Alexander Hoffmann - Publications

Affiliations: 
Chemistry and Biochemistry University of California, San Diego, La Jolla, CA 
Area:
signaling, transcription, computational network; stress and immune responses, apoptosis, proliferation
Website:
http://www-chem.ucsd.edu/faculty/profiles/hoffmann_alexander.html

105 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Mitchell S, Mercado EL, Adelaja A, Ho JQ, Cheng QJ, Ghosh G, Hoffmann A. An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct Mechanisms. Frontiers in Immunology. 10: 1425. PMID 31293585 DOI: 10.3389/fimmu.2019.01425  0.44
2019 Cheng Q, Behzadi F, Sen S, Ohta S, Spreafico R, Teles R, Modlin RL, Hoffmann A. Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions. Scientific Reports. 9: 5288. PMID 30918279 DOI: 10.1038/s41598-019-40503-y  0.48
2019 Davis-Turak J, Johnson TL, Hoffmann A. Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing. Nucleic Acids Research. PMID 30649426 DOI: 10.1093/nar/gkz013  0.36
2018 Davis-Turak J, Johnson TL, Hoffmann A. Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing. Nucleic Acids Research. PMID 30272246 DOI: 10.1093/nar/gky870  0.36
2018 Roy K, Shokhirev MN, Mitchell S, Hoffmann A. Deriving Quantitative Cell Biological Information from Dye-Dilution Lymphocyte Proliferation Experiments. Methods in Molecular Biology (Clifton, N.J.). 1707: 81-94. PMID 29388101 DOI: 10.1007/978-1-4939-7474-0_6  0.96
2017 Mognol GP, Spreafico R, Wong V, Scott-Browne JP, Togher S, Hoffmann A, Hogan PG, Rao A, Trifari S. Exhaustion-associated regulatory regions in CD8(+) tumor-infiltrating T cells. Proceedings of the National Academy of Sciences of the United States of America. PMID 28283662 DOI: 10.1073/pnas.1620498114  0.48
2017 Cheng CS, Behar MS, Suryawanshi GW, Feldman KE, Spreafico R, Hoffmann A. Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms. Cell Systems. PMID 28237795 DOI: 10.1016/j.cels.2017.01.012  0.48
2017 Dembinski HE, Wismer K, Vargas JD, Suryawanshi GW, Kern N, Kroon G, Dyson HJ, Hoffmann A, Komives EA. Functional importance of stripping in NFκB signaling revealed by a stripping-impaired IκBα mutant. Proceedings of the National Academy of Sciences of the United States of America. PMID 28167786 DOI: 10.1073/pnas.1610192114  0.48
2016 Inoue K, Shinohara H, Behar M, Yumoto N, Tanaka G, Hoffmann A, Aihara K, Okada-Hatakeyama M. Oscillation dynamics underlie functional switching of NF-κB for B-cell activation. Npj Systems Biology and Applications. 2: 16024. PMID 28725478 DOI: 10.1038/npjsba.2016.24  0.6
2016 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, et al. Early cytokine signatures of ischemia/reperfusion injury in human orthotopic liver transplantation. Jci Insight. 1: e89679. PMID 27942590 DOI: 10.1172/jci.insight.89679  0.48
2016 Junkin M, Kaestli AJ, Cheng Z, Jordi C, Albayrak C, Hoffmann A, Tay S. High-Content Quantification of Single-Cell Immune Dynamics. Cell Reports. PMID 27050527 DOI: 10.1016/j.celrep.2016.03.033  1
2016 Mitchell S, Vargas J, Hoffmann A. Signaling via the NFκB system. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. PMID 26990581 DOI: 10.1002/wsbm.1331  1
