Alexander Hoffmann*

The Hoffmann laboratory focuses on the signaling systems that control innate and adaptive immunity. A central theme is that signaling network dynamics determine biological specificity. We have contributed to an understanding of how NFκB and IRF signaling dynamics are regulated, how these are altered during cell differentiation and in human disease contexts, and how rational drug targeting strategies may be applied to correct misregulation. A wide range of experimental work in animals and cell culture, at single-molecule to genome-wide scales, is coordinated with computational modeling. The laboratory currently has three biological foci: 1) macrophages: how their functions are regulated in a stimulus-specific and context-dependent manner, and how prior history of exposure may be harnessed for innate immune training; 2) B-cells: how the intra-cellular molecular regulatory networks control fate decisions of cell death and cell division, and how inter-cellular networks in the germinal center generate the antibody repertoire in response to vaccination; 3) hematopoiesis: how signaling pathways inside and between cells regulate population dynamics via cell fate decisions of cell division, cell death, and differentiation.

Websites:

QCB Institute Website
Hoffmann Lab Website

Research Interests:

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

Publications:

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. 2024 Mar 31. view on PubMed

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 Rep. 2024 Mar 26; 43(3):113940. view on PubMed

Cheng CT, Hsiao JC, Hoffmann A, Tu HL. TNFR1 mediates heterogeneity in single-cell NF-κB activation. iScience. 2024 Apr 19; 27(4):109486. view on PubMed

Kröckert KW, Garg F, Heck J, Heinz MV, Lange J, Schmidt R, Hoffmann A, Herres-Pawlis S. ATRP catalysts of tetradentate guanidine ligands - do guanidine donors induce a faster atom transfer? Dalton Trans. 2024 Feb 13; 53(7):2973-2990. view on PubMed

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. Hepatol Commun. 2024 Jan 01; 8(1). view on PubMed

Thaden JT, Ahn R, Ruffin F, Gjertson DW, Hoffmann A, Fowler VG, Yeaman MR. Transcriptional signatures differentiate pathogen- and treatment-specific host responses in patients with bacterial bloodstream infections. J Infect Dis. 2023 Nov 24. view on PubMed

Grubwieser P, Hilbe R, Gehrer CM, Grander M, Brigo N, Hoffmann A, Seifert M, Berger S, Theurl I, Nairz M, Weiss G. Klebsiella pneumoniae manipulates human macrophages to acquire iron. Front Microbiol. 2023; 14:1223113. view on PubMed

Dalhoff R, Schmidt R, Steeb L, Rabatinova K, Witte M, Teeuwen S, Benjamaâ S, Hüppe H, Hoffmann A, Herres-Pawlis S. The bridge towards a more stable and active side-on-peroxido (Cu2II(µ-η2:η2-O2)) complex as a tyrosinase model system. Faraday Discuss. 2023 Aug 11; 244(0):134-153. view on PubMed

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. J Allergy Clin Immunol. 2023 11; 152(5):1261-1272. view on PubMed

Fuchs M, Schäfer PM, Wagner W, Krumm I, Walbeck M, Dietrich R, Hoffmann A, Herres-Pawlis S. A Multitool for Circular Economy: Fast Ring-Opening Polymerization and Chemical Recycling of (Bio)polyesters Using a Single Aliphatic Guanidine Carboxy Zinc Catalyst. ChemSusChem. 2023 Jun 22; 16(12):e202300779. view on PubMed

Fuchs M, Schäfer PM, Wagner W, Krumm I, Walbeck M, Dietrich R, Hoffmann A, Herres-Pawlis S. A Multitool for Circular Economy: Fast Ring-Opening Polymerization and Chemical Recycling of (Bio)polyesters Using a Single Aliphatic Guanidine Carboxy Zinc Catalyst. ChemSusChem. 2023 Jun 22; 16(12):e202300192. view on PubMed

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 Sci Educ. 2023 06; 22(2):ar25. view on PubMed

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 Rep. 2023 Jul 05; 24(7):e55986. view on PubMed

Hoffmann A. Designer genes courtesy of artificial intelligence. Genes Dev. 2023 05 01; 37(9-10):351-353. view on PubMed

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. Mol Syst Biol. 2023 05 09; 19(5):e11294. view on PubMed

Mitchell S, Tsui R, Tan ZC, Pack A, Hoffmann A. The NF-κB multidimer system model: A knowledge base to explore diverse biological contexts. Sci Signal. 2023 03 14; 16(776):eabo2838. view on PubMed

Hüppe HM, Iffland-Mühlhaus L, Heck J, Eilers M, Gildenast H, Schönfeld S, Dürrmann A, Hoffmann A, Weber B, Apfel UP, Herres-Pawlis S. Triflate vs Acetonitrile: Understanding the Iron(II)-Based Coordination Chemistry of Tri(quinolin-8-yl)amine. Inorg Chem. 2023 Mar 20; 62(11):4435-4455. view on PubMed

Ildefonso GV, Oliver Metzig M, Hoffmann A, Harris LA, Lopez CF. A biochemical necroptosis model explains cell-type-specific responses to cell death cues. Biophys J. 2023 03 07; 122(5):817-834. view on PubMed

