Hoffmann, A.
Immunity. 11 May 2021
 Quantifying information accumulation encoded in the dynamics of biochemical signalingTang, Y., Adelaja, A., Ye, F., Deeds, E., Wollman, R., Hoffmann, A.
Nature Communications volume 12, Article number: 1272 (2021)
 NF-κB responds to absolute differences in cytokine concentrations Son, M., Wang A.G., Tu, H., Metzig, M.O., Patel, P., Husain, K., Lin, J., Murugan, A., Hoffmann, A., Tay, S.
Science Signaling. 2021 Jan 19. Vol. 14, Issue 666
 NFκB dynamics determine the stimulus-specificity of epigenomic reprogramming in macrophageCheng, Q.J., Ohta, S., Sheu, K.M., Spreafico, R., Adelaja, A., Taylor, B., Hoffmann, A.
bioRxiv., 19 Feb 19 2020
 An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF-induced necroptosis decisionsMetzig, M.O., Tang, Y., Mitchell, S., Taylor, B., Foreman, R., Wollman, R., Hoffmann, A.
Mol Syst Biol. 2020 Dec;16(12):e9677
 IκBα Nuclear Export Enables 4-1BB-Induced cRel Activation and IL-2 Production to Promote CD8 T Cell ImmunityLisiero, D.N., Cheng, Z., Tejera, M.M., Neldner, B.T., Warrick, J.W., Wuerzberger-Davis, S.M., Hoffmann, A., Suresh, M., Miyamoto, S.
J Immunol August 14, 2020, ji2000039; DOI: https://doi.org/10.4049/jimmunol.2000039
 Dissecting the Regulatory Strategies of NFκB RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation LogicsNgo, K.A., Kishimoto, K., Davis-Turak, J., Pimplaskar, A., Cheng, Z., Spreafico, R., Chen, E.Y., Tam, A., Ghosh, G., Mitchell, S., Hoffmann, A.
Cell Rep., 25 Feb 2020; 30:2758-2775.
 Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene ExpressionSen, S., Cheng, Z., Sheu, K.M., Chen, Y., Hoffmann, A.
Cell syst., 22 Jan 2020; 10:1-14
 Stimulus-specificity in the responses of immune sentinel cellsSheu, K.M., Luecke, S., Hoffmann, A.
Current Opinions in Systems Biology, 18, pp.53-61
 Signaling crosstalk mechanisms that may fine-tune pathogen-receptive NFκBAdelaja, A., Hoffmann, A.
Front Immunol., 2 July 2019
 An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct MechanismsMitchell, S., Mercado, E.L., Adelaja, A., Ho, J.Q., Cheng, Q.J., Ghosh, G., Hoffmann, A.
Front. Immunol., 25 June 2019
 Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelBMitchell, S., Hoffmann, A
PNAS May 21, 2019 116 (21) 10592-10597
 Signaling via the NFκB systemMitchell S, Vargas J, Hoffmann A.
Wiley Interdiscip Rev Syst Biol Med. 2016 May,8(3):227-41
 The Reg-gamma-proteasome forms a regulatory circuit with IkBe and NFkB in experimental colitisXu, J., Zhou, L., Ji, L., Chen, F., Fortmann, K., Zhang, K., Liu, Q., Li, K., Wang, W., Wamg, H., Xie, W., Wang, Q., Liu, J., Zheng, B., Zhang, P., Huang, S., Shi, T., Zhang, B., Dang, Y., Chen, J., O'Malley, B.W., Moses, R.E., Wang, P., Li, L., Xiao, J., Hoffmann, A.*, Li, X.*
Nature Commun. 7, 10761
 The REGγ-proteasome forms a regulatory circuit with IκBɛ and NFκB in experimental colitisXu 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.
Nat Commun. (2016) Feb 22;7:10761. doi: 10.1038/ncomms10761
 Anatomy of a negative feedback loop: the case of IκBα.Fagerlund R, Behar M, Fortmann KT, Lin YE, Vargas JD, Hoffmann A.
J. R. Soc. Interface 12: 20150262. doi:10.1098/rsif.2015.0262
 A Regulated, Ubiquitin-Independent Degron in IκBα.Fortmann, K.T., Lewis, R.D., Ngo, K.A., Fagerlund, R., Hoffmann, A.
J. Molecular Biology (2015) Aug 28;427(17):2748-56. doi: 10.1016/j.jmb.2015.07.008
 IκBβ enhances the generation of the low-affinity NFκB/RelA homodimers.Tsui. R., Kearns, J.D., Lynch, C., Vu, D., Ngo, K., Basak, S., Ghosh, G., Hoffmann, A.
Nature Communications (2015) 6, 7068. PMID: 25946967
 Tunable signal processing through a kinase control cycle: the IKK signaling nodeBehar, M., Hoffmann, A.
J. Biophys. 105, pp.231-241
 A structural basis for IκB Kinase 2 Activation via oligomerization-dependent trans auto-phosphorylationPolley, S., Huang, D.-B., Hauenstein, A.V., Fusco, A.J., Zhong, X., Vu, D., Schroefelbauer, B., Kim, Y., Hoffmann, A., Verma, I.M., Ghosh, G., Huxford, T.
PLOS Biology, 11, e1001581
 A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways Loriaux, P., Hoffmann, A.
PLOS Comput Biol. 2013 February; 9(2): e1002932.
 Control of RelB during dendritic cell activation integrates canonical and non-canonical NFκB pathwaysShih, V.F.-S., Davis-Turak, J., Macal, M., Huang, J.Q., Ponomarenko, J., Kearns, J.D., Yu, T., Fagerlund, R., Asagiri, M., Zuniga, E.I., Hoffmann, A.
Nature Immunology, 2012 Dec;13(12):1162-70.
 ER stress activates NFκB by integrating functions of basal IKK activity, IRE1 and PERKTam, A., Mercado, E., Hoffmann, A., Niwa, M
PLOS ONE, 7, e45078.
 NEMO Ensures Signaling Specificity of the Pleiotropic IKKβ by Directing Its Kinase Activity toward IκBαSchröfelbauer B, Polley S, Behar M, Ghosh G, Hoffmann A.
Mol Cell. 2012 Jul 13;47(1):111-21. Epub 2012 May 24.
 Lessons from mathematically modeling the NF-κB pathwayBasak S, Behar M, Hoffmann A.
Immunol Rev. 2012 Mar;246(1):221-38. doi: 10.1111/j.1600-065X.2011.01092.x. Review.
 How do pleiotropic kinase hubs mediate specific signaling by TNFR superfamily members?Schröfelbauer, B., Hoffmann, A.
Immunol Rev. 2011 Nov;244(1):29-43
 A single NFκB system for both canonical and non-canonical signalingShih VF, Tsui R, Caldwell A, Hoffmann A.
Cell Res. 2011 Jan;21(1):86-102. Epub 2010 Nov 23. Review.
 Understanding the logic of IκB:NF-κB regulation in structural termsHuxford T, Hoffmann A, Ghosh G.
Curr Top Microbiol Immunol. 2011;349:1-24. Review.
 The regulatory logic of the NF-κB signaling systemO'Dea E, Hoffmann A.
Cold Spring Harb Perspect Biol. 2010 Jan;2(1):a000216. Review.
 Kinetic enhancement of NF-κBxDNA dissociation by IκBαBergqvist S, Alverdi V, Mengel B, Hoffmann A, Ghosh G, Komives EA.
Proc Natl Acad Sci U S A. 2009 Nov 17;106(46):19328-33. Epub 2009 Nov 3.
 NF-κB signalingO'Dea E, Hoffmann A.
Wiley Interdiscip Rev Syst Biol Med. 2009 Jul-Aug;1(1):107-15. Review.
 Kinetic control of negative feedback regulators of NF-κB/RelA determines their pathogen- and cytokine-receptor signaling specificityShih VF, Kearns JD, Basak S, Savinova OV, Ghosh G, Hoffmann A.
Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9619-24. Epub 2009 Jun 1.
 The NFκB1 and NFκB2 proteins p105 and p100 function as the core of high-molecular-weight heterogeneous complexesSavinova OV, Hoffmann A, Ghosh G.
Mol Cell. 2009 Jun 12;34(5):591-602.
 Integrating computational and biochemical studies to explore mechanisms in NF-κB signalingKearns JD, Hoffmann A.
J Biol Chem. 2009 Feb 27;284(9):5439-43. Epub 2008 Oct 20. Review. No abstract available.
 Crosstalk via the NF-κB signaling systemBasak S, Hoffmann A.
Cytokine Growth Factor Rev. 2008 Jun-Aug;19(3-4):187-97. Epub 2008 Jun 2. Review.
 UV as an amplifier rather than inducer of NF-κB activityO'Dea EL, Kearns JD, Hoffmann A.
Mol Cell. 2008 Jun 6;30(5):632-41.
 Understanding NF-κB signaling via mathematical modelingCheong R, Hoffmann A, Levchenko A.
Mol Syst Biol. 2008;4:192. Epub 2008 May 6.
 Stabilization of RelB requires multidomain interactions with p100/p52Fusco AJ, Savinova OV, Talwar R, Kearns JD, Hoffmann A, Ghosh G.
J Biol Chem. 2008 May 2;283(18):12324-32. Epub 2008 Mar 4.
 Generation and activation of multiple dimeric transcription factors within the NF-κB signaling systemBasak S, Shih VF, Hoffmann A.
Mol Cell Biol. 2008 May;28(10):3139-50. Epub 2008 Feb 25.
 NF-κB dictates the degradation pathway of IκBalphaMathes E, O'Dea EL, Hoffmann A, Ghosh G.
EMBO J. 2008 May 7;27(9):1357-67. Epub 2008 Apr 10. Erratum in: EMBO J. 2008 May 7;27(9):1421.
 A homeostatic model of IκB metabolism to control constitutive NF-κB activityO'Dea EL, Barken D, Peralta RQ, Tran KT, Werner SL, Kearns JD, Levchenko A, Hoffmann A.
Mol Syst Biol. 2007;3:111. Epub 2007 May 8.
 A fourth IκB protein within the NF-κB signaling moduleBasak S, Kim H, Kearns JD, Tergaonkar V, O'Dea E, Werner SL, Benedict CA, Ware CF, Ghosh G, Verma IM, Hoffmann A.
Cell. 2007 Jan 26;128(2):369-81.
 IκBepsilon provides negative feedback to control NF-κB oscillations, signaling dynamics, and inflammatory gene expressionKearns JD, Basak S, Werner SL, Huang CS, Hoffmann A.
J Cell Biol. 2006 Jun 5;173(5):659-64. Epub 2006 May 30.
 Circuitry of nuclear factor kappaB signalingHoffmann A, Baltimore D.
Immunol Rev. 2006 Apr;210:171-86. Review.
 CK2 Is a C-Terminal IκB Kinase Responsible for NF-κB Activation during the UV ResponseKato T Jr, Delhase M, Hoffmann A, Karin M.
Mol Cell. 2003 Oct;12(4):829-39.
 Genetic analysis of NF-κB/Rel transcription factors defines functional specificitiesHoffmann A, Leung TH, Baltimore D.
EMBO J. 2003 Oct 15;22(20):5530-9.
 The IκB-NF-κB signaling module: temporal control and selective gene activationHoffmann A, Levchenko A, Scott ML, Baltimore D.
Science. 2002 Nov 8;298(5596):1241-5.
 Nuclear localization of IκB alpha is mediated by the second ankyrin repeat: the IκB alpha ankyrin repeats define a novel class of cis-acting nuclear import sequencesSachdev S, Hoffmann A, Hannink M.
Mol Cell Biol. 1998 May;18(5):2524-34.