2016 Cheng Z, Hoffmann A. A stochastic spatio-temporal (SST) model to study cell-to-cell variability in HIV-1 infection. Journal of Theoretical Biology. PMID 26860658 DOI: 10.1016/j.jtbi.2016.02.001  1
2016 Almaden JV, Liu YC, Yang E, Otero D, Birnbaum H, Davis-Turak J, Asagiri M, David M, Goldrath AW, Hoffmann A. B cell survival and development controlled by the coordination of NFκB family members RelB and cRel. Blood. PMID 26773039 DOI: 10.1182/blood-2014-10-606988  1
2015 Suryawanshi GW, Hoffmann A. A multi-scale mathematical modeling framework to investigate anti-viral therapeutic opportunities in targeting HIV-1 accessory proteins. Journal of Theoretical Biology. 386: 89-104. PMID 26385832 DOI: 10.1016/j.jtbi.2015.08.032  1
2015 Fagerlund R, Behar M, Fortmann KT, Lin YE, Vargas JD, Hoffmann A. Anatomy of a negative feedback loop: the case of IκBα. Journal of the Royal Society, Interface / the Royal Society. 12. PMID 26311312 DOI: 10.1098/rsif.2015.0262  1
2015 Tsui R, Kearns JD, Lynch C, Vu D, Ngo KA, Basak S, Ghosh G, Hoffmann A. IκBβ enhances the generation of the low-affinity NFκB/RelA homodimer. Nature Communications. 6: 7068. PMID 25946967 DOI: 10.1038/ncomms8068  1
2015 Spreafico R, Mitchell S, Hoffmann A. Training the 21st Century Immunologist. Trends in Immunology. 36: 283-5. PMID 25911462 DOI: 10.1016/j.it.2015.04.001  1
2015 Ourthiague DR, Birnbaum H, Ortenlöf N, Vargas JD, Wollman R, Hoffmann A. Limited specificity of IRF3 and ISGF3 in the transcriptional innate-immune response to double-stranded RNA. Journal of Leukocyte Biology. 98: 119-28. PMID 25896227 DOI: 10.1189/jlb.4A1014-483RR  1
2015 Shokhirev MN, Almaden J, Davis-Turak J, Birnbaum HA, Russell TM, Vargas JA, Hoffmann A. A multi-scale approach reveals that NF-κB cRel enforces a B-cell decision to divide. Molecular Systems Biology. 11: 783. PMID 25680807  0.96
2015 Davis-Turak JC, Allison K, Shokhirev MN, Ponomarenko P, Tsimring LS, Glass CK, Johnson TL, Hoffmann A. Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing. Nucleic Acids Research. 43: 699-707. PMID 25541195 DOI: 10.1093/nar/gku1338  1
2015 Jiang M, Österlund P, Fagerlund R, Rios DN, Hoffmann A, Poranen MM, Bamford DH, Julkunen I. MAP kinase p38α regulates type III interferon (IFN-λ1) gene expression in human monocyte-derived dendritic cells in response to RNA stimulation. Journal of Leukocyte Biology. 97: 307-20. PMID 25473098 DOI: 10.1189/jlb.2A0114-059RR  1
2015 Shokhirev MN, Almaden J, Davis-Turak J, Birnbaum HA, Russell TM, Vargas JAD, Hoffmann A. A multi-scale approach reveals that NF-κB cRel enforces a B-cell decision to divide Molecular Systems Biology. 11. DOI: 10.15252/msb.20145554  1
2014 Selimkhanov J, Taylor B, Yao J, Pilko A, Albeck J, Hoffmann A, Tsimring L, Wollman R. Systems biology. Accurate information transmission through dynamic biochemical signaling networks. Science (New York, N.Y.). 346: 1370-3. PMID 25504722 DOI: 10.1126/science.1254933  1
2014 Almaden JV, Tsui R, Liu YC, Birnbaum H, Shokhirev MN, Ngo KA, Davis-Turak JC, Otero D, Basak S, Rickert RC, Hoffmann A. A pathway switch directs BAFF signaling to distinct NFκB transcription factors in maturing and proliferating B cells. Cell Reports. 9: 2098-111. PMID 25497099 DOI: 10.1016/j.celrep.2014.11.024  1