Sheu KM, Guru AA, Hoffmann A. Quantifying stimulus-response specificity to probe the functional state of macrophages. Cell Syst. 2023 03 15; 14(3):180-195.e5. view on PubMed

Burkart L, Eith A, Hoffmann A, Herres-Pawlis S. Open Loop Recycling - Guanidine Iron(II) Polymerization Catalyst for the Depolymerization of Polylactide. Chem Asian J. 2023 Mar 01; 18(5):e202201195. view on PubMed

De Souza LV, Hoffmann A, Fischer C, Petzer V, Asshoff M, Theurl I, Tymoszuk P, Seifert M, Brigo N, Hilbe R, Demetz E, Von Raffay L, Berger S, Barros-Pinkelnig M, Weiss G. Comparative analysis of oral and intravenous iron therapy in rat models of inflammatory anemia and iron deficiency. Haematologica. 2023 01 01; 108(1):135-149. view on PubMed

Lefaudeux D, Sen S, Jiang K, Hoffmann A, UCLA Ribonomics Group. Kinetics of mRNA nuclear export regulate innate immune response gene expression. Nat Commun. 2022 11 23; 13(1):7197. view on PubMed

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. J Autoimmun. 2023 May; 137:102946. view on PubMed

Gehrer CM, Hoffmann A, Hilbe R, Grubwieser P, Mitterstiller AM, Talasz H, Fang FC, Meyron-Holtz EG, Atkinson SH, Weiss G, Nairz M. Availability of Ferritin-Bound Iron to Enterobacteriaceae. Int J Mol Sci. 2022 Oct 28; 23(21). view on PubMed

Brammer JC, Blanke G, Kellner C, Hoffmann A, Herres-Pawlis S, Schatzschneider U. TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson. J Cheminform. 2022 Sep 28; 14(1):66. view on PubMed

Okumura A, Ghana P, Fink F, Schmidt R, Hoffmann A, Spaniol TP, Herres-Pawlis S, Okuda J. Formate complexes of tri- and tetravalent titanium supported by a tris(phenolato)amine ligand. Dalton Trans. 2022 Sep 26; 51(37):14345-14351. view on PubMed

Kröckert KW, Garg F, Heinz MV, Lange J, Simões PP, Schmidt R, Bienemann O, Hoffmann A, Herres-Pawlis S. Understanding the structure-activity relationship and performance of highly active novel ATRP catalysts. Dalton Trans. 2022 Sep 13; 51(35):13272-13287. view on PubMed

Hermann A, Becker T, Schäfer MA, Hoffmann A, Herres-Pawlis S. Effective Ligand Design: Zinc Complexes with Guanidine Hydroquinoline Ligands for Fast Lactide Polymerization and Chemical Recycling. ChemSusChem. 2022 Sep 20; 15(18):e202201603. view on PubMed

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 Syst Biol Appl. 2022 Aug 04; 8(1):26. view on PubMed

Hermann A, Becker T, Schäfer MA, Hoffmann A, Herres-Pawlis S. Effective Ligand Design: Zinc Complexes with Guanidine Hydroquinoline Ligands for Fast Lactide Polymerization and Chemical Recycling. ChemSusChem. 2022 Sep 20; 15(18):e202201075. view on PubMed

Tang Y, Hoffmann A. Quantifying information of intracellular signaling: progress with machine learning. Rep Prog Phys. 2022 07 12; 85(8). view on PubMed

Kim J, Sheu KM, Cheng QJ, Hoffmann A, Enciso G. Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling. Cell Rep. 2022 07 12; 40(2):111076. view on PubMed

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. Chem Sci. 2022 Jul 20; 13(28):8274-8288. view on PubMed

Grander M, Hoffmann A, Seifert M, Demetz E, Grubwieser P, Pfeifhofer-Obermair C, Haschka D, Weiss G. DMT1 Protects Macrophages from Salmonella Infection by Controlling Cellular Iron Turnover and Lipocalin 2 Expression. Int J Mol Sci. 2022 Jun 17; 23(12). view on PubMed

Raßpe-Lange L, Hoffmann A, Gertig C, Heck J, Leonhard K, Herres-Pawlis S. Geometrical benchmarking and analysis of redox potentials of copper(I/II) guanidine-quinoline complexes: Comparison of semi-empirical tight-binding and DFT methods and the challenge of describing the entatic state (part III). J Comput Chem. 2023 01 30; 44(3):319-328. view on PubMed

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; 17(5):e0268861. view on PubMed

Grubwieser P, Hoffmann A, Hilbe R, Seifert M, Sonnweber T, Böck N, Theurl I, Weiss G, Nairz M. Airway Epithelial Cells Differentially Adapt Their Iron Metabolism to Infection With Klebsiella pneumoniae and Escherichia coli In Vitro. Front Cell Infect Microbiol. 2022; 12:875543. view on PubMed

Vaidehi Narayanan H, Hoffmann A. From Antibody Repertoires to Cell-Cell Interactions to Molecular Networks: Bridging Scales in the Germinal Center. Front Immunol. 2022; 13:898078. view on PubMed

Sheu KM, Hoffmann A. Functional Hallmarks of Healthy Macrophage Responses: Their Regulatory Basis and Disease Relevance. Annu Rev Immunol. 2022 04 26; 40:295-321. view on PubMed