NFkB Signaling - Dynamical Code

Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responsesAdelaja, A., Taylor, B., Sheu, K.M., Liu, Y., Luecke, S., Hoffmann, A.
Immunity. 11 May 2021
 Quantifying information accumulation encoded in the dynamics of biochemical signalingTang, Y., Adelaja, A., Ye, F., Deeds, E., Wollman, R., Hoffmann, A.
Nature Communications volume 12, Article number: 1272 (2021)
 NF-κB responds to absolute differences in cytokine concentrations Son, M., Wang A.G., Tu, H., Metzig, M.O., Patel, P., Husain, K., Lin, J., Murugan, A., Hoffmann, A., Tay, S.
Science Signaling. 2021 Jan 19. Vol. 14, Issue 666
 NFκB dynamics determine the stimulus-specificity of epigenomic reprogramming in macrophageCheng, Q.J., Ohta, S., Sheu, K.M., Spreafico, R., Adelaja, A., Taylor, B., Hoffmann, A.
bioRxiv., 19 Feb 19 2020
 An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF-induced necroptosis decisionsMetzig, M.O., Tang, Y., Mitchell, S., Taylor, B., Foreman, R., Wollman, R., Hoffmann, A.
Mol Syst Biol. 2020 Dec;16(12):e9677
 Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene ExpressionSen, S., Cheng, Z., Sheu, K.M., Chen, Y., Hoffmann, A.
Cell syst., 22 Jan 2020; 10:1-14
 Stimulus-specificity in the responses of immune sentinel cellsSheu, K.M., Luecke, S., Hoffmann, A.
Current Opinions in Systems Biology, 18, pp.53-61
 Immune Response Signaling: Combinatorial and Dynamic ControlHoffmann, A.
Trends Immunol. 2016 Sep;37(9):570-2
 Signaling via the NFκB systemMitchell S, Vargas J, Hoffmann A.
Wiley Interdiscip Rev Syst Biol Med. 2016 May,8(3):227-41
 Oscillation dynamics underlie functional switching of NFkB for B-cell activation. Inoue, K., Shinohara, H., Behar, M., Yumoto, N., Tanaka, G., Hoffmann, A., Aihara, K., Okada-Hatakeyama, M.
Systems Biology and Applications, 2, 16024.
 High Content Quantification of Single-Cell Immune DynamicsJunkin M., Kaestli A.J., Cheng Z., Jordi C., Albayrak C., Hoffmann A., Tay S.
Cell Rep. 15, pp. 411-22. PMID: 27050527
 Distinct Single Cell Signaling Characteristics Conferred by the MyD88 and TRIF Pathways in TLR4 Activation.Cheng, Z*., Taylor, B.*, Ourthiague, D.N., Hoffmann, A.
Science Signaling (2015) Jul 14; 8(385):ra69. doi: 10.1126/scisignal.aaa5208
 Studying NFκB Signaling with mathematical models.Mitchell, S., Tsui, R., Hoffmann, A.
Methods in Molecular Biology, 1280, pp.647-661. PMID: 25736777
 Accurate information transmission through dynamic biochemical signaling networksSelimkhanov, S.*, Taylor, B.*, Yao, J., Pilko, A., Albeck, J., Hoffmann, A., Tsimring, L., Wollman, R.
Science, 346, pp.1270-3. PMID: 25504722
 Network dynamics determine the autocrine and paracrine signaling functions of TNFCaldwell, A.B., Cheng, Z., Vargas, J.D., Birnbaum, H.A., Hoffmann, A.
Genes and Development, 2014. 28: 2120-2133
 Positive feedback within a kinase signaling complex functions as a switch mechanism for NF-κB activationShinohara, H.*, Behar, M.*, Inoue, K., Hiroshima, M., Yasuda, T., Nagashima, T., Kmura, S., Sanjo, H., Maeda, S., Yumoto, N., Ki, S., Sako, Y., Hoffmann , A.+, Kurosaki, T.+, Okada-Hatakeyama, M.+
Science, 344, pp.760-764, PMID: 24833394
 The Dynamics of Signaling as a Pharmacological TargetBehar, M., Barken, D., Werner, S.L., Hoffmann, A
Cell, 155, pp.448-461
 Dual delayed feedback provides sensitivity and robustness to the NFκB signaling moduleLongo, D., Selimkhanov, J., Kearns, J.D., Hasty, J., Hoffmann, A., Tsimring, L.
PLOS Computational Biology, 9, e1003112
 Lessons from mathematically modeling the NF-κB pathwayBasak S, Behar M, Hoffmann A.
Immunol Rev. 2012 Mar;246(1):221-38. doi: 10.1111/j.1600-065X.2011.01092.x. Review.
 Understanding the temporal codes of intra-cellular signalsBehar M, Hoffmann A.
Curr Opin Genet Dev. 2010 Dec;20(6):684-93. Epub 2010 Oct 16.
 Systems Biology of cellular rhythms: from cacophony to symphonyHasty, J, Hoffmann, A., Golden, S.
Current Opinion in Genetics and Development, 20, pp.571-3.
 Coherent activation of a synthetic mammalian gene networkLongo DM, Hoffmann A, Tsimring LS, Hasty J.
Syst Synth Biol. 2010 Mar;4(1):15-23.
 Kinetic control of negative feedback regulators of NF-κB/RelA determines their pathogen- and cytokine-receptor signaling specificityShih VF, Kearns JD, Basak S, Savinova OV, Ghosh G, Hoffmann A.
Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9619-24. Epub 2009 Jun 1.
 Encoding NF-κB temporal control in response to TNF: distinct roles for the negative regulators IκBalpha and A20Werner SL, Kearns JD, Zadorozhnaya V, Lynch C, O'Dea E, Boldin MP, Ma A, Baltimore D, Hoffmann A.
Genes Dev. 2008 Aug 1;22(15):2093-101.
 A fourth IκB protein within the NF-κB signaling moduleBasak S, Kim H, Kearns JD, Tergaonkar V, O'Dea E, Werner SL, Benedict CA, Ware CF, Ghosh G, Verma IM, Hoffmann A.
Cell. 2007 Jan 26;128(2):369-81.
 IκBepsilon provides negative feedback to control NF-κB oscillations, signaling dynamics, and inflammatory gene expressionKearns JD, Basak S, Werner SL, Huang CS, Hoffmann A.
J Cell Biol. 2006 Jun 5;173(5):659-64. Epub 2006 May 30.
 Circuitry of nuclear factor kappaB signalingHoffmann A, Baltimore D.
Immunol Rev. 2006 Apr;210:171-86. Review.
 Transient IκB kinase activity mediates temporal NF-κB dynamics in response to a wide range of tumor necrosis factor-alpha dosesCheong R, Bergmann A, Werner SL, Regal J, Hoffmann A, Levchenko A.
J Biol Chem. 2006 Feb 3;281(5):2945-50. Epub 2005 Dec 1.
 Stimulus specificity of gene expression programs determined by temporal control of IKK activityWerner SL*, Barken D*, Hoffmann A.
Science. 2005 Sep 16;309(5742):1857-61.
 Comment on "Oscillations in NF-κB signaling control the dynamics of gene expression"Barken D, Wang CJ, Kearns J, Cheong R, Hoffmann A, Levchenko A.
Science. 2005 Apr 1;308(5718):52; author reply 52. No abstract available.
 The IκB-NF-κB signaling module: temporal control and selective gene activationHoffmann A, Levchenko A, Scott ML, Baltimore D.
Science. 2002 Nov 8;298(5596):1241-5.

