Alexander Hoffmann

Title(s)Professor, MIMG
SchoolMedicine
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    Bruins in Genomics: Dental, Oral & Craniofacial Research Training Program (BIG DOC)
    NIH R25DE030117Jan 15, 2021 - Dec 31, 2025
    Role: Co-Principal Investigator
    The NFkB System in Dendritic Cells
    NIH R01AI127867Apr 3, 2018 - Mar 31, 2023
    Role: Principal Investigator
    Cell decision underlying B-cell immune responses
    NIH R01AI132731Feb 1, 2018 - Jan 31, 2023
    Role: Principal Investigator
    Coordinated dynamic regulation and function of IRF transcription factors
    NIH R01AI132835Jun 20, 2017 - May 31, 2022
    Role: Principal Investigator
    Roles of RelB in tuning inflammatory and innate immune responses
    NIH R21AI128646Dec 19, 2016 - Nov 30, 2019
    Role: Principal Investigator
    NFkB Signaling in Macrophages
    NIH R01AI127864Nov 17, 2016 - Oct 31, 2021
    Role: Principal Investigator
    Understanding dynamical coding by NFkB
    NIH R01GM117134Feb 15, 2016 - Jan 31, 2021
    Role: Principal Investigator
    NGS Data Analysis Skills for the Biosciences Pipeline
    NIH R25EB022364Sep 30, 2015 - Jun 30, 2019
    Role: Principal Investigator
    Ribonomics of Gene Regulation to predict Innate Immune Responses
    NIH U01HG007912Jan 5, 2015 - Nov 30, 2018
    Role: Principal Investigator
    Epigenomic control of RNA splicing
    NIH R01ES024995Sep 5, 2014 - Aug 31, 2017
    Role: Co-Principal Investigator
    San Diego Center for Systems Biology: From Maps to Models
    NIH P50GM085764Sep 18, 2010 - May 31, 2019
    Role: Co-Principal Investigator
    Delays and variability in single-cell NFkB signaling
    NIH R01GM089976May 1, 2010 - Apr 30, 2015
    Role: Co-Principal Investigator
    The NF-kB signaling system as a regulator of B-cell activation
    NIH R01AI083453Dec 15, 2009 - Nov 30, 2014
    Role: Principal Investigator
    IKK:Biophysical basis of dynamic regulation
    NIH R01CA141722Jul 1, 2009 - May 31, 2015
    Role: Co-Principal Investigator
    NFkB during TLR signaling in macrophages
    NIH R01GM071573Jul 1, 2004 - Apr 30, 2014
    Role: Principal Investigator
    Graduate Training Program in Bioinformatics
    NIH T32GM008806Jul 1, 2001 - Jun 30, 2021
    Role: Co-Principal Investigator

    Collapse Bibliographic 
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    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Quantifying information of intracellular signaling: progress with machine learning. Rep Prog Phys. 2022 07 12; 85(8). Tang Y, Hoffmann A. PMID: 35724636.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    2. Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling. Cell Rep. 2022 Jul 12; 40(2):111076. Kim J, Sheu KM, Cheng QJ, Hoffmann A, Enciso G. PMID: 35830792.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    3. From Antibody Repertoires to Cell-Cell Interactions to Molecular Networks: Bridging Scales in the Germinal Center. Front Immunol. 2022; 13:898078. Vaidehi Narayanan H, Hoffmann A. PMID: 35603162; PMCID: PMC9114758.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. Functional Hallmarks of Healthy Macrophage Responses: Their Regulatory Basis and Disease Relevance. Annu Rev Immunol. 2022 04 26; 40:295-321. Sheu KM, Hoffmann A. PMID: 35471841.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    5. Pathogenic TNF-α drives peripheral nerve inflammation in an Aire-deficient model of autoimmunity. Proc Natl Acad Sci U S A. 2022 01 25; 119(4). Wang Y, Guo L, Yin X, McCarthy EC, Cheng MI, Hoang AT, Chen HC, Patel AY, Allard Trout D, Xu E, Yakobian N, Hugo W, Howard JF, Sheu KM, Hoffmann A, Lechner MG, Su MA. PMID: 35058362; PMCID: PMC8795502.