Oliver Metzig M, Hoffmann A. Controlling Cancer Cell Death Types to Optimize Anti-Tumor Immunity. Biomedicines. 2022 Apr 22; 10(5). view on PubMed

Fuchs M, Walbeck M, Jagla E, Hoffmann A, Herres-Pawlis S. Guanidine Carboxy Zinc Complexes for the Chemical Recycling of Renewable Polyesters. Chempluschem. 2022 05; 87(5):e202200029. view on PubMed

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 Sci Educ. 2022 03; 21(1):ar1. view on PubMed

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. Proc Natl Acad Sci U S A. 2022 01 25; 119(4). view on PubMed

Nairz M, Metzendorf C, Vujic-Spasic M, Mitterstiller AM, Schroll A, Haschka D, Hoffmann A, Von Raffay L, Sparla R, Huck CW, Talasz H, Moser PL, Muckenthaler MU, Weiss G. Cell-specific expression of Hfe determines the outcome of Salmonella enterica serovar Typhimurium infection in mice Haematologica. 2021 12 01; 106(12):3149-3161. view on PubMed

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 Syst Biol Appl. 2021 12 01; 7(1):42. view on PubMed

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. Front Immunol. 2021; 12:750659. view on PubMed

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 11 08; 6(21). view on PubMed

Luecke S, Sheu KM, Hoffmann A. Stimulus-specific responses in innate immunity: Multilayered regulatory circuits. Immunity. 2021 09 14; 54(9):1915-1932. view on PubMed

Hoffmann A, Haschka D, Valente de Souza L, Tymoszuk P, Seifert M, von Raffay L, Hilbe R, Petzer V, Moser PL, Nairz M, Weiss G. Baseline iron status and presence of anaemia determine the course of systemic Salmonella infection following oral iron supplementation in mice. EBioMedicine. 2021 Sep; 71:103568. view on PubMed

Rittinghaus RD, Karabulut A, Hoffmann A, Herres-Pawlis S. Active in Sleep: Iron Guanidine Catalyst Performs ROP on Dormant Side of ATRP. Angew Chem Int Ed Engl. 2021 09 27; 60(40):21795-21800. view on PubMed

Hoffmann A, de Souza LV, Seifert M, von Raffay L, Haschka D, Grubwieser P, Grander M, Mitterstiller AM, Nairz M, Poli M, Weiss G. Pharmacological Targeting of BMP6-SMAD Mediated Hepcidin Expression Does Not Improve the Outcome of Systemic Infections With Intra-Or Extracellular Gram-Negative Bacteria in Mice. Front Cell Infect Microbiol. 2021; 11:705087. view on PubMed

Paul M, Teubner M, Grimm-Lebsanft B, Buchenau S, Hoffmann A, Rübhausen M, Herres-Pawlis S. Influence of the amine donor on hybrid guanidine-stabilized Bis(μ-oxido) dicopper(III) complexes and their tyrosinase-like oxygenation activity towards polycyclic aromatic alcohols. J Inorg Biochem. 2021 11; 224:111541. view on PubMed

Wang N, Lefaudeux D, Mazumder A, Li JJ, Hoffmann A. Identifying the combinatorial control of signal-dependent transcription factors. PLoS Comput Biol. 2021 06; 17(6):e1009095. view on PubMed

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. 2021 06 18; 372(6548):1349-1353. view on PubMed

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. J Clin Invest. 2021 06 15; 131(12). view on PubMed

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 05 11; 54(5):916-930.e7. view on PubMed

Thomas F, Oster M, Schön F, Göbgen KC, Amarouch B, Steden D, Hoffmann A, Herres-Pawlis S. A new generation of terminal copper nitrenes and their application in aromatic C-H amination reactions. Dalton Trans. 2021 May 21; 50(19):6444-6462. view on PubMed

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. Front Immunol. 2021; 12:651254. view on PubMed

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. Proc Natl Acad Sci U S A. 2021 03 09; 118(10). view on PubMed

Tang Y, Adelaja A, Ye FX, Deeds E, Wollman R, Hoffmann A. Quantifying information accumulation encoded in the dynamics of biochemical signaling. Nat Commun. 2021 02 24; 12(1):1272. view on PubMed

Paul M, Hoffmann A, Herres-Pawlis S. Room temperature stable multitalent: highly reactive and versatile copper guanidine complexes in oxygenation reactions. J Biol Inorg Chem. 2021 05; 26(2-3):249-263. view on PubMed

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. Sci Signal. 2021 01 19; 14(666). view on PubMed

Haschka D, Hoffmann A, Weiss G. Iron in immune cell function and host defense. Semin Cell Dev Biol. 2021 07; 115:27-36. view on PubMed

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. Mol Syst Biol. 2020 12; 16(12):e9677. view on PubMed

Valente de Souza L, Hoffmann A, Weiss G. Impact of bacterial infections on erythropoiesis. Expert Rev Anti Infect Ther. 2021 05; 19(5):619-633. view on PubMed

Hermann A, Hill S, Metz A, Heck J, Hoffmann A, Hartmann L, Herres-Pawlis S. Next Generation of Zinc Bisguanidine Polymerization Catalysts towards Highly Crystalline, Biodegradable Polyesters. Angew Chem Int Ed Engl. 2020 11 23; 59(48):21778-21784. view on PubMed