NFkB Signaling - in Lymphoid cells

A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell DifferentiationRoy, K., Mitchell, S., Liu, Y., Ohta, S.,Lin, Y., Metzig, M.O., Nutt, S.L., Hoffmann, A.
Immunity. 2019 Mar 5.
 Identifying Noise Sources governing cell-to-cell variabilityMitchell, S., Hoffmann, A
Current Opinion in Systems Biology, 8, pp.39-45
 Nongenetic origins of cell-to-cell variability in B lymphocyte proliferationMitchell, S., Roy, K., Zangle, T.A., Hoffmann, A
Proc. Natl. Acad. Sci. USA,115.12 (2018): E2888-E2897.
 Deriving Quantitative Cell Biological Information from Dye-Dilution Lymphocyte Proliferation ExperimentsRoy, K., Shokhirev, M.N., Mitchell, S., Hoffmann, A
Methods Mol Biol. 1707:81-94.
 Oscillation dynamics underlie functional switching of NFkB for B-cell activation. Inoue, K., Shinohara, H., Behar, M., Yumoto, N., Tanaka, G., Hoffmann, A., Aihara, K., Okada-Hatakeyama, M.
Systems Biology and Applications, 2, 16024.
 A miR-155-Peli1-cRel pathway controls the generation and function of T follicular helper cellsLiu, W.H., Kang, S.G., Huang, Z., Wu, C.J., Jin, H.Y., Maine, C.J., Liu, Y., Shepherd, J., Sabouri-Ghomi, M., Gonzalez-Martin, A., Xu, S., Hoffmann, A., Zheng, Y., Lu, L.F., Xiao, N., Fu., G., Xiao, C.
J. Ex. Med. 213, pp.1901-19
 B-cell survival and development controlled by the coordination of NF-κB family members RelB and cRelAlmaden JV*, Liu YC*, Yang E, Otero DC, Birnbaum H, Davis-Turak J, Asagiri M, David M, Goldrath AW, Hoffmann, A.
Blood (2016) Mar 10; 127. doi: 10.1182/blood-2014-10-606988
 A multi-scale approach reveals that NF-κB cRel enforces a B-cell decision to divideShokhirev, M.N., Almaden, J., Davis‐Turak, J., Birnbaum, H.A., Russell, T.M., Vargas, J.A.D., Hoffmann, A.
Molecular Systems Biology (2015) 11: 783. DOI 10.15252/msb.20145554
 A pathway switch directs BAFF signaling to distinct NFκB transcription factors in maturing and proliferating B cells.Almaden, J., Tsui. J., Liu, Y.C., Birnbaum, H., Shokhirev, M.N., Ngo, K.A., Davis-Turak, J., Otero, D., Basak, S., Rickert, R., Hoffmann, A.
Cell Reports, 9, pp.2098-111. PMID: 25497099
 Positive feedback within a kinase signaling complex functions as a switch mechanism for NF-κB activationShinohara, H.*, Behar, M.*, Inoue, K., Hiroshima, M., Yasuda, T., Nagashima, T., Kmura, S., Sanjo, H., Maeda, S., Yumoto, N., Ki, S., Sako, Y., Hoffmann , A.+, Kurosaki, T.+, Okada-Hatakeyama, M.+
Science, 344, pp.760-764, PMID: 24833394
 IκBε is a key regulator of B-cell expansion by providing negative feedback on cRel and RelA in a stimulus-specific mannerAlves, B.N., Tsui, R., Almaden, J., Shokhirev, M.N., Davis-Turak, J., Fujimoto, J., Birnbaum, H., Ponomarenko, J., Hoffmann, A.
J. Immunol., 192, pp.3121-32. PMID: 24591377, PMC3965642
 FlowMax: a computational tool for maximum likelihood deconvolution of CFSE time courses.Shokhirev, M.N., Hoffmann, A.
PLOS ONE, 8, e67620
 NF-κB–inducing kinase plays an essential T cell–intrinsic role in graft-versus-host disease and lethal autoimmunity in miceMurray SE, Polesso F, Rowe AM, Basak S, Koguchi Y, Toren KG, Hoffmann A, Parker DC.
J Clin Invest. 2011 Dec;121(12):4775-86
 Nuclear export of the NF-κB inhibitor IκBα is required for proper B cell and secondary lymphoid tissue formationWuerzberger-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.
Immunity. 2011 Feb 25;34(2):188-200. Epub 2011 Feb 17. Erratum in: Immunity. 2011 Mar 25;34(3):449.
 Antigen-mediated T cell expansion regulated by parallel pathways of deathCh'en IL, Beisner DR, Degterev A, Lynch C, Yuan J, Hoffmann A, Hedrick SM.
Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17463-8. Epub 2008 Nov 3.
 Crosstalk via the NF-κB signaling systemBasak S, Hoffmann A.
Cytokine Growth Factor Rev. 2008 Jun-Aug;19(3-4):187-97. Epub 2008 Jun 2. Review.
 Coordination between NF-κB family members p50 and p52 is essential for mediating LTΒβR signals in the development and organization of secondary lymphoid tissuesLo JC, Basak S, James ES, Quiambo RS, Kinsella MC, Alegre ML, Weih F, Franzoso G, Hoffmann A, Fu YX.
Blood. 2006 Feb 1;107(3):1048-55. Epub 2005 Sep 29.
 Unique CD40-mediated biological program in B cell activation requires both type 1 and type 2 NF-κB activation pathwaysZarnegar B, He JQ, Oganesyan G, Hoffmann A, Baltimore D, Cheng G.
Proc Natl Acad Sci U S A. 2004 May 25;101(21):8108-13. Epub 2004 May 17.
 Cooperation of multiple signaling pathways in CD40-regulated gene expression in B lymphocytesDadgostar H, Zarnegar B, Hoffmann A, Qin XF, Truong U, Rao G, Baltimore D, Cheng G.
Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1497-502.