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    6. Acute and Chronic Changes in Gene Expression After CMV DNAemia in Kidney Transplant Recipients. Front Immunol. 2021; 12:750659. Ahn R, Schaenman J, Qian Z, Pickering H, Groysberg V, Rossetti M, Llamas M, Hoffmann A, Gjertson D, Deng M, Bunnapradist S, Reed EF, CMV Systems Immunobiology Group. PMID: 34867983; PMCID: PMC8634678.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    7. Stimulus-specific responses in innate immunity: Multilayered regulatory circuits. Immunity. 2021 09 14; 54(9):1915-1932. Luecke S, Sheu KM, Hoffmann A. PMID: 34525335; PMCID: PMC8452151.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    8. Identifying the combinatorial control of signal-dependent transcription factors. PLoS Comput Biol. 2021 06; 17(6):e1009095. Wang N, Lefaudeux D, Mazumder A, Li JJ, Hoffmann A. PMID: 34166361; PMCID: PMC8263068.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    9. NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages. Science. 2021 06 18; 372(6548):1349-1353. Cheng QJ, Ohta S, Sheu KM, Spreafico R, Adelaja A, Taylor B, Hoffmann A. PMID: 34140389; PMCID: PMC8489855.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    10. Melanoma dedifferentiation induced by IFN-γ epigenetic remodeling in response to anti-PD-1 therapy. J Clin Invest. 2021 06 15; 131(12). Kim YJ, Sheu KM, Tsoi J, Abril-Rodriguez G, Medina E, Grasso CS, Torrejon DY, Champhekar AS, Litchfield K, Swanton C, Speiser DE, Scumpia PO, Hoffmann A, Graeber TG, Puig-Saus C, Ribas A. PMID: 33914706; PMCID: PMC8203459.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    11. Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses. Immunity. 2021 05 11; 54(5):916-930.e7. Adelaja A, Taylor B, Sheu KM, Liu Y, Luecke S, Hoffmann A. PMID: 33979588; PMCID: PMC8184127.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    12. High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial Cells. Front Immunol. 2021; 12:651254. Kishimoto K, Wilder CL, Buchanan J, Nguyen M, Okeke C, Hoffmann A, Cheng QJ. PMID: 33897699; PMCID: PMC8062733.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    13. Quantifying information accumulation encoded in the dynamics of biochemical signaling. Nat Commun. 2021 02 24; 12(1):1272. Tang Y, Adelaja A, Ye FX, Deeds E, Wollman R, Hoffmann A. PMID: 33627672; PMCID: PMC7904837.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    14. An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF-induced necroptosis decisions. Mol Syst Biol. 2020 12; 16(12):e9677. Oliver Metzig M, Tang Y, Mitchell S, Taylor B, Foreman R, Wollman R, Hoffmann A. PMID: 33314666; PMCID: PMC7734648.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    15. Dissecting the Regulatory Strategies of NF-κB RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation Logics. Cell Rep. 2020 02 25; 30(8):2758-2775.e6. Ngo KA, Kishimoto K, Davis-Turak J, Pimplaskar A, Cheng Z, Spreafico R, Chen EY, Tam A, Ghosh G, Mitchell S, Hoffmann A. PMID: 32101750; PMCID: PMC7061728.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    16. Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene Expression. Cell Syst. 2020 02 26; 10(2):169-182.e5. Sen S, Cheng Z, Sheu KM, Chen YH, Hoffmann A. PMID: 31972132; PMCID: PMC7047529.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    17. Stimulus-specificity in the Responses of Immune Sentinel Cells. Curr Opin Syst Biol. 2019 Dec; 18:53-61. Sheu K, Luecke S, Hoffmann A. PMID: 32864512; PMCID: PMC7450653.