2014 Caldwell AB, Cheng Z, Vargas JD, Birnbaum HA, Hoffmann A. Network dynamics determine the autocrine and paracrine signaling functions of TNF. Genes & Development. 28: 2120-33. PMID 25274725 DOI: 10.1101/gad.244749.114  1
2014 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, et al. Positive feedback within a kinase signaling complex functions as a switch mechanism for NF-κB activation. Science (New York, N.Y.). 344: 760-4. PMID 24833394 DOI: 10.1126/science.1250020  0.6
2014 Alves BN, Tsui R, Almaden J, Shokhirev MN, Davis-Turak J, Fujimoto J, Birnbaum H, Ponomarenko J, Hoffmann A. IκBε is a key regulator of B cell expansion by providing negative feedback on cRel and RelA in a stimulus-specific manner. Journal of Immunology (Baltimore, Md. : 1950). 192: 3121-32. PMID 24591377 DOI: 10.4049/jimmunol.1302351  1
2014 Vogel CF, Khan EM, Leung PS, Gershwin ME, Chang WL, Wu D, Haarmann-Stemmann T, Hoffmann A, Denison MS. Cross-talk between aryl hydrocarbon receptor and the inflammatory response: a role for nuclear factor-κB. The Journal of Biological Chemistry. 289: 1866-75. PMID 24302727 DOI: 10.1074/jbc.M113.505578  1
2013 Behar M, Barken D, Werner SL, Hoffmann A. The dynamics of signaling as a pharmacological target. Cell. 155: 448-61. PMID 24120141 DOI: 10.1016/j.cell.2013.09.018  1
2013 Feldman KE, Loriaux PM, Saito M, Tuero I, Villaverde H, Siva T, Gotuzzo E, Gilman RH, Hoffmann A, Vinetz JM. Ex vivo innate immune cytokine signature of enhanced risk of relapsing brucellosis. Plos Neglected Tropical Diseases. 7: e2424. PMID 24040434 DOI: 10.1371/journal.pntd.0002424  1
2013 Mukherjee SP, Behar M, Birnbaum HA, Hoffmann A, Wright PE, Ghosh G. Analysis of the RelA:CBP/p300 interaction reveals its involvement in NF-κB-driven transcription. Plos Biology. 11: e1001647. PMID 24019758 DOI: 10.1371/journal.pbio.1001647  1
2013 Shokhirev MN, Hoffmann A. FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses. Plos One. 8: e67620. PMID 23826329 DOI: 10.1371/journal.pone.0067620  1
2013 Longo DM, Selimkhanov J, Kearns JD, Hasty J, Hoffmann A, Tsimring LS. Dual delayed feedback provides sensitivity and robustness to the NF-κB signaling module. Plos Computational Biology. 9: e1003112. PMID 23825938 DOI: 10.1371/journal.pcbi.1003112  1
2013 Behar M, Hoffmann A. Tunable signal processing through a kinase control cycle: the IKK signaling node. Biophysical Journal. 105: 231-41. PMID 23823243 DOI: 10.1016/j.bpj.2013.05.013  0.6
2013 Polley S, Huang DB, Hauenstein AV, Fusco AJ, Zhong X, Vu D, Schröfelbauer B, Kim Y, Hoffmann A, Verma IM, Ghosh G, Huxford T. A structural basis for IκB kinase 2 activation via oligomerization-dependent trans auto-phosphorylation. Plos Biology. 11: e1001581. PMID 23776406 DOI: 10.1371/journal.pbio.1001581  1
2013 Loriaux PM, Tesler G, Hoffmann A. Characterizing the relationship between steady state and response using analytical expressions for the steady states of mass action models. Plos Computational Biology. 9: e1002901. PMID 23509437 DOI: 10.1371/journal.pcbi.1002901  1