NFkB Signaling - in Myeloid cells

Immune Response Signaling: Combinatorial and Dynamic ControlHoffmann, A.
Trends Immunol. 2016 Sep;37(9):570-2
 Distinct Single Cell Signaling Characteristics Conferred by the MyD88 and TRIF Pathways in TLR4 Activation.Cheng, Z*., Taylor, B.*, Ourthiague, D.N., Hoffmann, A.
Science Signaling (2015) Jul 14; 8(385):ra69. doi: 10.1126/scisignal.aaa5208
 Network dynamics determine the autocrine and paracrine signaling functions of TNFCaldwell, A.B., Cheng, Z., Vargas, J.D., Birnbaum, H.A., Hoffmann, A.
Genes and Development, 2014. 28: 2120-2133
 Crosstalk-between Aryl Hydrocarbon Receptor and the inflammatory responses: a role for NFκBVogel, C.F.A, Kahn, E.M., Leung, P.S.C., Gershwin, M.E., Chang, W.L.W., Wu, D., Haarmann-Sternmann, T., Hoffmann, A., Denison, M.S
J. Biological Chemistry, 289, pp.1866-1875. PMID: 24302727, PMC3894361
 Control of RelB during dendritic cell activation integrates canonical and non-canonical NFκB pathwaysShih, V.F.-S., Davis-Turak, J., Macal, M., Huang, J.Q., Ponomarenko, J., Kearns, J.D., Yu, T., Fagerlund, R., Asagiri, M., Zuniga, E.I., Hoffmann, A.
Nature Immunology, 2012 Dec;13(12):1162-70.
 Crosstalk via the NF-κB signaling systemBasak S, Hoffmann A.
Cytokine Growth Factor Rev. 2008 Jun-Aug;19(3-4):187-97. Epub 2008 Jun 2. Review.
 Negative regulation of constitutive NF-κB and JNK signaling by PKN1-mediated phosphorylation of TRAF1Kato T Jr, Gotoh Y, Hoffmann A, Ono Y.
Genes Cells. 2008 May;13(5):509-20.
 Signaling pathways and genes that inhibit pathogen-induced macrophage apoptosis--CREB and NF-κB as key regulatorsPark JM, Greten FR, Wong A, Westrick RJ, Arthur JS, Otsu K, Hoffmann A, Montminy M, Karin M.
Immunity. 2005 Sep;23(3):319-29.
 Cutting edge: innate immunity conferred by B cells is regulated by caspase-8Beisner DR, Ch'en IL, Kolla RV, Hoffmann A, Hedrick SM.
J Immunol. 2005 Sep 15;175(6):3469-73.
 Induction of NR4A orphan nuclear receptor expression in macrophages in response to inflammatory stimuliPei L, Castrillo A, Chen M, Hoffmann A, Tontonoz P.
J Biol Chem. 2005 Aug 12;280(32):29256-62. Epub 2005 Jun 17.
 Subcytocidal attack by staphylococcal alpha-toxin activates NF-κB and induces interleukin-8 productionDragneva Y, Anuradha CD, Valeva A, Hoffmann A, Bhakdi S, Husmann M.
Infect Immun. 2001 Apr;69(4):2630-5.