Keisers K, Hüppe HM, Iffland-Mühlhaus L, Hoffmann A, Göbel C, Apfel UP, Weber B, Herres-Pawlis S. Interplay of Spin Crossover and Coordination-Induced Spin State Switch for Iron Bis(pyrazolyl)methanes in Solution. Inorg Chem. 2020 Oct 19; 59(20):15343-15354. view on PubMed

Petzer V, Tymoszuk P, Asshoff M, Carvalho J, Papworth J, Deantonio C, Bayliss L, Wake MS, Seifert M, Brigo N, Valente de Souza L, Hilbe R, Grubwieser P, Demetz E, Dichtl S, Volani C, Berger S, Böhm F, Hoffmann A, Pfeifhofer-Obermair C, von Raffay L, Sopper S, Arndt S, Bosserhoff A, Kautz L, Perrier P, Nairz M, Wolf D, Weiss G, Germaschewski V, Theurl I. A fully human anti-BMP6 antibody reduces the need for erythropoietin in rodent models of the anemia of chronic disease. Blood. 2020 08 27; 136(9):1080-1090. view on PubMed

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. J Immunol. 2020 09 15; 205(6):1540-1553. view on PubMed

Schäfer D, Fink F, Kleinschmidt D, Keisers K, Thomas F, Hoffmann A, Pich A, Herres-Pawlis S. Enhanced catalytic activity of copper complexes in microgels for aerobic oxidation of benzyl alcohols. Chem Commun (Camb). 2020 May 27; 56(42):5601-5604. view on PubMed

Paul M, Teubner M, Grimm-Lebsanft B, Golchert C, Meiners Y, Senft L, Keisers K, Liebhäuser P, Rösener T, Biebl F, Buchenau S, Naumova M, Murzin V, Krug R, Hoffmann A, Pietruszka J, Ivanovic-Burmazovic I, Rübhausen M, Herres-Pawlis S. Exceptional Substrate Diversity in Oxygenation Reactions Catalyzed by a Bis(μ-oxo) Copper Complex. Chemistry. 2020 Jun 18; 26(34):7556-7562. view on PubMed

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 Rep. 2020 02 25; 30(8):2758-2775.e6. view on PubMed

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 Syst. 2020 02 26; 10(2):169-182.e5. view on PubMed

Rittinghaus RD, Tremmel J, Ružicka A, Conrads C, Albrecht P, Hoffmann A, Ksiazkiewicz AN, Pich A, Jambor R, Herres-Pawlis S. Undiscovered Potential: Ge Catalysts for Lactide Polymerization. Chemistry. 2020 Jan 02; 26(1):212-221. view on PubMed

Sheu K, Luecke S, Hoffmann A. Stimulus-specificity in the Responses of Immune Sentinel Cells. Curr Opin Syst Biol. 2019 Dec; 18:53-61. view on PubMed

Mikkaichi T, Yeaman MR, Hoffmann A, MRSA Systems Immunobiology Group. Identifying determinants of persistent MRSA bacteremia using mathematical modeling. PLoS Comput Biol. 2019 07; 15(7):e1007087. view on PubMed

Adelaja A, Hoffmann A. Signaling Crosstalk Mechanisms That May Fine-Tune Pathogen-Responsive NFκB. Front Immunol. 2019; 10:433. view on PubMed

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. Front Immunol. 2019; 10:1425. view on PubMed

Brazeau SEN, Norwine EE, Hannigan SF, Orth N, Ivanovic-Burmazovic I, Rukser D, Biebl F, Grimm-Lebsanft B, Praedel G, Teubner M, Rübhausen M, Liebhäuser P, Rösener T, Stanek J, Hoffmann A, Herres-Pawlis S, Doerrer LH. Dual oxidase/oxygenase reactivity and resonance Raman spectra of {Cu3O2} moiety with perfluoro-t-butoxide ligands. Dalton Trans. 2019 May 21; 48(20):6899-6909. view on PubMed

Schäfer PM, McKeown P, Fuchs M, Rittinghaus RD, Hermann A, Henkel J, Seidel S, Roitzheim C, Ksiazkiewicz AN, Hoffmann A, Pich A, Jones MD, Herres-Pawlis S. Tuning a robust system: N,O zinc guanidine catalysts for the ROP of lactide. Dalton Trans. 2019 May 07; 48(18):6071-6082. view on PubMed

Mitchell S, Hoffmann A. 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. view on PubMed

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 03 27; 9(1):5288. view on PubMed

Rittinghaus RD, Schäfer PM, Albrecht P, Conrads C, Hoffmann A, Ksiazkiewicz AN, Bienemann O, Pich A, Herres-Pawlis S. New Kids in Lactide Polymerization: Highly Active and Robust Iron Guanidine Complexes as Superior Catalysts. ChemSusChem. 2019 May 21; 12(10):2161-2165. view on PubMed

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 03 19; 50(3):616-628.e6. view on PubMed

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 Res. 2019 Feb 20; 47(3):1602-1603. view on PubMed

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 02 05; 10(1). view on PubMed

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 Res. 2018 11 16; 46(20):10598-10607. view on PubMed