2013 Loriaux PM, Hoffmann A. A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways. Plos Computational Biology. 9: e1002932. PMID 23468615 DOI: 10.1371/journal.pcbi.1002932  1
2012 Tam AB, Mercado EL, Hoffmann A, Niwa M. ER stress activates NF-κB by integrating functions of basal IKK activity, IRE1 and PERK. Plos One. 7: e45078. PMID 23110043 DOI: 10.1371/journal.pone.0045078  1
2012 Shih VF, Davis-Turak J, Macal M, Huang JQ, Ponomarenko J, Kearns JD, Yu T, Fagerlund R, Asagiri M, Zuniga EI, Hoffmann A. Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways. Nature Immunology. 13: 1162-70. PMID 23086447 DOI: 10.1038/ni.2446  1
2012 Wang VY, Huang W, Asagiri M, Spann N, Hoffmann A, Glass C, Ghosh G. The transcriptional specificity of NF-κB dimers is coded within the κB DNA response elements. Cell Reports. 2: 824-39. PMID 23063365 DOI: 10.1016/j.celrep.2012.08.042  1
2012 Schröfelbauer B, Polley S, Behar M, Ghosh G, Hoffmann A. NEMO ensures signaling specificity of the pleiotropic IKKβ by directing its kinase activity toward IκBα. Molecular Cell. 47: 111-21. PMID 22633953 DOI: 10.1016/j.molcel.2012.04.020  1
2012 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. Paternal RLIM/Rnf12 is a survival factor for milk-producing alveolar cells. Cell. 149: 630-41. PMID 22541433 DOI: 10.1016/j.cell.2012.02.056  1
2012 Loriaux PM, Hoffmann A. A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness. Methods in Cell Biology. 110: 81-109. PMID 22482946 DOI: 10.1016/B978-0-12-388403-9.00004-7  1
2012 Basak S, Behar M, Hoffmann A. Lessons from mathematically modeling the NF-κB pathway. Immunological Reviews. 246: 221-38. PMID 22435558 DOI: 10.1111/j.1600-065X.2011.01092.x  0.6
2012 Busino L, Millman SE, Scotto L, Kyratsous CA, Basrur V, O'Connor O, Hoffmann A, Elenitoba-Johnson KS, Pagano M. Fbxw7α- and GSK3-mediated degradation of p100 is a pro-survival mechanism in multiple myeloma. Nature Cell Biology. 14: 375-85. PMID 22388891 DOI: 10.1038/ncb2463  1
2011 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, et al. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. Plos Genetics. 7: e1002401. PMID 22174696 DOI: 10.1371/journal.pgen.1002401  1
2011 Murray SE, Polesso F, Rowe AM, Basak S, Koguchi Y, Toren KG, Hoffmann A, Parker DC. NF-κB–inducing kinase plays an essential T cell–intrinsic role in graft-versus-host disease and lethal autoimmunity in mice. The Journal of Clinical Investigation. 121: 4775-86. PMID 22045568 DOI: 10.1172/JCI44943  1
2011 Ho JQ, Asagiri M, Hoffmann A, Ghosh G. NF-κB potentiates caspase independent hydrogen peroxide induced cell death. Plos One. 6: e16815. PMID 21347231 DOI: 10.1371/journal.pone.0016815  1
2011 Cheng CS, Feldman KE, Lee J, Verma S, Huang DB, Huynh K, Chang M, Ponomarenko JV, Sun SC, Benedict CA, Ghosh G, Hoffmann A. The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50. Science Signaling. 4: ra11. PMID 21343618 DOI: 10.1126/scisignal.2001501  1
2011 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. Nuclear export of the NF-κB inhibitor IκBα is required for proper B cell and secondary lymphoid tissue formation. Immunity. 34: 188-200. PMID 21333553 DOI: 10.1016/j.immuni.2011.01.014  1
