Alexander Hoffmann

Professor, MIMG, University of California Los Angeles

UC Profile
QCBio Institute Website
Hoffmann Lab Website

Interests

IRF signaling system, Macrophages: innate immunity, B-cells: control vaccine responses, hematopoiesis: age-associated immune dysregulation, NFkB signaling system

Education and Training

California Institute of Technologypostdoc05/2003NFkB, Systems Immunology
Massachusetts Institute of Technologypostdoc01/1998HIV, control of latency
Rockefeller UniversityPhD06/1994Biochemistry of TFIID
Cambridge UniversityBA06/1988Physics

Awards and Honors

  • UCLA Undergraduate Research Mentor Award, 2023.
  • Thomas M Asher endowed chair in Microbiology, 2014-now.
  • Hellman Fellow, 2007-2008.
  • Ellison Medical Foundation Scholar in Aging Research, 2005-2009.
  • Gordon Ross Medical Foundation post-doctoral fellow, 1999-2002.
  • Arnold and Mabel Beckman graduate fellowship, 1992-1994.
  • Boehringer Ingelheim graduate fellowship, 1990-1992.
  • Institut Jacques Monod Summer Research Award, 1988.
  • Johns Hopkins Summer Research Award, 1987.

Publications

  1. Wang AG, Son M, Gorin A, Kenna E, Padhi A, Keisham B, Schauer A, Hoffmann A, Tay S. Macrophage memory emerges from coordinated transcription factor and chromatin dynamics.. Cell systems, 2025.
  2. Navarro HI, Daly AE, Rodriguez B, Wu S, Ngo KA, Fraser A, Schiffman A, Liu Y, Smale ST, Chia JJ, Hoffmann A. NF-κB RelB suppresses the inflammatory gene expression programs of dendritic cells by competing with RelA for binding to target gene promoters.. Cell discovery, 2025.
  3. Schiffman A, Cheng Z, Ourthiague D, Hoffmann A. Gene regulatory logic of the interferon-β enhancer contains multiple selectively deployed modes of transcription factor synergy.. bioRxiv : the preprint server for biology, 2025.
  4. Seitz T, Karabulut A, Suzuki RM, Hoffmann A, Heck J, Herres-Pawlis S. The golden goal of entatic state model design: lowering the internal reorganization energy leads to exponential increase in electron transfer rate.. Chemical communications (Cambridge, England), 2025.
  5. 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. Enhancing FAIRdata by providing digital workflows from data generation to the publication of data: an open source approach described for cyclic voltammetry.. Chemical science, 2025.
  6. Vareli A, Narayanan HV, Clark H, Jayawant E, Zhou H, Liu Y, Stott L, Simoes F, Hoffmann A, Pepper A, Pepper C, Mitchell S. Systems biology-enabled targeting of NF-κΒ and BCL2 overcomes microenvironment-mediated BH3-mimetic resistance in DLBCL.. bioRxiv : the preprint server for biology, 2025.
  7. Chia JJ, Singh A, Lin Y, Popko N, Mastro D, Liu Y, Tran T, King JK, Rao DS, Hoffmann A. Distinct causes of three phenotypic hallmarks of hematopoietic aging.. bioRxiv : the preprint server for biology, 2025.
  8. Chavez C, Lin K, Malveaux A, Gorin A, Brizuela S, Cheng QJ, Hoffmann A. IRF1 cooperates with ISGF3 or GAF to form innate immune de novo enhancers in macrophages.. Science signaling, 2025.
  9. Singh A, Chia JJ, Rao DS, Hoffmann A. Population dynamics modeling reveals that myeloid bias involves both HSC differentiation and progenitor proliferation biases.. Blood, 2024.
  10. Yuan Kueh H, Handel A, Hoffmann A, Chowell D, Gottschalk RA, Singh H, Germain RN, Meier-Schellersheim M, Miller-Jensen K, Altan-Bonnet G. What unique insights can modeling approaches capture about the immune system?. Cell systems, 2024.
