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Hoffmann, Alexander

Title(s)Professor, Mimg
Phone3107949925
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    Collapse Research 
    Collapse Research Activities and Funding
    The NFkB System in Dendritic Cells
    NIH/NIAID R01AI127867Apr 3, 2018 - Mar 31, 2023
    Role: Principal Investigator
    Cell decision underlying B-cell immune responses
    NIH/NIAID R01AI132731Feb 1, 2018 - Jan 31, 2023
    Role: Principal Investigator
    Coordinated dynamic regulation and function of IRF transcription factors
    NIH/NIAID R01AI132835Jun 20, 2017 - May 31, 2022
    Role: Principal Investigator
    Roles of RelB in tuning inflammatory and innate immune responses
    NIH/NIAID R21AI128646Dec 19, 2016 - Nov 30, 2018
    Role: Principal Investigator
    NFkB Signaling in Macrophages
    NIH/NIAID R01AI127864Nov 17, 2016 - Oct 31, 2021
    Role: Principal Investigator
    Understanding dynamical coding by NFkB
    NIH/NIGMS R01GM117134Feb 15, 2016 - Jan 31, 2020
    Role: Principal Investigator
    NGS Data Analysis Skills for the Biosciences Pipeline
    NIH/NIBIB R25EB022364Sep 30, 2015 - Jun 30, 2018
    Role: Principal Investigator
    Ribonomics of Gene Regulation to predict Innate Immune Responses
    NIH/NHGRI U01HG007912Jan 5, 2015 - Nov 30, 2017
    Role: Principal Investigator
    Epigenomic control of RNA splicing
    NIH/NIEHS R01ES024995Sep 5, 2014 - Aug 31, 2016
    Role: Co-Principal Investigator
    Delays and variability in single-cell NFkB signaling
    NIH/NIGMS R01GM089976May 1, 2010 - Apr 30, 2014
    Role: Co-Principal Investigator
    The NF-kB signaling system as a regulator of B-cell activation
    NIH/NIAID R01AI083453Dec 15, 2009 - Nov 30, 2014
    Role: Principal Investigator
    Graduate Training Program in Bioinformatics
    NIH/NIGMS T32GM008806Aug 3, 2009 - Jun 30, 2021
    Role: Co-Principal Investigator
    IKK:Biophysical basis of dynamic regulation
    NIH/NCI R01CA141722Jul 1, 2009 - May 31, 2014
    Role: Co-Principal Investigator
    San Diego Center for Systems Biology: From Maps to Models
    NIH/NIGMS P50GM085764Jul 1, 2008 - May 31, 2019
    Role: Co-Principal Investigator
    NFkB during TLR signaling in macrophages
    NIH/NIGMS R01GM071573Jul 1, 2004 - Apr 30, 2014
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. 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-?B RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation Logics. Cell Rep. 2020 Feb 25; 30(8):2758-2775.e6. PMID: 32101750.
      View in: PubMed
    2. Sen S, Cheng Z, Sheu KM, Chen YH, Hoffmann A. Gene Regulatory Strategies that Decode the Duration of NF?B Dynamics Contribute to LPS- versus TNF-Specific Gene Expression. Cell Syst. 2020 Feb 26; 10(2):169-182.e5. PMID: 31972132.
      View in: PubMed
    3. Mikkaichi T, Yeaman MR, Hoffmann A. Identifying determinants of persistent MRSA bacteremia using mathematical modeling. PLoS Comput Biol. 2019 07; 15(7):e1007087. PMID: 31295255.
      View in: PubMed
    4. Adelaja A, Hoffmann A. Signaling Crosstalk Mechanisms That May Fine-Tune Pathogen-Responsive NF?B. Front Immunol. 2019; 10:433. PMID: 31312197.
      View in: PubMed
    5. Mitchell S, Mercado EL, Adelaja A, Ho JQ, Cheng QJ, Ghosh G, Hoffmann A. An NF?B Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NF?B via Distinct Mechanisms. Front Immunol. 2019; 10:1425. PMID: 31293585.
      View in: PubMed
    6. Mitchell S, Hoffmann A. Substrate complex competition is a regulatory motif that allows NF?B RelA to license but not amplify NF?B RelB. Proc Natl Acad Sci U S A. 2019 05 21; 116(21):10592-10597. PMID: 31048505.
      View in: PubMed
    7. 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. Sci Rep. 2019 Mar 27; 9(1):5288. PMID: 30918279.
      View in: PubMed
    8. Roy K, Mitchell S, Liu Y, Ohta S, Lin YS, Metzig MO, Nutt SL, Hoffmann A. A Regulatory Circuit Controlling the Dynamics of NF?B cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation. Immunity. 2019 03 19; 50(3):616-628.e6. PMID: 30850343.
      View in: PubMed
    9. 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. Proc Natl Acad Sci U S A. 2018 11 20; 115(47):E11061-E11070. PMID: 30401736.