      View in: PubMed   Mentions: 1  
    18. Identifying determinants of persistent MRSA bacteremia using mathematical modeling. PLoS Comput Biol. 2019 07; 15(7):e1007087. Mikkaichi T, Yeaman MR, Hoffmann A, MRSA Systems Immunobiology Group. PMID: 31295255; PMCID: PMC6622483.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    19. Signaling Crosstalk Mechanisms That May Fine-Tune Pathogen-Responsive NFκB. Front Immunol. 2019; 10:433. Adelaja A, Hoffmann A. PMID: 31312197; PMCID: PMC6614373.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    20. An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct Mechanisms. Front Immunol. 2019; 10:1425. Mitchell S, Mercado EL, Adelaja A, Ho JQ, Cheng QJ, Ghosh G, Hoffmann A. PMID: 31293585; PMCID: PMC6604663.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    21. Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB. Proc Natl Acad Sci U S A. 2019 05 21; 116(21):10592-10597. Mitchell S, Hoffmann A. PMID: 31048505; PMCID: PMC6535030.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    22. Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions. Sci Rep. 2019 03 27; 9(1):5288. Cheng Q, Behzadi F, Sen S, Ohta S, Spreafico R, Teles R, Modlin RL, Hoffmann A. PMID: 30918279; PMCID: PMC6437173.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    23. A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation. Immunity. 2019 03 19; 50(3):616-628.e6. Roy K, Mitchell S, Liu Y, Ohta S, Lin YS, Metzig MO, Nutt SL, Hoffmann A. PMID: 30850343; PMCID: PMC6955201.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    24. Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. Proc Natl Acad Sci U S A. 2018 11 20; 115(47):E11061-E11070. Yeom KH, Mitchell S, Linares AJ, Zheng S, Lin CH, Wang XJ, Hoffmann A, Black DL. PMID: 30401736; PMCID: PMC6255174.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    25. Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation. Proc Natl Acad Sci U S A. 2018 03 20; 115(12):E2888-E2897. Mitchell S, Roy K, Zangle TA, Hoffmann A. PMID: 29514960; PMCID: PMC5866559.
      View in: PubMed   Mentions: 23     Fields:    Translation:AnimalsCells
    26. Deriving Quantitative Cell Biological Information from Dye-Dilution Lymphocyte Proliferation Experiments. Methods Mol Biol. 2018; 1707:81-94. Roy K, Shokhirev MN, Mitchell S, Hoffmann A. PMID: 29388101; PMCID: PMC8363314.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    27. Identifying Noise Sources governing cell-to-cell variability. Curr Opin Syst Biol. 2018 Apr; 8:39-45. Mitchell S, Hoffmann A. PMID: 29623300; PMCID: PMC5879788.
      View in: PubMed   Mentions: 8  
    28. Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX. Trends Biotechnol. 2017 10; 35(10):901-903. Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E. PMID: 28720283.
      View in: PubMed   Mentions: 7     Fields:    
    29. Immune Response Signaling: Combinatorial and Dynamic Control. Trends Immunol. 2016 09; 37(9):570-572. Hoffmann A. PMID: 27461000; PMCID: PMC5003693.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    30. High-Content Quantification of Single-Cell Immune Dynamics. Cell Rep. 2016 Apr 12; 15(2):411-22. Junkin M, Kaestli AJ, Cheng Z, Jordi C, Albayrak C, Hoffmann A, Tay S. PMID: 27050527; PMCID: PMC4835544.
      View in: PubMed   Mentions: 44     Fields:    Translation:AnimalsCells
    31. Signaling via the NFκB system. Wiley Interdiscip Rev Syst Biol Med. 2016 05; 8(3):227-41. Mitchell S, Vargas J, Hoffmann A. PMID: 26990581; PMCID: PMC8363188.
      View in: PubMed   Mentions: 283     Fields:    Translation:HumansAnimalsCells
    32. A stochastic spatio-temporal (SST) model to study cell-to-cell variability in HIV-1 infection. J Theor Biol. 2016 Apr 21; 395:87-96. Cheng Z, Hoffmann A. PMID: 26860658.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    33. A multi-scale mathematical modeling framework to investigate anti-viral therapeutic opportunities in targeting HIV-1 accessory proteins. J Theor Biol. 2015 Dec 07; 386:89-104. Suryawanshi GW, Hoffmann A. PMID: 26385832; PMCID: PMC4685255.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    34. Distinct single-cell signaling characteristics are conferred by the MyD88 and TRIF pathways during TLR4 activation. Sci Signal. 2015 Jul 14; 8(385):ra69. Cheng Z, Taylor B, Ourthiague DR, Hoffmann A. PMID: 26175492; PMCID: PMC6764925.