  11. Sheu KM, Pimplaskar A, Hoffmann A. Single-cell stimulus-response gene expression trajectories reveal the stimulus specificities of dynamic responses by single macrophages.. Molecular cell, 2024.
  12. Zhang J, Griffin J, Roy K, Hoffmann A, Zangle TA. Tracking of lineage mass via quantitative phase imaging and confinement in low refractive index microwells.. Lab on a chip, 2024.
  13. Daly AE, Schiffman A, Hoffmann A, Smale ST. Examining NF-κB genomic interactions by ChIP-seq and CUT&Tag.. bioRxiv : the preprint server for biology, 2024.
  14. Huang H, Narayanan HV, Hoffmann A. Synergy and antagonism in the integration of BCR and CD40 signals that control B-cell proliferation.. bioRxiv : the preprint server for biology, 2024.
  15. Vaidehi Narayanan H, Xiang MY, Chen Y, Huang H, Roy S, Makkar H, Hoffmann A, Roy K. Direct observation correlates NFκB cRel in B cells with activating and terminating their proliferative program.. Proceedings of the National Academy of Sciences of the United States of America, 2024.
  16. Luecke S, Guo X, Sheu KM, Singh A, Lowe SC, Han M, Diaz J, Lopes F, Wollman R, Hoffmann A. Dynamical and combinatorial coding by MAPK p38 and NFκB in the inflammatory response of macrophages.. Molecular systems biology, 2024.
  17. Singh A, Sen S, Iter M, Adelaja A, Luecke S, Guo X, Hoffmann A. Stimulus-response signaling dynamics characterize macrophage polarization states.. Cell systems, 2024.
  18. Thaden JT, Ahn R, Ruffin F, Gjertson DW, Hoffmann A, Fowler VG, Yeaman MR. Use of Transcriptional Signatures to Differentiate Pathogen-Specific and Treatment-Specific Host Responses in Patients With Bacterial Bloodstream Infections.. The Journal of infectious diseases, 2024.
  19. 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 . Tensor modeling of MRSA bacteremia cytokine and transcriptional patterns reveals coordinated, outcome-associated immunological programs.. PNAS nexus, 2024.
  20. Rodriguez BN, Huang H, Chia JJ, Hoffmann A. The noncanonical NFκB pathway: Regulatory mechanisms in health and disease.. WIREs mechanisms of disease, 2024.
  21. 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. The metabolic cofactor Coenzyme A enhances alternative macrophage activation via MyD88-linked signaling.. bioRxiv : the preprint server for biology, 2024.
  22. Rahman SMT, Singh A, Lowe S, Aqdas M, Jiang K, Vaidehi Narayanan H, Hoffmann A, Sung MH. Co-imaging of RelA and c-Rel reveals features of NF-κB signaling for ligand discrimination.. Cell reports, 2024.
  23. Cheng CT, Hsiao JC, Hoffmann A, Tu HL. TNFR1 mediates heterogeneity in single-cell NF-κB activation.. iScience, 2024.
  24. 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. Myeloid spatial and transcriptional molecular signature of ischemia-reperfusion injury in human liver transplantation.. Hepatology communications, 2024.
  25. Navarro HI, Liu Y, Fraser A, Lefaudeux D, Chia JJ, Vong L, Roifman CM, Hoffmann A. RelB-deficient autoinflammatory pathology presents as interferonopathy, but in mice is interferon-independent.. The Journal of allergy and clinical immunology, 2023.
  26. 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. Virtually the Same? Evaluating the Effectiveness of Remote Undergraduate Research Experiences.. CBE life sciences education, 2023.
  27. Luecke S, Adelaja A, Guo X, Sen S, Spreafico R, Singh A, Liu Y, Taylor B, Diaz J, Cheng Q, Hoffmann A. Tonic TNF conditioning of macrophages safeguards stimulus-specific inflammatory responses.. EMBO reports, 2023.