NFkB Signaling - in Disease

Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responsesAdelaja, A., Taylor, B., Sheu, K.M., Liu, Y., Luecke, S., Hoffmann, A.
Immunity. 11 May 2021
 The Reg-gamma-proteasome forms a regulatory circuit with IkBe and NFkB in experimental colitisXu, J., Zhou, L., Ji, L., Chen, F., Fortmann, K., Zhang, K., Liu, Q., Li, K., Wang, W., Wamg, H., Xie, W., Wang, Q., Liu, J., Zheng, B., Zhang, P., Huang, S., Shi, T., Zhang, B., Dang, Y., Chen, J., O'Malley, B.W., Moses, R.E., Wang, P., Li, L., Xiao, J., Hoffmann, A.*, Li, X.*
Nature Commun. 7, 10761
 The REGγ-proteasome forms a regulatory circuit with IκBɛ and NFκB in experimental colitisXu 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.
Nat Commun. (2016) Feb 22;7:10761. doi: 10.1038/ncomms10761
 Regulation and Function of the Caspase-1 in an Inflammatory Microenvironment.Lee, D.-J., Du, F., Chen, S.-W., Nakasako, M., Rana, I., Shih, V. F.-S., Hoffmann, A., Jamora, C.
J. Investigative Dermatology, in press PMID: 25815426
 The Dynamics of Signaling as a Pharmacological TargetBehar, M., Barken, D., Werner, S.L., Hoffmann, A
Cell, 155, pp.448-461
 Ex Vivo Innate Immune Cytokine Signature of Enhanced Risk of Relapsing BrucellosisFeldman, K., E., Loriaux, P.M., Saito, M., Tuero, I., Villaverde, H., Siva, T., Gotuzzo, E., Gilman, R.H., Vinetz, J.M., Hoffmann, A.
PLOS Neglected Tropical Diseases, 7:e2424
 Chromatin-bound IκBα regulates a subset of plycomb-target genes in differentiation and cancerMulero, M.C., Ferres-Marco, D., Islam, A., Margalef, P., Pecoraro, M., Toll, A., Drechsel, N., Charneco, C., Davis, S., Bellora, N., Gallardo, F., Lopez-Arribillaga, E., Asensio, E., Rodilla, V., Gonzalez, J., Iglesias, M., Shoh, V., Alba, M., Dr Croce, L., Hoffmann, A., Miyamoto, S., Villa-Feixa, J., Lopez-Bigas, N., Keyes, W.M., Dominguez, M., Bigas, A., Espinosa, L.
Cancer Cell, 24, pp.151-66
 Fbxw7α- and GSK3-mediated degradation of p100 is a pro-survival mechanism in multiple myeloma.Busino, L., Millman, S.E., Scotto, L., Kyratsous, C.A., Basrur, V., O’Connor, O., Hoffmann, A., Elenitoba-Johnson, K.S., Pagano, M.
Nat Cell Biol. 14, pp.375-85.
 NF-κB potentiates caspase independent hydrogen peroxide induced cell deathHo JQ, Asagiri M, Hoffmann A, Ghosh G.
PLoS One. 2011 Feb 15;6(2):e16815.
 IκBbeta acts to inhibit and activate gene expression during the inflammatory responseRao P, Hayden MS, Long M, Scott ML, West AP, Zhang D, Oeckinghaus A, Lynch C, Hoffmann A, Baltimore D, Ghosh S.
Nature. 2010 Aug 26;466(7310):1115-9.
 Defective regulation of CXCR2 facilitates neutrophil release from bone marrow causing spontaneous inflammation in severely NF-kappa B-deficient micevon Vietinghoff S, Asagiri M, Azar D, Hoffmann A, Ley K.
J Immunol. 2010 Jul 1;185(1):670-8. Epub 2010 Jun 2.
 Differential activation and antagonistic function of HIF-α isoforms in macrophages are essential for NO homeostasisTakeda N, O'Dea EL, Doedens A, Kim JW, Weidemann A, Stockmann C, Asagiri M, Simon MC, Hoffmann A, Johnson RS.
Genes Dev. 2010 Mar 1;24(5):491-501.
 NF-κB as a determinant of distinct cell death pathwaysCh'en IL, Hedrick SM, Hoffmann A.
Methods Enzymol. 2008;446:175-87.
 Inflammatory tales of liver cancerHoffmann A, Xia Y, Verma IM.
Cancer Cell. 2007 Feb;11(2):99-101.
 Coordination between NF-κB family members p50 and p52 is essential for mediating LTΒβR signals in the development and organization of secondary lymphoid tissuesLo JC, Basak S, James ES, Quiambo RS, Kinsella MC, Alegre ML, Weih F, Franzoso G, Hoffmann A, Fu YX.
Blood. 2006 Feb 1;107(3):1048-55. Epub 2005 Sep 29.
 Immortalized fibroblasts from NF-κB RelA knockout mice show phenotypic heterogeneity and maintain increased sensitivity to tumor necrosis factor alpha after transformation by v-RasGapuzan ME, Schmah O, Pollock AD, Hoffmann A, Gilmore TD.
Oncogene. 2005 Sep 29;24(43):6574-83.
 Initiation and termination of NF-κB signaling by the intracellular protozoan parasite Toxoplasma gondiiShapira S, Harb OS, Margarit J, Matrajt M, Han J, Hoffmann A, Freedman B, May MJ, Roos DS, Hunter CA.
J Cell Sci. 2005 Aug 1;118(Pt 15):3501-8.
 Double-stranded RNA-dependent protein kinase (pkr) is essential for thermotolerance, accumulation of HSP70, and stabilization of ARE-containing HSP70 mRNA during stressZhao M, Tang D, Lechpammer S, Hoffmann A, Asea A, Stevenson MA, Calderwood SK.
J Biol Chem. 2002 Nov 15;277(46):44539-47. Epub 2002 Aug 30
 Subcytocidal attack by staphylococcal alpha-toxin activates NF-κB and induces interleukin-8 productionDragneva Y, Anuradha CD, Valeva A, Hoffmann A, Bhakdi S, Husmann M.
Infect Immun. 2001 Apr;69(4):2630-5.
 Regulation of IL-6 and IL-8 expression in rheumatoid arthritis synovial fibroblasts: the dominant role for NF-kappa B but not C/EBP beta or c-JunGeorganas C, Liu H, Perlman H, Hoffmann A, Thimmapaya B, Pope RM.
J Immunol. 2000 Dec 15;165(12):7199-206.
 Suppression of steady-state, but not stimulus-induced NF-κB activity inhibits alphavirus-induced apoptosisLin KI, DiDonato JA, Hoffmann A, Hardwick JM, Ratan RR.
J Cell Biol. 1998 Jun 29;141(7):1479-87.

Gene Expression - by NFkB

Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responsesAdelaja, A., Taylor, B., Sheu, K.M., Liu, Y., Luecke, S., Hoffmann, A.
Immunity. 11 May 2021
 High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial CellsKishimoto, K., Wilder, C.L., Buchanan, J., Nguyen, M., Okeke, C., Hoffmann, A., Cheng, Q.J.
Front Immunol., 9 April 2021
 NFκB dynamics determine the stimulus-specificity of epigenomic reprogramming in macrophageCheng, Q.J., Ohta, S., Sheu, K.M., Spreafico, R., Adelaja, A., Taylor, B., Hoffmann, A.
bioRxiv., 19 Feb 19 2020
 Dissecting the Regulatory Strategies of NFκB RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation LogicsNgo, K.A., Kishimoto, K., Davis-Turak, J., Pimplaskar, A., Cheng, Z., Spreafico, R., Chen, E.Y., Tam, A., Ghosh, G., Mitchell, S., Hoffmann, A.
Cell Rep., 25 Feb 2020; 30:2758-2775.
 Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene ExpressionSen, S., Cheng, Z., Sheu, K.M., Chen, Y., Hoffmann, A.
Cell syst., 22 Jan 2020; 10:1-14
 Stimulus-specificity in the responses of immune sentinel cellsSheu, K.M., Luecke, S., Hoffmann, A.
Current Opinions in Systems Biology, 18, pp.53-61
 Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms.Cheng CS, Behar MS, Suryawanshi GW, Feldman KE, Spreafico R, Hoffmann A.
Cell Syst. 2017 Mar 22;4(3):330-343.e5
 Analysis of the RelA:CBP/p300 interaction reveals its involvement in NFκB-driven transcriptionMukherjee, S.P., Behar, M., Birnbaum, H.A, Hoffmann, A., Wright, P.E., Ghosh, G.
PLOS Biology, 11:e1001647
 Chromatin-bound IκBα regulates a subset of plycomb-target genes in differentiation and cancerMulero, M.C., Ferres-Marco, D., Islam, A., Margalef, P., Pecoraro, M., Toll, A., Drechsel, N., Charneco, C., Davis, S., Bellora, N., Gallardo, F., Lopez-Arribillaga, E., Asensio, E., Rodilla, V., Gonzalez, J., Iglesias, M., Shoh, V., Alba, M., Dr Croce, L., Hoffmann, A., Miyamoto, S., Villa-Feixa, J., Lopez-Bigas, N., Keyes, W.M., Dominguez, M., Bigas, A., Espinosa, L.
Cancer Cell, 24, pp.151-66
 The transcriptional specificity of NF-κB dimers is coded within the kB DNA response elementsWang, V.Y.-F., Huang, W., Asagiri, M., Spann, N., Hoffmann, A., Glass, C.K, Ghosh, G.
Cell Reports, 2, pp.824-839.
 Mechanisms establishing TLR4-responsive activation states of inflammatory response genesEscoubet-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.
PLOS Genet. 2011 Dec;7(12):e1002401
 The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50Cheng CS, Feldman KE, Lee J, Verma S, Huang DB, Huynh K, Chang M, Ponomarenko JV, Sun SC, Benedict CA, Ghosh G, Hoffmann A.
Sci Signal. 2011 Feb 22;4(161):ra11.
 Transcriptional regulation via the NF-κB signaling moduleHoffmann A, Natoli G, Ghosh G.
Oncogene. 2006 Oct 30;25(51):6706-16. Review.
 Stimulus specificity of gene expression programs determined by temporal control of IKK activityWerner SL*, Barken D*, Hoffmann A.
Science. 2005 Sep 16;309(5742):1857-61.
 A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activationSanjabi S, Williams KJ, Saccani S, Zhou L, Hoffmann A, Ghosh G, Gerondakis S, Natoli G, Smale ST.
Genes Dev. 2005 Sep 15;19(18):2138-51.
 Molecular determinants of crosstalk between nuclear receptors and toll-like receptorsOgawa S, Lozach J, Benner C, Pascual G, Tangirala RK, Westin S, Hoffmann A, Subramaniam S, David M, Rosenfeld MG, Glass CK.
Cell. 2005 Sep 9;122(5):707-21.
 One nucleotide in a kappaB site can determine cofactor specificity for NF-κB dimersLeung TH, Hoffmann A, Baltimore D.
Cell. 2004 Aug 20;118(4):453-64.
 Genetic analysis of NF-κB/Rel transcription factors defines functional specificitiesHoffmann A, Leung TH, Baltimore D.
EMBO J. 2003 Oct 15;22(20):5530-9.
 Nucleosome remodeling at the IL-12 p40 promoter is a TLR-dependent, Rel-independent eventWeinmann AS, Mitchell DM, Sanjabi S, Bradley MN, Hoffmann A, Liou HC, Smale ST.
Nat Immunol. 2001 Jan;2(1):51-7.
 Regulation of IL-6 and IL-8 expression in rheumatoid arthritis synovial fibroblasts: the dominant role for NF-kappa B but not C/EBP beta or c-JunGeorganas C, Liu H, Perlman H, Hoffmann A, Thimmapaya B, Pope RM.
J Immunol. 2000 Dec 15;165(12):7199-206.
 LBP-p40 binds DNA tightly through associations with histones H2A. H2B, and H4.Kinoshita K, Kaneda Y, Sato M, Saeki Y, Wataya-Kaneda M, Hoffmann A, Kaneda Y.
Biophys. Biochem. Res. Commun. 1998. 253, pp. 277-282.