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. view on PubMed

Moegling J, Hoffmann A, Thomas F, Orth N, Liebhäuser P, Herber U, Rampmaier R, Stanek J, Fink G, Ivanovic-Burmazovic I, Herres-Pawlis S. Designed To React: Terminal Copper Nitrenes and Their Application in Catalytic C-H Aminations. Angew Chem Int Ed Engl. 2018 Jul 16; 57(29):9154-9159. view on PubMed

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. view on PubMed

Zöller T, Dietz C, Winter F, Pöttgen R, Gorelsky SI, Hoffmann A, Herres-Pawlis S, Jurkschat K. Rational Syntheses and Serendipity: Complexes [LSnPtCl2 (SMe2 )]2 , [{LSnPtCl(SMe2 )}2 SnCl2 ], [(LSn)3 (PtCl2 )(PtClSnCl){LSn(Cl)OH}], and [O(SnCl)2 (SnL)2 ] with L=MeN(CH2 CMe2 O)2. Chemistry. 2018 Apr 11; 24(21):5551-5561. view on PubMed

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. view on PubMed

Mitchell S, Hoffmann A. Identifying Noise Sources governing cell-to-cell variability. Curr Opin Syst Biol. 2018 Apr; 8:39-45. view on PubMed

Schäfer PM, Fuchs M, Ohligschläger A, Rittinghaus R, McKeown P, Akin E, Schmidt M, Hoffmann A, Liauw MA, Jones MD, Herres-Pawlis S. Corrigendum: Highly Active N,O Zinc Guanidine Catalysts for the Ring-Opening Polymerization of Lactide. ChemSusChem. 2017 12 08; 10(23):4799. view on PubMed

Stanek J, Sackers N, Fink F, Paul M, Peters L, Grunzke R, Hoffmann A, Herres-Pawlis S. Copper Guanidinoquinoline Complexes as Entatic State Models of Electron-Transfer Proteins. Chemistry. 2017 Nov 07; 23(62):15738-15745. view on PubMed

Schäfer PM, Fuchs M, Ohligschläger A, Rittinghaus R, McKeown P, Akin E, Schmidt M, Hoffmann A, Liauw MA, Jones MD, Herres-Pawlis S. Highly Active N,O Zinc Guanidine Catalysts for the Ring-Opening Polymerization of Lactide. ChemSusChem. 2017 09 22; 10(18):3547-3556. view on PubMed

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. view on PubMed

Liebhäuser P, Keisers K, Hoffmann A, Schnappinger T, Sommer I, Thoma A, Wilfer C, Schoch R, Stührenberg K, Bauer M, Dürr M, Ivanovic-Burmazovic I, Herres-Pawlis S. Record Broken: A Copper Peroxide Complex with Enhanced Stability and Faster Hydroxylation Catalysis. Chemistry. 2017 Sep 07; 23(50):12171-12183. view on PubMed

Hannigan SF, Arnoff AI, Neville SE, Lum JS, Golen JA, Rheingold AL, Orth N, Ivanovic-Burmazovic I, Liebhäuser P, Rösener T, Stanek J, Hoffmann A, Herres-Pawlis S, Doerrer LH. On the Way to a Trisanionic {Cu3 O2 } Core for Oxidase Catalysis: Evidence of an Asymmetric Trinuclear Precursor Stabilized by Perfluoropinacolate Ligands. Chemistry. 2017 Jun 16; 23(34):8212-8224. view on PubMed

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. Proc Natl Acad Sci U S A. 2017 03 28; 114(13):E2776-E2785. view on PubMed

Cheng CS, Behar MS, Suryawanshi GW, Feldman KE, Spreafico R, Hoffmann A. Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms. Cell Syst. 2017 03 22; 4(3):330-343.e5. view on PubMed

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. Proc Natl Acad Sci U S A. 2017 02 21; 114(8):1916-1921. view on PubMed

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 12 08; 1(20):e89679. view on PubMed

Vollmers NJ, Müller P, Hoffmann A, Herres-Pawlis S, Rohrmüller M, Schmidt WG, Gerstmann U, Bauer M. Experimental and Theoretical High-Energy-Resolution X-ray Absorption Spectroscopy: Implications for the Investigation of the Entatic State. Inorg Chem. 2016 Nov 21; 55(22):11694-11706. view on PubMed

Arshad J, Hoffmann A, Gesing S, Grunzke R, Krüger J, Kiss T, Herres-Pawlis S, Terstyanszky G. Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry. J Cheminform. 2016; 8:58. view on PubMed

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 Syst Biol Appl. 2016; 2:16024. view on PubMed

Hejda M, Lycka A, Mikysek T, Jambor R, Ružicka A, Vinklárek J, Wilfer C, Hoffmann A, Herres-Pawlis S, Dostál L. Homolytic, Heterolytic, Mesolytic - As You Like It: Steering the Cleavage of a HC(sp3 )-C(sp3 )H Bond in Bis(1H-2,1-benzazaborole) Derivatives. Chemistry. 2016 Oct 17; 22(43):15340-15349. view on PubMed