  28. Hoffmann A. Designer genes courtesy of artificial intelligence.. Genes & development, 2023.
  29. Wilder CL, Lefaudeux D, Mathenge R, Kishimoto K, Zuniga Munoz A, Nguyen MA, Meyer AS, Cheng QJ, Hoffmann A. A stimulus-contingent positive feedback loop enables IFN-β dose-dependent activation of pro-inflammatory genes.. Molecular systems biology, 2023.
  30. Mitchell S, Tsui R, Tan ZC, Pack A, Hoffmann A. The NF-κB multidimer system model: A knowledge base to explore diverse biological contexts.. Science signaling, 2023.
  31. Ildefonso GV, Oliver Metzig M, Hoffmann A, Harris LA, Lopez CF. A biochemical necroptosis model explains cell-type-specific responses to cell death cues.. Biophysical journal, 2023.
  32. Sheu KM, Guru AA, Hoffmann A. Quantifying stimulus-response specificity to probe the functional state of macrophages.. Cell systems, 2023.
  33. Lefaudeux D, Sen S, Jiang K, Hoffmann A, UCLA Ribonomics Group. Kinetics of mRNA nuclear export regulate innate immune response gene expression.. Nature communications, 2022.
  34. 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. NFκB pathway dysregulation due to reduced RelB expression leads to severe autoimmune disorders and declining immunity.. Journal of autoimmunity, 2022.
  35. Ando M, Magi S, Seki M, Suzuki Y, Kasukawa T, Lefaudeux D, Hoffmann A, Okada M. Author Correction: IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells.. NPJ systems biology and applications, 2022.
  36. Tang Y, Hoffmann A. Quantifying information of intracellular signaling: progress with machine learning.. Reports on progress in physics. Physical Society (Great Britain), 2022.
  37. Kim J, Sheu KM, Cheng QJ, Hoffmann A, Enciso G. Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling.. Cell reports, 2022.
  38. Heck J, Metz F, Buchenau S, Teubner M, Grimm-Lebsanft B, Spaniol TP, Hoffmann A, Rübhausen MA, Herres-Pawlis S. Manipulating electron transfer - the influence of substituents on novel copper guanidine quinolinyl complexes.. Chemical science, 2022.
  39. Coller HA, Beggs S, Andrews S, Maloy J, Chiu A, Sankararaman S, Pellegrini M, Freimer N, Johnson T, Papp J, Eskin E, Hoffmann A. Bruins-in-Genomics: Evaluation of the impact of a UCLA undergraduate summer program in computational biology on participating students.. PloS one, 2022.
  40. Vaidehi Narayanan H, Hoffmann A. From Antibody Repertoires to Cell-Cell Interactions to Molecular Networks: Bridging Scales in the Germinal Center.. Frontiers in immunology, 2022.
  41. Sheu KM, Hoffmann A. Functional Hallmarks of Healthy Macrophage Responses: Their Regulatory Basis and Disease Relevance.. Annual review of immunology, 2022.
  42. Oliver Metzig M, Hoffmann A. Controlling Cancer Cell Death Types to Optimize Anti-Tumor Immunity.. Biomedicines, 2022.
  43. 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. "How Do We Do This at a Distance?!" A Descriptive Study of Remote Undergraduate Research Programs during COVID-19.. CBE life sciences education, 2022.
  44. 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. Pathogenic TNF-α drives peripheral nerve inflammation in an Aire-deficient model of autoimmunity.. Proceedings of the National Academy of Sciences of the United States of America, 2022.
  45. Ando M, Magi S, Seki M, Suzuki Y, Kasukawa T, Lefaudeux D, Hoffmann A, Okada M. IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells.. NPJ systems biology and applications, 2021.
  46. 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. Acute and Chronic Changes in Gene Expression After CMV DNAemia in Kidney Transplant Recipients.. Frontiers in immunology, 2021.