2011 Huxford T, Hoffmann A, Ghosh G. Understanding the logic of IκB:NF-κB regulation in structural terms. Current Topics in Microbiology and Immunology. 349: 1-24. PMID 20845107 DOI: 10.1007/82_2010_99  1
2010 Hasty J, Hoffmann A, Golden S. Systems biology of cellular rhythms: from cacophony to symphony. Current Opinion in Genetics & Development. 20: 571-3. PMID 21036033 DOI: 10.1016/j.gde.2010.10.003  1
2010 Behar M, Hoffmann A. Understanding the temporal codes of intra-cellular signals. Current Opinion in Genetics & Development. 20: 684-93. PMID 20956081 DOI: 10.1016/j.gde.2010.09.007  0.6
2010 Rao P, Hayden MS, Long M, Scott ML, West AP, Zhang D, Oeckinghaus A, Lynch C, Hoffmann A, Baltimore D, Ghosh S. IkappaBbeta acts to inhibit and activate gene expression during the inflammatory response. Nature. 466: 1115-9. PMID 20740013 DOI: 10.1038/nature09283  1
2010 Takeda N, O'Dea EL, Doedens A, Kim JW, Weidemann A, Stockmann C, Asagiri M, Simon MC, Hoffmann A, Johnson RS. Differential activation and antagonistic function of HIF-{alpha} isoforms in macrophages are essential for NO homeostasis. Genes & Development. 24: 491-501. PMID 20194441 DOI: 10.1101/gad.1881410  0.48
2010 O'Dea E, Hoffmann A. The regulatory logic of the NF-kappaB signaling system. Cold Spring Harbor Perspectives in Biology. 2: a000216. PMID 20182598 DOI: 10.1101/cshperspect.a000216  0.4
2010 Longo DM, Hoffmann A, Tsimring LS, Hasty J. Coherent activation of a synthetic mammalian gene network. Systems and Synthetic Biology. 4: 15-23. PMID 19757189 DOI: 10.1007/s11693-009-9044-5  1
2009 O'Dea E, Hoffmann A. NF-κB signaling. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 1: 107-15. PMID 20151024 DOI: 10.1002/wsbm.30  0.4
2009 Bergqvist S, Alverdi V, Mengel B, Hoffmann A, Ghosh G, Komives EA. Kinetic enhancement of NF-kappaBxDNA dissociation by IkappaBalpha. Proceedings of the National Academy of Sciences of the United States of America. 106: 19328-33. PMID 19887633 DOI: 10.1073/pnas.0908797106  1
2009 Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell. 138: 114-28. PMID 19596239 DOI: 10.1016/j.cell.2009.04.020  0.48
2009 Savinova OV, Hoffmann A, Ghosh G. The Nfkb1 and Nfkb2 proteins p105 and p100 function as the core of high-molecular-weight heterogeneous complexes. Molecular Cell. 34: 591-602. PMID 19524538 DOI: 10.1016/j.molcel.2009.04.033  1
2009 Shih VF, Kearns JD, Basak S, Savinova OV, Ghosh G, Hoffmann A. Kinetic control of negative feedback regulators of NF-kappaB/RelA determines their pathogen- and cytokine-receptor signaling specificity. Proceedings of the National Academy of Sciences of the United States of America. 106: 9619-24. PMID 19487661 DOI: 10.1073/pnas.0812367106  1
2009 Kearns JD, Hoffmann A. Integrating computational and biochemical studies to explore mechanisms in NF-{kappa}B signaling. The Journal of Biological Chemistry. 284: 5439-43. PMID 18940809 DOI: 10.1074/jbc.R800008200  1
2008 Ch'en IL, Beisner DR, Degterev A, Lynch C, Yuan J, Hoffmann A, Hedrick SM. Antigen-mediated T cell expansion regulated by parallel pathways of death. Proceedings of the National Academy of Sciences of the United States of America. 105: 17463-8. PMID 18981423 DOI: 10.1073/pnas.0808043105  1