Rösener T, Bienemann O, Sigl K, Schopp N, Schnitter F, Flörke U, Hoffmann A, Döring A, Kuckling D, Herres-Pawlis S. A Comprehensive Study of Copper Guanidine Quinoline Complexes: Predicting the Activity of Catalysts in ATRP with DFT. Chemistry. 2016 Sep 12; 22(38):13550-62. view on PubMed

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. J Exp Med. 2016 08 22; 213(9):1901-19. view on PubMed

Hoffmann A. Immune Response Signaling: Combinatorial and Dynamic Control. Trends Immunol. 2016 09; 37(9):570-572. view on PubMed

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. view on PubMed

Mitchell S, Vargas J, Hoffmann A. Signaling via the NFκB system. Wiley Interdiscip Rev Syst Biol Med. 2016 05; 8(3):227-41. view on PubMed

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. Nat Commun. 2016 Feb 22; 7:10761. view on PubMed

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. view on PubMed

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 Mar 10; 127(10):1276-86. view on PubMed

Herres-Pawlis S, Haase R, Verma P, Hoffmann A, Kang P, Stack TD. Formation of hybrid guanidine-stabilized bis(μ-oxo)dicopper cores in solution: Electronic and steric perturbations. Eur J Inorg Chem. 2015 Nov; 2015(32):5426-5436. view on PubMed

Wilfer C, Liebhäuser P, Hoffmann A, Erdmann H, Grossmann O, Runtsch L, Paffenholz E, Schepper R, Dick R, Bauer M, Dürr M, Ivanovic-Burmazovic I, Herres-Pawlis S. Efficient Biomimetic Hydroxylation Catalysis with a Bis(pyrazolyl)imidazolylmethane Copper Peroxide Complex. Chemistry. 2015 Dec 01; 21(49):17639-49. view on PubMed

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. view on PubMed

Fagerlund R, Behar M, Fortmann KT, Lin YE, Vargas JD, Hoffmann A. Anatomy of a negative feedback loop: the case of IκBα. J R Soc Interface. 2015 Sep 06; 12(110):0262. view on PubMed

Fortmann KT, Lewis RD, Ngo KA, Fagerlund R, Hoffmann A. A Regulated, Ubiquitin-Independent Degron in IκBα. J Mol Biol. 2015 Aug 28; 427(17):2748-56. view on PubMed

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. view on PubMed

Rohrmüller M, Hoffmann A, Thierfelder C, Herres-Pawlis S, Schmidt WG. The Cu2O2 torture track for a real-life system: [Cu2(btmgp)2O2](2+) oxo and peroxo species in density functional calculations. J Comput Chem. 2015 Aug 15; 36(22):1672-85. view on PubMed

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. Nat Commun. 2015 May 07; 6:7068. view on PubMed

Spreafico R, Mitchell S, Hoffmann A. Training the 21st Century Immunologist. Trends Immunol. 2015 May; 36(5):283-5. view on PubMed

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. view on PubMed

Novák M, Bouška M, Dostál L, Ružicka A, Hoffmann A, Herres-Pawlis S, Jambor R. Less is more: three-coordinate c,n-chelated distannynes and digermynes. Chemistry. 2015 May 18; 21(21):7820-9. view on PubMed

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. J Invest Dermatol. 2015 Aug; 135(8):2012-2020. view on PubMed

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. Mol Syst Biol. 2015 Feb 13; 11(1):783. view on PubMed

Vránová I, Jambor R, Ružicka A, Hoffmann A, Herres-Pawlis S, Dostál L. Antimony(III) and bismuth(III) amides containing pendant N-donor groups--a combined experimental and theoretical study. Dalton Trans. 2015 Jan 07; 44(1):395-400. view on PubMed

Mitchell S, Tsui R, Hoffmann A. Studying NF-κB signaling with mathematical models. Methods Mol Biol. 2015; 1280:647-61. view on PubMed

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 Res. 2015 Jan; 43(2):699-707. view on PubMed

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. 2014 Dec 12; 346(6215):1370-3. view on PubMed

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 Rep. 2014 Dec 24; 9(6):2098-111. view on PubMed

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. J Leukoc Biol. 2015 Feb; 97(2):307-20. view on PubMed

Caldwell AB, Cheng Z, Vargas JD, Birnbaum HA, Hoffmann A. Network dynamics determine the autocrine and paracrine signaling functions of TNF. Genes Dev. 2014 Oct 01; 28(19):2120-33. view on PubMed

Hoffmann A, Rohrmüller M, Jesser A, dos Santos Vieira I, Schmidt WG, Herres-Pawlis S. Geometrical and optical benchmarking of copper(II) guanidine-quinoline complexes: insights from TD-DFT and many-body perturbation theory (part II). J Comput Chem. 2014 Nov 05; 35(29):2146-61. view on PubMed

Hoffmann A, Grunzke R, Herres-Pawlis S. Insights into the influence of dispersion correction in the theoretical treatment of guanidine-quinoline copper(I) complexes. J Comput Chem. 2014 Oct 15; 35(27):1943-50. view on PubMed

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 Res Int. 2014; 2014:624024. view on PubMed

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. 2014 May 16; 344(6185):760-4. view on PubMed

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. J Immunol. 2014 Apr 01; 192(7):3121-32. view on PubMed