  47. 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. NK and CD8+ T cell phenotypes predict onset and control of CMV viremia after kidney transplant.. JCI insight, 2021.
  48. Luecke S, Sheu KM, Hoffmann A. Stimulus-specific responses in innate immunity: Multilayered regulatory circuits.. Immunity, 2021.
  49. Wang N, Lefaudeux D, Mazumder A, Li JJ, Hoffmann A. Identifying the combinatorial control of signal-dependent transcription factors.. PLoS computational biology, 2021.
  50. Cheng QJ, Ohta S, Sheu KM, Spreafico R, Adelaja A, Taylor B, Hoffmann A. NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages.. Science (New York, N.Y.), 2021.
  51. 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. Melanoma dedifferentiation induced by IFN-γ epigenetic remodeling in response to anti-PD-1 therapy.. The Journal of clinical investigation, 2021.
  52. Adelaja A, Taylor B, Sheu KM, Liu Y, Luecke S, Hoffmann A. Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses.. Immunity, 2021.
  53. Kishimoto K, Wilder CL, Buchanan J, Nguyen M, Okeke C, Hoffmann A, Cheng QJ. High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial Cells.. Frontiers in immunology, 2021.
  54. 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. Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremia.. Proceedings of the National Academy of Sciences of the United States of America, 2021.
  55. Tang Y, Adelaja A, Ye FX, Deeds E, Wollman R, Hoffmann A. Quantifying information accumulation encoded in the dynamics of biochemical signaling.. Nature communications, 2021.
  56. Son M, Wang AG, Tu HL, Metzig MO, Patel P, Husain K, Lin J, Murugan A, Hoffmann A, Tay S. NF-κB responds to absolute differences in cytokine concentrations.. Science signaling, 2021.
  57. Oliver Metzig M, Tang Y, Mitchell S, Taylor B, Foreman R, Wollman R, Hoffmann A. An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF-induced necroptosis decisions.. Molecular systems biology, 2020.
  58. Lisiero DN, Cheng Z, Tejera MM, Neldner BT, Warrick JW, Wuerzberger-Davis SM, Hoffmann A, Suresh M, Miyamoto S. IκBα Nuclear Export Enables 4-1BB-Induced cRel Activation and IL-2 Production to Promote CD8 T Cell Immunity.. Journal of immunology (Baltimore, Md. : 1950), 2020.
  59. Ghana P, Hoffmann A, Spaniol TP, Okuda J. Reduced Arene Complexes of Scandium.. Chemistry (Weinheim an der Bergstrasse, Germany), 2020.
  60. Ngo KA, Kishimoto K, Davis-Turak J, Pimplaskar A, Cheng Z, Spreafico R, Chen EY, Tam A, Ghosh G, Mitchell S, Hoffmann A. Dissecting the Regulatory Strategies of NF-κB RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation Logics.. Cell reports, 2020.
  61. Sen S, Cheng Z, Sheu KM, Chen YH, Hoffmann A. Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene Expression.. Cell systems, 2020.
  62. Sheu K, Luecke S, Hoffmann A. Stimulus-specificity in the Responses of Immune Sentinel Cells.. Current opinion in systems biology, 2019.
  63. Mikkaichi T, Yeaman MR, Hoffmann A, MRSA Systems Immunobiology Group. Identifying determinants of persistent MRSA bacteremia using mathematical modeling.. PLoS computational biology, 2019.
  64. Adelaja A, Hoffmann A. Signaling Crosstalk Mechanisms That May Fine-Tune Pathogen-Responsive NFκB.. Frontiers in immunology, 2019.
  65. 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, 2019.
  66. Mitchell S, Hoffmann A. Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB.. Proceedings of the National Academy of Sciences of the United States of America, 2019.
  67. 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, 2019.
  68. Roy K, Mitchell S, Liu Y, Ohta S, Lin YS, Metzig MO, Nutt SL, Hoffmann A. A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation.. Immunity, 2019.