2008 Werner SL, Kearns JD, Zadorozhnaya V, Lynch C, O'Dea E, Boldin MP, Ma A, Baltimore D, Hoffmann A. Encoding NF-kappaB temporal control in response to TNF: distinct roles for the negative regulators IkappaBalpha and A20. Genes & Development. 22: 2093-101. PMID 18676814 DOI: 10.1101/gad.1680708  1
2008 O'Dea EL, Kearns JD, Hoffmann A. UV as an amplifier rather than inducer of NF-kappaB activity. Molecular Cell. 30: 632-41. PMID 18538661 DOI: 10.1016/j.molcel.2008.03.017  1
2008 Basak S, Hoffmann A. Crosstalk via the NF-kappaB signaling system. Cytokine & Growth Factor Reviews. 19: 187-97. PMID 18515173 DOI: 10.1016/j.cytogfr.2008.04.005  1
2008 Cheong R, Hoffmann A, Levchenko A. Understanding NF-kappaB signaling via mathematical modeling. Molecular Systems Biology. 4: 192. PMID 18463616 DOI: 10.1038/msb.2008.30  0.48
2008 Cheng CS, Johnson TL, Hoffmann A. Epigenetic control: slow and global, nimble and local. Genes & Development. 22: 1110-4. PMID 18451102 DOI: 10.1101/gad.1677008  1
2008 Mathes E, O'Dea EL, Hoffmann A, Ghosh G. NF-kappaB dictates the degradation pathway of IkappaBalpha. The Embo Journal. 27: 1357-67. PMID 18401342 DOI: 10.1038/emboj.2008.73  1
2008 Fusco AJ, Savinova OV, Talwar R, Kearns JD, Hoffmann A, Ghosh G. Stabilization of RelB requires multidomain interactions with p100/p52. The Journal of Biological Chemistry. 283: 12324-32. PMID 18321863 DOI: 10.1074/jbc.M707898200  1
2008 Basak S, Shih VF, Hoffmann A. Generation and activation of multiple dimeric transcription factors within the NF-kappaB signaling system. Molecular and Cellular Biology. 28: 3139-50. PMID 18299388 DOI: 10.1128/MCB.01469-07  0.36
2007 O'Dea EL, Barken D, Peralta RQ, Tran KT, Werner SL, Kearns JD, Levchenko A, Hoffmann A. A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity. Molecular Systems Biology. 3: 111. PMID 17486138 DOI: 10.1038/msb4100148  1
2007 Hoffmann A, Xia Y, Verma IM. Inflammatory tales of liver cancer. Cancer Cell. 11: 99-101. PMID 17292819 DOI: 10.1016/j.ccr.2007.01.008  1
2007 Basak S, Kim H, Kearns JD, Tergaonkar V, O'Dea E, Werner SL, Benedict CA, Ware CF, Ghosh G, Verma IM, Hoffmann A. A fourth IkappaB protein within the NF-kappaB signaling module. Cell. 128: 369-81. PMID 17254973 DOI: 10.1016/j.cell.2006.12.033  1
2006 Kearns JD, Basak S, Werner SL, Huang CS, Hoffmann A. IkappaBepsilon provides negative feedback to control NF-kappaB oscillations, signaling dynamics, and inflammatory gene expression. The Journal of Cell Biology. 173: 659-64. PMID 16735576 DOI: 10.1083/jcb.200510155  1
2006 Hoffmann A, Baltimore D. Circuitry of nuclear factor kappaB signaling. Immunological Reviews. 210: 171-86. PMID 16623771 DOI: 10.1111/j.0105-2896.2006.00375.x  1
2006 Cheong R, Bergmann A, Werner SL, Regal J, Hoffmann A, Levchenko A. Transient IkappaB kinase activity mediates temporal NF-kappaB dynamics in response to a wide range of tumor necrosis factor-alpha doses. The Journal of Biological Chemistry. 281: 2945-50. PMID 16321974 DOI: 10.1074/jbc.M510085200  1