Gene Expression - in immunity

High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial CellsKishimoto, K., Wilder, C.L., Buchanan, J., Nguyen, M., Okeke, C., Hoffmann, A., Cheng, Q.J.
Front Immunol., 9 April 2021
 NFκB dynamics determine the stimulus-specificity of epigenomic reprogramming in macrophageCheng, Q.J., Ohta, S., Sheu, K.M., Spreafico, R., Adelaja, A., Taylor, B., Hoffmann, A.
bioRxiv., 19 Feb 19 2020
 Dissecting the Regulatory Strategies of NFκB RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation LogicsNgo, K.A., Kishimoto, K., Davis-Turak, J., Pimplaskar, A., Cheng, Z., Spreafico, R., Chen, E.Y., Tam, A., Ghosh, G., Mitchell, S., Hoffmann, A.
Cell Rep., 25 Feb 2020; 30:2758-2775.
 Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene ExpressionSen, S., Cheng, Z., Sheu, K.M., Chen, Y., Hoffmann, A.
Cell syst., 22 Jan 2020; 10:1-14
 Stimulus-specificity in the responses of immune sentinel cellsSheu, K.M., Luecke, S., Hoffmann, A.
Current Opinions in Systems Biology, 18, pp.53-61
 Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functionsCheng, Q., Behzadi, F., Sen, S., Ohta, S., Spreafico, R., Teles, R., Modlin, R.L., Hoffmann, A.
Scientific reports 9.1 (2019): 5288.
 Immune Response Signaling: Combinatorial and Dynamic ControlHoffmann, A.
Trends Immunol. 2016 Sep;37(9):570-2
 A pathway switch directs BAFF signaling to distinct NFκB transcription factors in maturing and proliferating B cells.Almaden, J., Tsui. J., Liu, Y.C., Birnbaum, H., Shokhirev, M.N., Ngo, K.A., Davis-Turak, J., Otero, D., Basak, S., Rickert, R., Hoffmann, A.
Cell Reports, 9, pp.2098-111. PMID: 25497099
 Crosstalk-between Aryl Hydrocarbon Receptor and the inflammatory responses: a role for NFκBVogel, C.F.A, Kahn, E.M., Leung, P.S.C., Gershwin, M.E., Chang, W.L.W., Wu, D., Haarmann-Sternmann, T., Hoffmann, A., Denison, M.S
J. Biological Chemistry, 289, pp.1866-1875. PMID: 24302727, PMC3894361
 Mechanisms establishing TLR4-responsive activation states of inflammatory response genesEscoubet-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.
PLOS Genet. 2011 Dec;7(12):e1002401
 The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50Cheng CS, Feldman KE, Lee J, Verma S, Huang DB, Huynh K, Chang M, Ponomarenko JV, Sun SC, Benedict CA, Ghosh G, Hoffmann A.
Sci Signal. 2011 Feb 22;4(161):ra11.
 A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodelingRamirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST.
Cell. 2009 Jul 10;138(1):114-28.
 Epigenetic control: slow and global, nimble and localCheng CS, Johnson TL, Hoffmann A.
Genes Dev. 2008 May 1;22(9):1110-4.
 Signaling pathways and genes that inhibit pathogen-induced macrophage apoptosis--CREB and NF-κB as key regulatorsPark JM, Greten FR, Wong A, Westrick RJ, Arthur JS, Otsu K, Hoffmann A, Montminy M, Karin M.
Immunity. 2005 Sep;23(3):319-29.
 Molecular determinants of crosstalk between nuclear receptors and toll-like receptorsOgawa S, Lozach J, Benner C, Pascual G, Tangirala RK, Westin S, Hoffmann A, Subramaniam S, David M, Rosenfeld MG, Glass CK.
Cell. 2005 Sep 9;122(5):707-21.
 Subcytocidal attack by staphylococcal alpha-toxin activates NF-κB and induces interleukin-8 productionDragneva Y, Anuradha CD, Valeva A, Hoffmann A, Bhakdi S, Husmann M.
Infect Immun. 2001 Apr;69(4):2630-5.
 Regulation of IL-6 and IL-8 expression in rheumatoid arthritis synovial fibroblasts: the dominant role for NF-kappa B but not C/EBP beta or c-JunGeorganas C, Liu H, Perlman H, Hoffmann A, Thimmapaya B, Pope RM.
J Immunol. 2000 Dec 15;165(12):7199-206.

Gene Expression - transcription and splicing

High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial CellsKishimoto, K., Wilder, C.L., Buchanan, J., Nguyen, M., Okeke, C., Hoffmann, A., Cheng, Q.J.
Front Immunol., 9 April 2021
 Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms.Cheng CS, Behar MS, Suryawanshi GW, Feldman KE, Spreafico R, Hoffmann A.
Cell Syst. 2017 Mar 22;4(3):330-343.e5
 Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing.Davis-Turak JC, Allison K, Shokhirev MN, Ponomarenko P, Tsimring LS, Glass CK, Johnson TL, Hoffmann A.
Nucleic Acids Res. 2015 Jan 30;43(2):699-707. doi: 10.1093/nar/gku1338. PubMed PMID: 25541195.