  69. 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, 2019.
  70. 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. Dopamine Is a Siderophore-Like Iron Chelator That Promotes Salmonella enterica Serovar Typhimurium Virulence in Mice.. mBio, 2019.
  71. Ritter F, Mukherjee D, Spaniol TP, Hoffmann A, Okuda J. A Masked Cuprous Hydride as a Catalyst for Carbonyl Hydrosilylation in Aqueous Solutions.. Angewandte Chemie (International ed. in English), 2019.
  72. 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, 2018.
  73. Yeom KH, Mitchell S, Linares AJ, Zheng S, Lin CH, Wang XJ, Hoffmann A, Black DL. Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse.. Proceedings of the National Academy of Sciences of the United States of America, 2018.
  74. Mitchell S, Roy K, Zangle TA, Hoffmann A. Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation.. Proceedings of the National Academy of Sciences of the United States of America, 2018.
  75. 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.), 2018.
  76. Mitchell S, Hoffmann A. Identifying Noise Sources governing cell-to-cell variability.. Current opinion in systems biology, 2017.
  77. Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E. Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX.. Trends in biotechnology, 2017.
  78. 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, 2017.
  79. Cheng CS, Behar MS, Suryawanshi GW, Feldman KE, Spreafico R, Hoffmann A. Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms.. Cell systems, 2017.
  80. 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, 2017.
  81. 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. Early cytokine signatures of ischemia/reperfusion injury in human orthotopic liver transplantation.. JCI insight, 2016.
  82. 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, 2016.
  83. 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. A miR-155-Peli1-c-Rel pathway controls the generation and function of T follicular helper cells.. The Journal of experimental medicine, 2016.
  84. Hoffmann A. Immune Response Signaling: Combinatorial and Dynamic Control.. Trends in immunology, 2016.
  85. Junkin M, Kaestli AJ, Cheng Z, Jordi C, Albayrak C, Hoffmann A, Tay S. High-Content Quantification of Single-Cell Immune Dynamics.. Cell reports, 2016.
  86. Mitchell S, Vargas J, Hoffmann A. Signaling via the NFκB system.. Wiley interdisciplinary reviews. Systems biology and medicine, 2016.
  87. 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. The REGγ-proteasome forms a regulatory circuit with IκBɛ and NFκB in experimental colitis.. Nature communications, 2016.
  88. Cheng Z, Hoffmann A. A stochastic spatio-temporal (SST) model to study cell-to-cell variability in HIV-1 infection.. Journal of theoretical biology, 2016.
  89. Almaden JV, Liu YC, Yang E, Otero DC, Birnbaum H, Davis-Turak J, Asagiri M, David M, Goldrath AW, Hoffmann A. B-cell survival and development controlled by the coordination of NF-κB family members RelB and cRel.. Blood, 2016.
  90. 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, 2015.
  91. 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, 2015.
  92. Fortmann KT, Lewis RD, Ngo KA, Fagerlund R, Hoffmann A. A Regulated, Ubiquitin-Independent Degron in IκBα.. Journal of molecular biology, 2015.
  93. Cheng Z, Taylor B, Ourthiague DR, Hoffmann A. Distinct single-cell signaling characteristics are conferred by the MyD88 and TRIF pathways during TLR4 activation.. Science signaling, 2015.
  94. 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, 2015.
  95. Spreafico R, Mitchell S, Hoffmann A. Training the 21st Century Immunologist.. Trends in immunology, 2015.
  96. 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, 2015.
  97. Lee DJ, Du F, Chen SW, Nakasaki M, Rana I, Shih VFS, Hoffmann A, Jamora C. Regulation and Function of the Caspase-1 in an Inflammatory Microenvironment.. The Journal of investigative dermatology, 2015.
  98. 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, 2015.
  99. Mitchell S, Tsui R, Hoffmann A. Studying NF-κB signaling with mathematical models.. Methods in molecular biology (Clifton, N.J.), 2015.