2006 Lo JC, Basak S, James ES, Quiambo RS, Kinsella MC, Alegre ML, Weih F, Franzoso G, Hoffmann A, Fu YX. 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. 107: 1048-55. PMID 16195333 DOI: 10.1182/blood-2005-06-2452  1
2005 Werner SL, Barken D, Hoffmann A. Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science (New York, N.Y.). 309: 1857-61. PMID 16166517 DOI: 10.1126/science.1113319  1
2005 Sanjabi S, Williams KJ, Saccani S, Zhou L, Hoffmann A, Ghosh G, Gerondakis S, Natoli G, Smale ST. A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activation. Genes & Development. 19: 2138-51. PMID 16166378 DOI: 10.1101/gad.1329805  0.44
2005 Ogawa S, Lozach J, Benner C, Pascual G, Tangirala RK, Westin S, Hoffmann A, Subramaniam S, David M, Rosenfeld MG, Glass CK. Molecular determinants of crosstalk between nuclear receptors and toll-like receptors. Cell. 122: 707-21. PMID 16143103 DOI: 10.1016/j.cell.2005.06.029  1
2005 Shapira S, Harb OS, Margarit J, Matrajt M, Han J, Hoffmann A, Freedman B, May MJ, Roos DS, Hunter CA. Initiation and termination of NF-kappaB signaling by the intracellular protozoan parasite Toxoplasma gondii. Journal of Cell Science. 118: 3501-8. PMID 16079291 DOI: 10.1242/jcs.02428  1
2005 Gapuzan ME, Schmah O, Pollock AD, Hoffmann A, Gilmore TD. 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. 24: 6574-83. PMID 16027734 DOI: 10.1038/sj.onc.1208809  1
2005 Barken D, Wang CJ, Kearns J, Cheong R, Hoffmann A, Levchenko A. Comment on "Oscillations in NF-kappaB signaling control the dynamics of gene expression". Science (New York, N.Y.). 308: 52; author reply 52. PMID 15802586 DOI: 10.1126/science.1107904  1
2004 Leung TH, Hoffmann A, Baltimore D. One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers. Cell. 118: 453-64. PMID 15315758 DOI: 10.1016/j.cell.2004.08.007  1
2004 Zarnegar B, He JQ, Oganesyan G, Hoffmann A, Baltimore D, Cheng G. Unique CD40-mediated biological program in B cell activation requires both type 1 and type 2 NF-kappaB activation pathways. Proceedings of the National Academy of Sciences of the United States of America. 101: 8108-13. PMID 15148378 DOI: 10.1073/pnas.0402629101  1
2003 Hoffmann A, Leung TH, Baltimore D. Genetic analysis of NF-kappaB/Rel transcription factors defines functional specificities. The Embo Journal. 22: 5530-9. PMID 14532125 DOI: 10.1093/emboj/cdg534  1
2002 Hoffmann A, Levchenko A, Scott ML, Baltimore D. The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science (New York, N.Y.). 298: 1241-5. PMID 12424381 DOI: 10.1126/science.1071914  1
2002 Dadgostar H, Zarnegar B, Hoffmann A, Qin XF, Truong U, Rao G, Baltimore D, Cheng G. Cooperation of multiple signaling pathways in CD40-regulated gene expression in B lymphocytes. Proceedings of the National Academy of Sciences of the United States of America. 99: 1497-502. PMID 11830667 DOI: 10.1073/pnas.032665099  1
2000 Sanjabi S, Hoffmann A, Liou HC, Baltimore D, Smale ST. Selective requirement for c-Rel during IL-12 P40 gene induction in macrophages. Proceedings of the National Academy of Sciences of the United States of America. 97: 12705-10. PMID 11058167 DOI: 10.1073/pnas.230436397  1