Gene Expression - core promoter fundamentals

High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial CellsKishimoto, K., Wilder, C.L., Buchanan, J., Nguyen, M., Okeke, C., Hoffmann, A., Cheng, Q.J.
Front Immunol., 9 April 2021
 Dissecting the Regulatory Strategies of NFκB RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation LogicsNgo, K.A., Kishimoto, K., Davis-Turak, J., Pimplaskar, A., Cheng, Z., Spreafico, R., Chen, E.Y., Tam, A., Ghosh, G., Mitchell, S., Hoffmann, A.
Cell Rep., 25 Feb 2020; 30:2758-2775.
 Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells.Mognol GP, Spreafico R, Wong V, Scott-Browne JP, Togher S, Hoffmann A, Hogan PG, Rao A, Trifari S.
Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2776-E2785
 Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms.Cheng CS, Behar MS, Suryawanshi GW, Feldman KE, Spreafico R, Hoffmann A.
Cell Syst. 2017 Mar 22;4(3):330-343.e5
 Mitotic regulation of TFIID: Inhibition of activator-dependent transcription and changes in sub-cellular localizationSegil N, Guermah M, Hoffmann A, Roeder RG, Heintz N.
Genes & Development 1996. 10, pp. 2389-2400.
 Cloning and characterization of human TAF20/15: multiple interactions suggest a central role in TFIID complex formation.Hoffmann A and Roeder RG.
J. Biol. Chem. 1996. 271, pp. 18194-18202.
 Crystal structure of a human TATA box-binding protein/TATA element complex.Nikolov DB, Chen H, Halay ED, Hoffmann A, Roeder RG, Burley SK.
Proc. Natl. Acad. Sci. 1996. USA 93, pp. 4862-4867.
 A histone octamer-like structure within TFIID.Hoffmann A, Chiang CM, Oelgeschlager T, Burley SK, Nakatani Y, Roeder RG.
Nature 1996. 380, No.6572, pp. 356-359.
 Structural similarity between TAFs and the heterotetrameric core of the histone octamer.Xie XL, Kokubo T, Cohen S, Mirza UA, Hoffmann A, Chait BT, Roeder RG, Nakatani Y, Burley SK.
Nature 1996. 380, No.6572, pp. 316-322.
 Unique TATA-binding protein-containing complexes and cofactors involved in transcription by RNA polymerases II and IIIChiang CM, Ge H, Wang Z, Hoffmann A, Roeder RG.
EMBO J. 1993. 12, pp. 2749-2762.
 Identification of human TFIID components and direct interaction between a 250-kDa polypeptide and the TATA box-binding protein (TFIIDt)Takada R, Nakatani Y, Hoffmann A, Kokubo T, Hasegawa S, Roeder RG, Horikoshi M.
Proc. Natl. Acad. Sci. 1992. USA 89, pp. 11809-11813.
 Crystal structure of TFIID TATA-box binding proteinNikolov DB, Hu SH, Lin J, Gasch A, Hoffmann A, Horikoshi M, Chua NH, Roeder RG, Burley SK.
Nature 1992. 360, pp. 40-46.
 Structural motifs and potential homologies in the large subunit of human general transcription factor TFIIEOhkuma Y, Sumimoto H, Hoffmann A, Shimazaki S, Horikoshi M, Roeder RG.
Nature 1991. 354, pp. 398-401.
 Purification of his-tagged proteins in non-denaturing conditions suggests a convenient method for protein interaction studies.Hoffmann , Roeder RG.
Nucleic Acids Research 1991. 19, No.22, pp. 6337-6338.
 Striking homology of the 'variable' N-terminal as well as the 'conserved core' domains of the mouse and human TATA-factors (TFIID).Tamura, T., Sumita, K., Fujino, I., Aoyama, A., Horikoshi, M., Hoffmann, A., Roeder, R.G., Mikoshiba, K. 1991.
Nucleic Acids Research 1991. 19, No.14, pp. 3861-3865.
 Arabidopsis thaliana contains two genes for TFIIDGasch A, Hoffmann A, Horikoshi M, Roeder RG, Chua NH.
Nature 1990. 346, No.6282, pp.390-394.
 Highly conserved core domain and unique N-terminus with presumptive regulatory motifs in a human TATA factor (TFIID)Hoffmann A, Sinn E, Yamamoto T, Wang J, Roy A, Horikoshi M, Roeder RG.
Nature 1990. 346, No.6282, pp.387-390.
 Cloning of the Schizosaccharomyces pombe TFIID gene reveals a strong conservation of functional domains present in Saccharomyces cerevisiae TFIIDHoffmann A, Horikoshi M, Wang CK, Schroeder S, Weil PA, Roeder RG.
Genes & Development 1990. 4, pp. 1141-1148.

IRF Signaling - fundamentals

Limited specificity of IRF3 and ISGF3 in the transcriptional innate –immune response to double –stranded RNA.Ourthiague, D.N., Birnbaum H., Ortenlöf, N., Vargas, J.D., Wollman , R., Hoffmann, A.
Journal of Leukocyte Biology (2015) 98, pp.119-28. PMID: 25896227
 MAP kinase p38α regulates type III interferon (IFN-λ1) gene expression in human monocyte-derived dendritic cells in response to RNA stimulation.Jiang M, Osterlund P, Fagerlund R, Rios DN, Hoffmann A, Poranen MM, Bamford DH, Julkunen I.
J Leukoc Biol. 2015 Feb;97(2):307-20. doi: 10.1189/jlb.2A0114-059RR. Epub 2014 Dec 3. PubMed PMID: 25473098.

HIV and Infectious Disease Modeling

Identifying determinants of persistent MRSA bacteremia using mathematical modelingMikkaichi, T., Yeaman, M.R., Hoffmann, A., MRSA Systems Immunobiology Group
PLoS Comput Biol. 2019 Jul; 15(7): e1007087
 A stochastic spatio-temporal (SST) model to study cell-to-cell variability in HIV-1 infectionCheng Z, Hoffmann, A.
J Theor Biol. (2016) Apr 21; 395:87-96. doi: 10.1016/j.jtbi.2016.02.001
 A multi-scale mathematical modeling framework to investigate anti-viral therapeutic opportunities in targeting HIV-1 accessory proteinsGajendra W. Suryawanshi and Alexander Hoffmann
J. Theor. Biol. 386 (2015) 89-104. doi:10.1016/j.jtbi.2015.08.032
 Ex Vivo Innate Immune Cytokine Signature of Enhanced Risk of Relapsing BrucellosisFeldman, K., E., Loriaux, P.M., Saito, M., Tuero, I., Villaverde, H., Siva, T., Gotuzzo, E., Gilman, R.H., Vinetz, J.M., Hoffmann, A.
PLOS Neglected Tropical Diseases, 7:e2424

Theory - Software

Quantifying information accumulation encoded in the dynamics of biochemical signalingTang, Y., Adelaja, A., Ye, F., Deeds, E., Wollman, R., Hoffmann, A.
Nature Communications volume 12, Article number: 1272 (2021)
 Deriving Quantitative Cell Biological Information from Dye-Dilution Lymphocyte Proliferation ExperimentsRoy, K., Shokhirev, M.N., Mitchell, S., Hoffmann, A
Methods Mol Biol. 1707:81-94.
 Addressing the digital divide in contemporary biology: Lessons from teaching UNIXMangul, S., Martin, L., Hoffmann, A., Pellegrini, M., Eskin, E.
BioRxiv
 Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing.Davis-Turak JC, Allison K, Shokhirev MN, Ponomarenko P, Tsimring LS, Glass CK, Johnson TL, Hoffmann A.
Nucleic Acids Res. 2015 Jan 30;43(2):699-707. doi: 10.1093/nar/gku1338. PubMed PMID: 25541195.
 FlowMax: a computational tool for maximum likelihood deconvolution of CFSE time courses.Shokhirev, M.N., Hoffmann, A.
PLOS ONE, 8, e67620
 A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways Loriaux, P., Hoffmann, A.
PLOS Comput Biol. 2013 February; 9(2): e1002932.
 Characterizing the Relationship Between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action ModelsLoriaux, P., Tesler, G., Hoffmann, A.
PLOS Comput Biol. 2013 February; 9(2): e1002901.
 A framework for modeling the relationship between cellular steady-state and stimulus-responsivenessLoriaux, P. Hoffmann, A
Methods Cell Biol. 2012;110:81-109