  100. 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, 2014.
  101. 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.), 2014.
  102. 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, 2014.
  103. 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, 2014.
  104. Caldwell AB, Cheng Z, Vargas JD, Birnbaum HA, Hoffmann A. Network dynamics determine the autocrine and paracrine signaling functions of TNF.. Genes & development, 2014.
  105. Krüger J, Grunzke R, Herres-Pawlis S, Hoffmann A, de la Garza L, Kohlbacher O, Nagel WE, Gesing S. Performance studies on distributed virtual screening.. BioMed research international, 2014.
  106. 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. Positive feedback within a kinase signaling complex functions as a switch mechanism for NF-κB activation.. Science (New York, N.Y.), 2014.
  107. 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), 2014.
  108. 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, 2013.
  109. Behar M, Barken D, Werner SL, Hoffmann A. The dynamics of signaling as a pharmacological target.. Cell, 2013.
  110. 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, 2013.
  111. 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, 2013.
  112. 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. Chromatin-bound IκBα regulates a subset of polycomb target genes in differentiation and cancer.. Cancer cell, 2013.
  113. Behar M, Hoffmann A. Tunable signal processing through a kinase control cycle: the IKK signaling node.. Biophysical journal, 2013.
  114. 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, 2013.
  115. Shokhirev MN, Hoffmann A. FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses.. PloS one, 2013.
  116. 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, 2013.
  117. Loriaux PM, Hoffmann A. A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways.. PLoS computational biology, 2013.
  118. 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, 2013.
  119. 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, 2012.
  120. 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, 2012.
  121. 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, 2012.
  122. 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, 2012.
  123. 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, 2012.
  124. Basak S, Behar M, Hoffmann A. Lessons from mathematically modeling the NF-κB pathway.. Immunological reviews, 2012.
  125. Loriaux PM, Hoffmann A. A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness.. Methods in cell biology, 2012.
  126. 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. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes.. PLoS genetics, 2011.
  127. 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, 2011.
  128. Schröfelbauer B, Hoffmann A. How do pleiotropic kinase hubs mediate specific signaling by TNFR superfamily members?. Immunological reviews, 2011.
  129. 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, 2011.
  130. 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, 2011.
  131. Ho JQ, Asagiri M, Hoffmann A, Ghosh G. NF-κB potentiates caspase independent hydrogen peroxide induced cell death.. PloS one, 2011.
  132. Huxford T, Hoffmann A, Ghosh G. Understanding the logic of IκB:NF-κB regulation in structural terms.. Current topics in microbiology and immunology, 2011.
  133. Shih VF, Tsui R, Caldwell A, Hoffmann A. A single NFκB system for both canonical and non-canonical signaling.. Cell research, 2010.
  134. Hasty J, Hoffmann A, Golden S. Systems biology of cellular rhythms: from cacophony to symphony.. Current opinion in genetics & development, 2010.
  135. Behar M, Hoffmann A. Understanding the temporal codes of intra-cellular signals.. Current opinion in genetics & development, 2010.
  136. 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, 2010.
  137. von Vietinghoff S, Asagiri M, Azar D, Hoffmann A, Ley K. Defective regulation of CXCR2 facilitates neutrophil release from bone marrow causing spontaneous inflammation in severely NF-kappa B-deficient mice.. Journal of immunology (Baltimore, Md. : 1950), 2010.
  138. 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, 2010.
  139. O'Dea E, Hoffmann A. The regulatory logic of the NF-kappaB signaling system.. Cold Spring Harbor perspectives in biology, 2010.
  140. 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, 2009.
  141. Longo DM, Hoffmann A, Tsimring LS, Hasty J. Coherent activation of a synthetic mammalian gene network.. Systems and synthetic biology, 2009.
  142. 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, 2009.
  143. O'Dea E, Hoffmann A. NF-κB signaling.. Wiley interdisciplinary reviews. Systems biology and medicine, 2009.
  144. 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, 2009.