      View in: PubMed
    10. Mitchell S, Roy K, Zangle TA, Hoffmann A. Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation. Proc Natl Acad Sci U S A. 2018 03 20; 115(12):E2888-E2897. PMID: 29514960.
      View in: PubMed
    11. Roy K, Shokhirev MN, Mitchell S, Hoffmann A. Deriving Quantitative Cell Biological Information from Dye-Dilution Lymphocyte Proliferation Experiments. Methods Mol Biol. 2018; 1707:81-94. PMID: 29388101.
      View in: PubMed
    12. Mitchell S, Hoffmann A. Identifying Noise Sources governing cell-to-cell variability. Curr Opin Syst Biol. 2018 Apr; 8:39-45. PMID: 29623300.
      View in: PubMed
    13. Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E. Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX. Trends Biotechnol. 2017 10; 35(10):901-903. PMID: 28720283.
      View in: PubMed
    14. Hoffmann A. Immune Response Signaling: Combinatorial and Dynamic Control. Trends Immunol. 2016 09; 37(9):570-572. PMID: 27461000.
      View in: PubMed
    15. Junkin M, Kaestli AJ, Cheng Z, Jordi C, Albayrak C, Hoffmann A, Tay S. High-Content Quantification of Single-Cell Immune Dynamics. Cell Rep. 2016 Apr 12; 15(2):411-22. PMID: 27050527.
      View in: PubMed
    16. Mitchell S, Vargas J, Hoffmann A. Signaling via the NF?B system. Wiley Interdiscip Rev Syst Biol Med. 2016 05; 8(3):227-41. PMID: 26990581.
      View in: PubMed
    17. Cheng Z, Hoffmann A. A stochastic spatio-temporal (SST) model to study cell-to-cell variability in HIV-1 infection. J Theor Biol. 2016 Apr 21; 395:87-96. PMID: 26860658.
      View in: PubMed
    18. Suryawanshi GW, Hoffmann A. A multi-scale mathematical modeling framework to investigate anti-viral therapeutic opportunities in targeting HIV-1 accessory proteins. J Theor Biol. 2015 Dec 07; 386:89-104. PMID: 26385832.
      View in: PubMed
    19. Cheng Z, Taylor B, Ourthiague DR, Hoffmann A. Distinct single-cell signaling characteristics are conferred by the MyD88 and TRIF pathways during TLR4 activation. Sci Signal. 2015 Jul 14; 8(385):ra69. PMID: 26175492.
      View in: PubMed
    20. Spreafico R, Mitchell S, Hoffmann A. Training the 21st Century Immunologist. Trends Immunol. 2015 May; 36(5):283-5. PMID: 25911462.
      View in: PubMed
    21. 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. J Leukoc Biol. 2015 Jul; 98(1):119-28. PMID: 25896227.
      View in: PubMed
    22. Mitchell S, Tsui R, Hoffmann A. Studying NF-?B signaling with mathematical models. Methods Mol Biol. 2015; 1280:647-61. PMID: 25736777.
      View in: PubMed
    23. Jiang M, Österlund P, Fagerlund R, Rios DN, Hoffmann A, Poranen MM, Bamford DH, Julkunen I. MAP kinase p38a regulates type III interferon (IFN-?1) gene expression in human monocyte-derived dendritic cells in response to RNA stimulation. J Leukoc Biol. 2015 Feb; 97(2):307-20. PMID: 25473098.
      View in: PubMed
    24. Behar M, Barken D, Werner SL, Hoffmann A. The dynamics of signaling as a pharmacological target. Cell. 2013 Oct 10; 155(2):448-61. PMID: 24120141.
      View in: PubMed
    25. 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 Genet. 2011 Dec; 7(12):e1002401. PMID: 22174696.
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    26. 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 Jul 10; 138(1):114-28. PMID: 19596239.
      View in: PubMed
    27. Werner SL, Barken D, Hoffmann A. Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science. 2005 Sep 16; 309(5742):1857-61. PMID: 16166517.
      View in: PubMed
    28. 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 Dev. 2005 Sep 15; 19(18):2138-51. PMID: 16166378.
      View in: PubMed
    29. 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 Sep 09; 122(5):707-21. PMID: 16143103.
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    30. Pei L, Castrillo A, Chen M, Hoffmann A, Tontonoz P. Induction of NR4A orphan nuclear receptor expression in macrophages in response to inflammatory stimuli. J Biol Chem. 2005 Aug 12; 280(32):29256-62. PMID: 15964844.
      View in: PubMed
    31. 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. Proc Natl Acad Sci U S A. 2004 May 25; 101(21):8108-13. PMID: 15148378.
      View in: PubMed
    32. 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. Proc Natl Acad Sci U S A. 2002 Feb 05; 99(3):1497-502. PMID: 11830667.
      View in: PubMed