Other

Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremiaChang, Y., Rossetti, M., Gjertson, D.W., Rubbi, L., Thompson, M., Montoya, D.J., Morselli, M., Ruffin, F., Hoffmann, A., Pellegrini, M., Fowler, V.G., yeaman, M.R., Reed, E.F.
PNAS March 9, 2021 118 (10) e2000663118
 Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells.Mognol GP, Spreafico R, Wong V, Scott-Browne JP, Togher S, Hoffmann A, Hogan PG, Rao A, Trifari S.
Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2776-E2785
 Functional importance of stripping in NFκB signaling revealed by a stripping-impaired IκBα mutant.Dembinski, HE. Wismer, K., Vargas JD., Suryawanshi, GW., Kern, N., Kroon, G., Dyson, HJ., Hoffmann, A., Komives, EA.
Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):1916-1921.
 Addressing the digital divide in contemporary biology: Lessons from teaching UNIXMangul, S., Martin, L., Hoffmann, A., Pellegrini, M., Eskin, E.
BioRxiv
 Early Cytokine Signatures of Ischemia Reperfusion Injury in Human Orthotopic Liver TransplantationSosa, R., Zarrinpar, A., Rossetti, M., Lassman, C., Naini, B., Datta, N., Rao, P., Harre, N., Zheng, Y., Spreafico, R., Hoffmann, A., Busuttil, R., Gjertson, D., Zhai, Y., Kupiec-Weglinski, J.W., Reed., E.
Journal of Clinical Immunology Insight, 1(20):e89679.
 Training the 21st Century Immunologist.Spreafico, R., Mitchell, S., Hoffmann, A.
Trends in Immunology, 1280, pp.647-61. PMID: 25736777
 Ex Vivo Innate Immune Cytokine Signature of Enhanced Risk of Relapsing BrucellosisFeldman, K., E., Loriaux, P.M., Saito, M., Tuero, I., Villaverde, H., Siva, T., Gotuzzo, E., Gilman, R.H., Vinetz, J.M., Hoffmann, A.
PLOS Neglected Tropical Diseases, 7:e2424
 Paternal RLIM/Rnf12 is a survival factor for milk-producing alveolar cellsJiao, B., Ma, H., Shokhirev, M., Drung, A., Yang, Q, Shin, J., Lu, S., Byron, M., Kalantry, S. Mercurio, A.M., Lawrence, J.B., Hoffmann, A., Bach, I.
Cell, 149, pp.630-641, 2012
 Differential activation and antagonistic function of HIF-α isoforms in macrophages are essential for NO homeostasisTakeda N, O'Dea EL, Doedens A, Kim JW, Weidemann A, Stockmann C, Asagiri M, Simon MC, Hoffmann A, Johnson RS.
Genes Dev. 2010 Mar 1;24(5):491-501.
 Coherent activation of a synthetic mammalian gene networkLongo DM, Hoffmann A, Tsimring LS, Hasty J.
Syst Synth Biol. 2010 Mar;4(1):15-23.
 Antigen-mediated T cell expansion regulated by parallel pathways of deathCh'en IL, Beisner DR, Degterev A, Lynch C, Yuan J, Hoffmann A, Hedrick SM.
Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17463-8. Epub 2008 Nov 3.
 Cutting edge: innate immunity conferred by B cells is regulated by caspase-8Beisner DR, Ch'en IL, Kolla RV, Hoffmann A, Hedrick SM.
J Immunol. 2005 Sep 15;175(6):3469-73.
 Induction of NR4A orphan nuclear receptor expression in macrophages in response to inflammatory stimuliPei L, Castrillo A, Chen M, Hoffmann A, Tontonoz P.
J Biol Chem. 2005 Aug 12;280(32):29256-62. Epub 2005 Jun 17.
 Selective requirement for c-Rel during IL-12 P40 gene induction in macrophagesSanjabi S, Hoffmann A, Liou HC, Baltimore D, Smale ST.
Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12705-10.
 LBP-p40 binds DNA tightly through associations with histones H2A. H2B, and H4.Kinoshita K, Kaneda Y, Sato M, Saeki Y, Wataya-Kaneda M, Hoffmann A, Kaneda Y.
Biophys. Biochem. Res. Commun. 1998. 253, pp. 277-282.
 Human autoantibody to topoisomerase IIHoffmann A, Heck MMS, Bordwell BJ, Rothfield NF, Earnshaw WC
Exp. Cell Res. 1989. 180, pp. 409-418.

Reviews

Stimulus-specificity in the responses of immune sentinel cellsSheu, K.M., Luecke, S., Hoffmann, A.
Current Opinions in Systems Biology, 18, pp.53-61
 Signaling crosstalk mechanisms that may fine-tune pathogen-receptive NFκBAdelaja, A., Hoffmann, A.
Front Immunol., 2 July 2019
 Identifying Noise Sources governing cell-to-cell variabilityMitchell, S., Hoffmann, A
Current Opinion in Systems Biology, 8, pp.39-45
 Immune Response Signaling: Combinatorial and Dynamic ControlHoffmann, A.
Trends Immunol. 2016 Sep;37(9):570-2
 Signaling via the NFκB systemMitchell S, Vargas J, Hoffmann A.
Wiley Interdiscip Rev Syst Biol Med. 2016 May,8(3):227-41
 Training the 21st Century Immunologist.Spreafico, R., Mitchell, S., Hoffmann, A.
Trends in Immunology, 1280, pp.647-61. PMID: 25736777
 Studying NFκB Signaling with mathematical models.Mitchell, S., Tsui, R., Hoffmann, A.
Methods in Molecular Biology, 1280, pp.647-661. PMID: 25736777
 Lessons from mathematically modeling the NF-κB pathwayBasak S, Behar M, Hoffmann A.
Immunol Rev. 2012 Mar;246(1):221-38. doi: 10.1111/j.1600-065X.2011.01092.x. Review.
 How do pleiotropic kinase hubs mediate specific signaling by TNFR superfamily members?Schröfelbauer, B., Hoffmann, A.
Immunol Rev. 2011 Nov;244(1):29-43
 A single NFκB system for both canonical and non-canonical signalingShih VF, Tsui R, Caldwell A, Hoffmann A.
Cell Res. 2011 Jan;21(1):86-102. Epub 2010 Nov 23. Review.
 Understanding the logic of IκB:NF-κB regulation in structural termsHuxford T, Hoffmann A, Ghosh G.
Curr Top Microbiol Immunol. 2011;349:1-24. Review.
 Understanding the temporal codes of intra-cellular signalsBehar M, Hoffmann A.
Curr Opin Genet Dev. 2010 Dec;20(6):684-93. Epub 2010 Oct 16.
 Systems Biology of cellular rhythms: from cacophony to symphonyHasty, J, Hoffmann, A., Golden, S.
Current Opinion in Genetics and Development, 20, pp.571-3.
 The regulatory logic of the NF-κB signaling systemO'Dea E, Hoffmann A.
Cold Spring Harb Perspect Biol. 2010 Jan;2(1):a000216. Review.
 NF-κB signalingO'Dea E, Hoffmann A.
Wiley Interdiscip Rev Syst Biol Med. 2009 Jul-Aug;1(1):107-15. Review.
 Of Elections and Cell Death DecisionsLoriaux P, Hoffmann A.
Mol Cell. 2009 May 15;34(3):257-8.
 Integrating computational and biochemical studies to explore mechanisms in NF-κB signalingKearns JD, Hoffmann A.
J Biol Chem. 2009 Feb 27;284(9):5439-43. Epub 2008 Oct 20. Review. No abstract available.
 NF-κB as a determinant of distinct cell death pathwaysCh'en IL, Hedrick SM, Hoffmann A.
Methods Enzymol. 2008;446:175-87.
 Crosstalk via the NF-κB signaling systemBasak S, Hoffmann A.
Cytokine Growth Factor Rev. 2008 Jun-Aug;19(3-4):187-97. Epub 2008 Jun 2. Review.
 Understanding NF-κB signaling via mathematical modelingCheong R, Hoffmann A, Levchenko A.
Mol Syst Biol. 2008;4:192. Epub 2008 May 6.
 Epigenetic control: slow and global, nimble and localCheng CS, Johnson TL, Hoffmann A.
Genes Dev. 2008 May 1;22(9):1110-4.
 Inflammatory tales of liver cancerHoffmann A, Xia Y, Verma IM.
Cancer Cell. 2007 Feb;11(2):99-101.
 Transcriptional regulation via the NF-κB signaling moduleHoffmann A, Natoli G, Ghosh G.
Oncogene. 2006 Oct 30;25(51):6706-16. Review.
 Circuitry of nuclear factor kappaB signalingHoffmann A, Baltimore D.
Immunol Rev. 2006 Apr;210:171-86. Review.