1. Hoffmann, A. & Baltimore, D. Circuitry of nuclear factor κB signaling. Immunol.Rev. 210, 171–186 (2006).
2. Lee, S. H. & Hannink, M. Characterization of the nuclear import and export functions of IκBε. J. Biol. Chem. 277, 23358–23366 (2002).
3. Tam, W. F., Lee, L. H., Davis, L. & Sen, R. Cytoplasmic Sequestration of Rel Proteins by IκBα Requires CRM1-Dependent Nuclear Export. Mol. Cell. Biol. 20, 2269–2284 (2000).
4. Hoffmann, A., Levchenko, A., Scott, M. L. & Baltimore, D. The IκB-NF-κB signaling module: Temporal control and selective gene activation. Science (80-. ). 298, 1241–1245 (2002).
5. Gilmore, T. D. Introduction to NF-κB: Players, pathways, perspectives.Oncogene 25, 6680–6684 (2006).
6. Basak, S., Shih, V. F.-S. & Hoffmann, A. Generation and Activation of Multiple Dimeric Transcription Factors within the NF-κB Signaling System. Mol. Cell. Biol. 28, 3139–3150 (2008).
7. Bours, V. et al. The oncoprotein Bcl-3 directly transactivates through κB motifs via association with DNA-binding p50B homodimers. Cell (1993) doi:10.1016/0092-8674(93)90401-B.
8. Claudio, E., Brown, K. & Siebenlist, U. NF-κB guides the survival and differentiation of developing lymphocytes. Cell Death Differ. 13, 697–701 (2006).
9. Dejardin, E. et al. The Lymphotoxin-Receptor Induces Different Patterns of Gene Expression via Two NF-B Pathways quire LTR signaling for their expression in development (Ngo et al The NF-B family of transcription factors regulates expression of genes crucial to innate and ad. Immunity 17, 525–535 (2002).
10. Hoffmann, A., Natoli, G. & Ghosh, G. Transcriptional regulation via the NF-κB signaling module. Oncogene 25, 6706–6716 (2006).
11. Oeckinghaus, A. & Ghosh, S. The NF-kappaB family of transcription factors and its regulation. Cold Spring Harbor perspectives in biology (2009) doi:10.1101/cshperspect.a000034.
12. Sarnico, I. et al. Activation of NF-κB p65/c-Rel dimer is associated with neuroprotection elicited by mGlu5 receptor agonists against MPP+ toxicity in SK-N-SH cells. J. Neural Transm. 115, 669–676 (2008).
13. Weih, D. S., Yilmaz, Z. B. & Weih, F. Essential Role of RelB in Germinal Center and Marginal Zone Formation and Proper Expression of Homing Chemokines. J. Immunol. 167, 1909–1919 (2001).
14. Yilmaz, Z. B., Weih, D. S., Sivakumar, V. & Weih, F. RelB is required for Peyer’s patch development: Differential regulation of p52-RelB by lymphotoxin and TNF. EMBO J. 22, 121–130 (2003).
15. Werner, S. L. et al. Encoding NF-κB temporal control in response to TNF: Distinct roles for the negative regulators IκBα and A20. Genes Dev. 22, 2093– 2101 (2008).
16. Basak, S., Behar, M. & Hoffmann, A. Lessons from mathematically modeling the NF-κB pathway. Immunol. Rev. (2012) doi:10.1111/j.1600-065X.2011.01092.x.
17. O’Dea, E. & Hoffmann, A. NF-κ B signaling. Wiley Interdiscip. Rev. Syst. Biol.Med. (2009) doi:10.1002/wsbm.30.
18. Beg, A. A., Finco, T. S., Nantermet, P. V & Baldwin, A. S. Tumor necrosis factor and interleukin-1 lead to phosphorylation and loss of I kappa B alpha: a mechanism for NF-kappa B activation. Mol. Cell. Biol. 13, 3301–3310 (1993).
19. Henkel, T. et al. Rapid proteolysis of IκB-α is necessary for activation of transcription factor NF-κB. Nature (1993) doi:10.1038/365182a0.
20. Kearns, J. D., Basak, S., Werner, S. L., Huang, C. S. & Hoffmann, A. IκBε provides negative feedback to control NF-κB oscillations, signaling dynamics, and inflammatory gene expression. J. Cell Biol. 173, 659–664 (2006).