1997 Hoffmann A, Oelgeschläger T, Roeder RG. Considerations of transcriptional control mechanisms: do TFIID-core promoter complexes recapitulate nucleosome-like functions? Proceedings of the National Academy of Sciences of the United States of America. 94: 8928-35. PMID 9256411  0.32
1996 Segil N, Guermah M, Hoffmann A, Roeder RG, Heintz N. Mitotic regulation of TFIID: inhibition of activator-dependent transcription and changes in subcellular localization. Genes & Development. 10: 2389-400. PMID 8843192  1
1996 Hoffmann A, Roeder RG. Cloning and characterization of human TAF20/15. Multiple interactions suggest a central role in TFIID complex formation. The Journal of Biological Chemistry. 271: 18194-202. PMID 8663456 DOI: 10.1074/jbc.271.30.18194  1
1996 Hoffmann A, Chiang CM, Oelgeschläger T, Xie X, Burley SK, Nakatani Y, Roeder RG. A histone octamer-like structure within TFIID. Nature. 380: 356-9. PMID 8598932 DOI: 10.1038/380356a0  0.32
1996 Xie X, Kokubo T, Cohen SL, Mirza UA, Hoffmann A, Chait BT, Roeder RG, Nakatani Y, Burley SK. Structural similarity between TAFs and the heterotetrameric core of the histone octamer. Nature. 380: 316-22. PMID 8598927 DOI: 10.1038/380316a0  0.32
1993 Chiang CM, Ge H, Wang Z, Hoffmann A, Roeder RG. Unique TATA-binding protein-containing complexes and cofactors involved in transcription by RNA polymerases II and III. The Embo Journal. 12: 2749-62. PMID 7687540  1
1992 Takada R, Nakatani Y, Hoffmann A, Kokubo T, Hasegawa S, Roeder RG, Horikoshi M. Identification of human TFIID components and direct interaction between a 250-kDa polypeptide and the TATA box-binding protein (TFIID tau). Proceedings of the National Academy of Sciences of the United States of America. 89: 11809-13. PMID 1465404  0.32
1992 Nikolov DB, Hu SH, Lin J, Gasch A, Hoffmann A, Horikoshi M, Chua NH, Roeder RG, Burley SK. Crystal structure of TFIID TATA-box binding protein. Nature. 360: 40-6. PMID 1436073 DOI: 10.1038/360040a0  0.32
1991 Hoffmann A, Roeder RG. Purification of his-tagged proteins in non-denaturing conditions suggests a convenient method for protein interaction studies. Nucleic Acids Research. 19: 6337-8. PMID 1956801 DOI: 10.1093/nar/19.22.6337  1
1991 Ohkuma Y, Sumimoto H, Hoffmann A, Shimasaki S, Horikoshi M, Roeder RG. Structural motifs and potential sigma homologies in the large subunit of human general transcription factor TFIIE. Nature. 354: 398-401. PMID 1956403 DOI: 10.1038/354398a0  0.32
1991 Tamura T, Sumita K, Fujino I, Aoyama A, Horikoshi M, Hoffmann A, Roeder RG, Muramatsu M, Mikoshiba K. Striking homology of the 'variable' N-terminal as well as the 'conserved core' domains of the mouse and human TATA-factors (TFIID). Nucleic Acids Research. 19: 3861-5. PMID 1861978  0.32
1990 Hoffmann A, Horikoshi M, Wang CK, Schroeder S, Weil PA, Roeder RG. Cloning of the Schizosaccharomyces pombe TFIID gene reveals a strong conservation of functional domains present in Saccharomyces cerevisiae TFIID. Genes & Development. 4: 1141-8. PMID 2210373  0.32
1990 Gasch A, Hoffmann A, Horikoshi M, Roeder RG, Chua NH. Arabidopsis thaliana contains two genes for TFIID. Nature. 346: 390-4. PMID 2197561 DOI: 10.1038/346390a0  0.32
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