      View in: PubMed   Mentions: 50     Fields:    Translation:AnimalsCells
    35. Training the 21st Century Immunologist. Trends Immunol. 2015 May; 36(5):283-5. Spreafico R, Mitchell S, Hoffmann A. PMID: 25911462.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    36. Limited specificity of IRF3 and ISGF3 in the transcriptional innate-immune response to double-stranded RNA. J Leukoc Biol. 2015 Jul; 98(1):119-28. Ourthiague DR, Birnbaum H, Ortenlöf N, Vargas JD, Wollman R, Hoffmann A. PMID: 25896227; PMCID: PMC4467169.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    37. Studying NF-κB signaling with mathematical models. Methods Mol Biol. 2015; 1280:647-61. Mitchell S, Tsui R, Hoffmann A. PMID: 25736777.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    38. MAP kinase p38α regulates type III interferon (IFN-λ1) gene expression in human monocyte-derived dendritic cells in response to RNA stimulation. J Leukoc Biol. 2015 Feb; 97(2):307-20. Jiang M, Österlund P, Fagerlund R, Rios DN, Hoffmann A, Poranen MM, Bamford DH, Julkunen I. PMID: 25473098.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    39. The dynamics of signaling as a pharmacological target. Cell. 2013 Oct 10; 155(2):448-61. Behar M, Barken D, Werner SL, Hoffmann A. PMID: 24120141; PMCID: PMC3856316.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansAnimalsCells
    40. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS Genet. 2011 Dec; 7(12):e1002401. Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, Heinz S, Spann NJ, Crotti A, Stender J, Ghisletti S, Reichart D, Cheng CS, Luna R, Ludka C, Sasik R, Garcia-Bassets I, Hoffmann A, Subramaniam S, Hardiman G, Rosenfeld MG, Glass CK. PMID: 22174696; PMCID: PMC3234212.
      View in: PubMed   Mentions: 76     Fields:    Translation:HumansAnimalsCells
    41. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell. 2009 Jul 10; 138(1):114-28. Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST. PMID: 19596239; PMCID: PMC2712736.
      View in: PubMed   Mentions: 303     Fields:    Translation:HumansAnimalsCells
    42. Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science. 2005 Sep 16; 309(5742):1857-61. Werner SL, Barken D, Hoffmann A. PMID: 16166517.
      View in: PubMed   Mentions: 238     Fields:    Translation:AnimalsCells
    43. A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activation. Genes Dev. 2005 Sep 15; 19(18):2138-51. Sanjabi S, Williams KJ, Saccani S, Zhou L, Hoffmann A, Ghosh G, Gerondakis S, Natoli G, Smale ST. PMID: 16166378; PMCID: PMC1221885.
      View in: PubMed   Mentions: 61     Fields:    Translation:AnimalsCells
    44. Molecular determinants of crosstalk between nuclear receptors and toll-like receptors. Cell. 2005 Sep 09; 122(5):707-21. Ogawa S, Lozach J, Benner C, Pascual G, Tangirala RK, Westin S, Hoffmann A, Subramaniam S, David M, Rosenfeld MG, Glass CK. PMID: 16143103; PMCID: PMC1430687.
      View in: PubMed   Mentions: 252     Fields:    Translation:AnimalsCells
    45. Induction of NR4A orphan nuclear receptor expression in macrophages in response to inflammatory stimuli. J Biol Chem. 2005 Aug 12; 280(32):29256-62. Pei L, Castrillo A, Chen M, Hoffmann A, Tontonoz P. PMID: 15964844.
      View in: PubMed   Mentions: 110     Fields:    Translation:HumansAnimalsCells
    46. Unique CD40-mediated biological program in B cell activation requires both type 1 and type 2 NF-kappaB activation pathways. Proc Natl Acad Sci U S A. 2004 May 25; 101(21):8108-13. Zarnegar B, He JQ, Oganesyan G, Hoffmann A, Baltimore D, Cheng G. PMID: 15148378; PMCID: PMC419565.
      View in: PubMed   Mentions: 38     Fields:    Translation:AnimalsCells
    47. Cooperation of multiple signaling pathways in CD40-regulated gene expression in B lymphocytes. Proc Natl Acad Sci U S A. 2002 Feb 05; 99(3):1497-502. Dadgostar H, Zarnegar B, Hoffmann A, Qin XF, Truong U, Rao G, Baltimore D, Cheng G. PMID: 11830667; PMCID: PMC122219.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
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