Hoffmann A, Herres-Pawlis S. Hiking on the potential energy surface of a functional tyrosinase model--implications of singlet, broken-symmetry and triplet description. Chem Commun (Camb). 2014 Jan 14; 50(4):403-5. view on PubMed

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. J Biol Chem. 2014 Jan 17; 289(3):1866-75. view on PubMed

Hoffmann A, Binder S, Jesser A, Haase R, Flörke U, Gnida M, Salomone Stagni M, Meyer-Klaucke W, Lebsanft B, Grünig LE, Schneider S, Hashemi M, Goos A, Wetzel A, Rübhausen M, Herres-Pawlis S. Catching an entatic state--a pair of copper complexes. Angew Chem Int Ed Engl. 2014 Jan 03; 53(1):299-304. view on PubMed

Behar M, Barken D, Werner SL, Hoffmann A. The dynamics of signaling as a pharmacological target. Cell. 2013 Oct 10; 155(2):448-61. view on PubMed

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 Negl Trop Dis. 2013; 7(9):e2424. view on PubMed

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 Biol. 2013 Sep; 11(9):e1001647. view on PubMed

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 Aug 12; 24(2):151-66. view on PubMed

Behar M, Hoffmann A. Tunable signal processing through a kinase control cycle: the IKK signaling node. Biophys J. 2013 Jul 02; 105(1):231-41. view on PubMed

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 Comput Biol. 2013; 9(6):e1003112. view on PubMed

Shokhirev MN, Hoffmann A. FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses. PLoS One. 2013; 8(6):e67620. view on PubMed

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 Biol. 2013; 11(6):e1001581. view on PubMed

Hoffmann A, Citek C, Binder S, Goos A, Rübhausen M, Troeppner O, Ivanovic-Burmazovic I, Wasinger EC, Stack TD, Herres-Pawlis S. Catalytic phenol hydroxylation with dioxygen: extension of the tyrosinase mechanism beyond the protein matrix. Angew Chem Int Ed Engl. 2013 May 10; 52(20):5398-401. view on PubMed

Loriaux PM, Hoffmann A. A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways. PLoS Comput Biol. 2013; 9(2):e1002932. view on PubMed

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 Comput Biol. 2013; 9(2):e1002901. view on PubMed

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; 7(10):e45078. view on PubMed

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. Nat Immunol. 2012 Dec; 13(12):1162-70. view on PubMed

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 Rep. 2012 Oct 25; 2(4):824-39. view on PubMed

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. Mol Cell. 2012 Jul 13; 47(1):111-21. view on PubMed

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 Apr 27; 149(3):630-41. view on PubMed

Basak S, Behar M, Hoffmann A. Lessons from mathematically modeling the NF-κB pathway. Immunol Rev. 2012 Mar; 246(1):221-38. view on PubMed

Loriaux PM, Hoffmann A. A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness. Methods Cell Biol. 2012; 110:81-109. view on PubMed

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. view on PubMed

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. J Clin Invest. 2011 Dec; 121(12):4775-86. view on PubMed

Schröfelbauer B, Hoffmann A. How do pleiotropic kinase hubs mediate specific signaling by TNFR superfamily members? Immunol Rev. 2011 Nov; 244(1):29-43. view on PubMed

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. Sci Signal. 2011 Feb 22; 4(161):ra11. view on PubMed

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 Feb 25; 34(2):188-200. view on PubMed

Ho JQ, Asagiri M, Hoffmann A, Ghosh G. NF-κB potentiates caspase independent hydrogen peroxide induced cell death. PLoS One. 2011 Feb 15; 6(2):e16815. view on PubMed

Huxford T, Hoffmann A, Ghosh G. Understanding the logic of IκB:NF-κB regulation in structural terms. Curr Top Microbiol Immunol. 2011; 349:1-24. view on PubMed

Shih VF, Tsui R, Caldwell A, Hoffmann A. A single NFκB system for both canonical and non-canonical signaling. Cell Res. 2011 Jan; 21(1):86-102. view on PubMed

Hasty J, Hoffmann A, Golden S. Systems biology of cellular rhythms: from cacophony to symphony. Curr Opin Genet Dev. 2010 Dec; 20(6):571-3. view on PubMed

Behar M, Hoffmann A. Understanding the temporal codes of intra-cellular signals. Curr Opin Genet Dev. 2010 Dec; 20(6):684-93. view on PubMed

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 Aug 26; 466(7310):1115-9. view on PubMed

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. J Immunol. 2010 Jul 01; 185(1):670-8. view on PubMed

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 Dev. 2010 Mar 01; 24(5):491-501. view on PubMed

O'Dea E, Hoffmann A. The regulatory logic of the NF-kappaB signaling system. Cold Spring Harb Perspect Biol. 2010 Jan; 2(1):a000216. view on PubMed

Bergqvist S, Alverdi V, Mengel B, Hoffmann A, Ghosh G, Komives EA. Kinetic enhancement of NF-kappaBxDNA dissociation by IkappaBalpha. Proc Natl Acad Sci U S A. 2009 Nov 17; 106(46):19328-33. view on PubMed

Longo DM, Hoffmann A, Tsimring LS, Hasty J. Coherent activation of a synthetic mammalian gene network. Syst Synth Biol. 2010 Mar; 4(1):15-23. view on PubMed