  145. 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, 2009.
  146. Loriaux P, Hoffmann A. Of elections and cell-death decisions.. Molecular cell, 2009.
  147. 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, 2008.
  148. Kearns JD, Hoffmann A. Integrating computational and biochemical studies to explore mechanisms in NF-{kappa}B signaling.. The Journal of biological chemistry, 2008.
  149. 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, 2008.
  150. O'Dea EL, Kearns JD, Hoffmann A. UV as an amplifier rather than inducer of NF-kappaB activity.. Molecular cell, 2008.
  151. Basak S, Hoffmann A. Crosstalk via the NF-kappaB signaling system.. Cytokine & growth factor reviews, 2008.
  152. Cheong R, Hoffmann A, Levchenko A. Understanding NF-kappaB signaling via mathematical modeling.. Molecular systems biology, 2008.
  153. Cheng CS, Johnson TL, Hoffmann A. Epigenetic control: slow and global, nimble and local.. Genes & development, 2008.
  154. Kato T, Gotoh Y, Hoffmann A, Ono Y. Negative regulation of constitutive NF-kappaB and JNK signaling by PKN1-mediated phosphorylation of TRAF1.. Genes to cells : devoted to molecular & cellular mechanisms, 2008.
  155. Mathes E, O'Dea EL, Hoffmann A, Ghosh G. NF-kappaB dictates the degradation pathway of IkappaBalpha.. The EMBO journal, 2008.
  156. 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, 2008.
  157. Basak S, Shih VF, Hoffmann A. Generation and activation of multiple dimeric transcription factors within the NF-kappaB signaling system.. Molecular and cellular biology, 2008.
  158. Ch'en IL, Hedrick SM, Hoffmann A. NF-kappaB as a determinant of distinct cell death pathways.. Methods in enzymology, 2008.
  159. 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, 2007.
  160. Hoffmann A, Xia Y, Verma IM. Inflammatory tales of liver cancer.. Cancer cell, 2007.
  161. 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, 2007.
  162. 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, 2006.
  163. Hoffmann A, Baltimore D. Circuitry of nuclear factor kappaB signaling.. Immunological reviews, 2006.
  164. 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, 2005.
  165. 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, 2005.
  166. 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, 2005.
  167. Werner SL, Barken D, Hoffmann A. Stimulus specificity of gene expression programs determined by temporal control of IKK activity.. Science (New York, N.Y.), 2005.
  168. 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, 2005.
  169. Beisner DR, Ch'en IL, Kolla RV, Hoffmann A, Hedrick SM. Cutting edge: innate immunity conferred by B cells is regulated by caspase-8.. Journal of immunology (Baltimore, Md. : 1950), 2005.
  170. 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, 2005.
  171. Park JM, Greten FR, Wong A, Westrick RJ, Arthur JS, Otsu K, Hoffmann A, Montminy M, Karin M. Signaling pathways and genes that inhibit pathogen-induced macrophage apoptosis--CREB and NF-kappaB as key regulators.. Immunity, 2005.
  172. 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, 2005.
  173. Pei L, Castrillo A, Chen M, Hoffmann A, Tontonoz P. Induction of NR4A orphan nuclear receptor expression in macrophages in response to inflammatory stimuli.. The Journal of biological chemistry, 2005.
  174. 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.), 2005.
  175. Leung TH, Hoffmann A, Baltimore D. One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers.. Cell, 2004.
  176. 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, 2004.
  177. Hoffmann A, Leung TH, Baltimore D. Genetic analysis of NF-kappaB/Rel transcription factors defines functional specificities.. The EMBO journal, 2003.
  178. Kato T, Delhase M, Hoffmann A, Karin M. CK2 Is a C-Terminal IkappaB Kinase Responsible for NF-kappaB Activation during the UV Response.. Molecular cell, 2003.
  179. 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.), 2002.
  180. 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, 2002.