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. view on PubMed

O'Dea E, Hoffmann A. NF-κB signaling. Wiley Interdiscip Rev Syst Biol Med. 2009 Jul-Aug; 1(1):107-115. view on PubMed

Savinova OV, Hoffmann A, Ghosh G. The Nfkb1 and Nfkb2 proteins p105 and p100 function as the core of high-molecular-weight heterogeneous complexes. Mol Cell. 2009 Jun 12; 34(5):591-602. view on PubMed

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. Proc Natl Acad Sci U S A. 2009 Jun 16; 106(24):9619-24. view on PubMed

Loriaux P, Hoffmann A. Of elections and cell-death decisions. Mol Cell. 2009 May 15; 34(3):257-8. view on PubMed

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. Proc Natl Acad Sci U S A. 2008 Nov 11; 105(45):17463-8. view on PubMed

Kearns JD, Hoffmann A. Integrating computational and biochemical studies to explore mechanisms in NF-{kappa}B signaling. J Biol Chem. 2009 Feb 27; 284(9):5439-43. view on PubMed

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 Dev. 2008 Aug 01; 22(15):2093-101. view on PubMed

O'Dea EL, Kearns JD, Hoffmann A. UV as an amplifier rather than inducer of NF-kappaB activity. Mol Cell. 2008 Jun 06; 30(5):632-41. view on PubMed

Basak S, Hoffmann A. Crosstalk via the NF-kappaB signaling system. Cytokine Growth Factor Rev. 2008 Jun-Aug; 19(3-4):187-97. view on PubMed

Cheong R, Hoffmann A, Levchenko A. Understanding NF-kappaB signaling via mathematical modeling. Mol Syst Biol. 2008; 4:192. view on PubMed

Cheng CS, Johnson TL, Hoffmann A. Epigenetic control: slow and global, nimble and local. Genes Dev. 2008 May 01; 22(9):1110-4. view on PubMed

Kato T, Gotoh Y, Hoffmann A, Ono Y. Negative regulation of constitutive NF-kappaB and JNK signaling by PKN1-mediated phosphorylation of TRAF1. Genes Cells. 2008 May; 13(5):509-20. view on PubMed

Mathes E, O'Dea EL, Hoffmann A, Ghosh G. NF-kappaB dictates the degradation pathway of IkappaBalpha. EMBO J. 2008 May 07; 27(9):1357-67. view on PubMed

Fusco AJ, Savinova OV, Talwar R, Kearns JD, Hoffmann A, Ghosh G. Stabilization of RelB requires multidomain interactions with p100/p52. J Biol Chem. 2008 May 02; 283(18):12324-32. view on PubMed

Basak S, Shih VF, Hoffmann A. Generation and activation of multiple dimeric transcription factors within the NF-kappaB signaling system. Mol Cell Biol. 2008 May; 28(10):3139-50. view on PubMed

Ch'en IL, Hedrick SM, Hoffmann A. NF-kappaB as a determinant of distinct cell death pathways. Methods Enzymol. 2008; 446:175-87. view on PubMed

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. Mol Syst Biol. 2007; 3:111. view on PubMed

Hoffmann A, Xia Y, Verma IM. Inflammatory tales of liver cancer. Cancer Cell. 2007 Feb; 11(2):99-101. view on PubMed

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 Jan 26; 128(2):369-81. view on PubMed

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. J Cell Biol. 2006 Jun 05; 173(5):659-64. view on PubMed

Hoffmann A, Baltimore D. Circuitry of nuclear factor kappaB signaling. Immunol Rev. 2006 Apr; 210:171-86. view on PubMed

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. J Biol Chem. 2006 Feb 03; 281(5):2945-50. view on PubMed

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. 2006 Feb 01; 107(3):1048-55. view on PubMed

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 Sep 29; 24(43):6574-83. view on PubMed

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. view on PubMed

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. view on PubMed

Beisner DR, Ch'en IL, Kolla RV, Hoffmann A, Hedrick SM. Cutting edge: innate immunity conferred by B cells is regulated by caspase-8. J Immunol. 2005 Sep 15; 175(6):3469-73. view on PubMed

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. view on PubMed

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 Sep; 23(3):319-29. view on PubMed

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. J Cell Sci. 2005 Aug 01; 118(Pt 15):3501-8. view on PubMed

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. view on PubMed

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. 2005 Apr 01; 308(5718):52; author reply 52. view on PubMed

Leung TH, Hoffmann A, Baltimore D. One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers. Cell. 2004 Aug 20; 118(4):453-64. view on PubMed

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. view on PubMed

Hoffmann A, Leung TH, Baltimore D. Genetic analysis of NF-kappaB/Rel transcription factors defines functional specificities. EMBO J. 2003 Oct 15; 22(20):5530-9. view on PubMed

Kato T, Delhase M, Hoffmann A, Karin M. CK2 Is a C-Terminal IkappaB Kinase Responsible for NF-kappaB Activation during the UV Response. Mol Cell. 2003 Oct; 12(4):829-39. view on PubMed

Hoffmann A, Levchenko A, Scott ML, Baltimore D. The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science. 2002 Nov 08; 298(5596):1241-5. view on PubMed

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. view on PubMed