21. Dembinski, H. E. et al. Functional importance of stripping in NFκB signaling revealed by a stripping-impaired IκBα mutant. Proc. Natl. Acad. Sci. U. S. A. 114, 1916–1921 (2017).
22. Mitchell, S., Vargas, J. & Hoffmann, A. Signaling via the NFκB system. Wiley Interdisciplinary Reviews: Systems Biology and Medicine (2016) doi:10.1002/wsbm.1331.
23. Sen, S., Cheng, Z., Sheu, K. M., Chen, Y. H. & Hoffmann, A. Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene Expression. Cell Syst. (2020) doi:10.1016/j.cels.2019.12.004.
24. Cheng, Q. J. et al. NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages. Science (80-. ). (2021) doi:10.1126/science.abc0269.
25. Adelaja, A. et al. Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses. Immunity (2021) doi:10.1016/j.immuni.2021.04.011.
26. Nalbandian, A. et al. Post-acute COVID-19 syndrome. Nat. Med. 27, 601–615 (2021).
27. Carfi, A.; Bernabei, R. and Landi, F. Persistent Symptoms in Patients After Acute COVID-19. JAMA 324, 603–605 (2020).
28. Tenforde, M. W. et al. Symptom Duration and Risk Factors for Delayed Return to Usual Health Among[1] M. W. Tenforde et al., “Symptom Duration and Risk Factors for Delayed Return to Usual Health Among Outpatients with COVID-19 in a Multistate Health Care Systems Network — United. MMWR. Morb. Mortal. Wkly. Rep. 69, 993–998 (2020).
29. Ramanathan, K. et al. 6-month consequences of COVID-19 in patients discharged from hospital: a cohort study. Lancet 397, 19–21 (2020).
30. McElvaney, O. J. et al. Characterization of the inflammatory response to severe COVID-19 Illness. Am. J. Respir. Crit. Care Med. 202, 812–821 (2020).
31. Sungnak, W. et al. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat. Med. 26, 681–687 (2020).
32. Tang, N., Li, D., Wang, X. & Sun, Z. Abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia. J. Thromb. Haemost. 18, 844–847 (2020).
33. Hirano, T. & Murakami, M. COVID-19: A New Virus, but a Familiar Receptor and Cytokine Release Syndrome. Immunity 52, 731–733 (2020).
34. Ren, X. et al. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. Cell 184, 1895-1913.e19 (2021).
35. Magi, S. et al. Transcriptionally inducible pleckstrin homology-like domain,family a, member 1, attenuates ERBB receptor activity by inhibiting receptor oligomerization. J. Biol. Chem. (2018) doi:10.1074/jbc.M117.778399.
36. Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015).
37. Kim, D., Langmead, B. & Salzberg, S. L. Hisat2. Nat. Methods (2015).
38. Krueger, F. Trim Galore!: A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. Babraham Inst. (2015).
39. Liao, Y., Smyth, G. K. & Shi, W. FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics (2014) doi:10.1093/bioinformatics/btt656.
40. Robinson, M., Mccarthy, D. & Smyth, G. K. edgeR. Most (2010).
41. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. (2014) doi:10.1186/s13059-014-0550-8.
42. Benner, C., Heinz, S. & Glass, C. K. HOMER - Software for motif discovery and next generation sequencing analysis. Http://Homer.Ucsd.Edu/ (2017).
43. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory- efficient alignment of short DNA sequences to the human genome. Genome Biol. (2009) doi:10.1186/gb-2009-10-3-r25.
44. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics(2009) doi:10.1093/bioinformatics/btp352.
45. Ramírez, F., Dündar, F., Diehl, S., Grüning, B. A. & Manke, T. DeepTools: A flexible platform for exploring deep-sequencing data. Nucleic Acids Res. (2014)doi:10.1093/nar/gku365.
46. Lee, R. E. C., Walker, S. R., Savery, K., Frank, D. A. & Gaudet, S. Fold change of nuclear NF-κB determines TNF-induced transcription in single cells. Mol. Cell 53, 867–879 (2014).
47. Cartwright, T., Perkins, N. D. & L Wilson, C. NFKB1: a suppressor of inflammation, ageing and cancer. The FEBS journal (2016) doi:10.1111/febs.13627.
48. Moorthy, A. K. et al. The 20S proteasome processes NF-κB1 p105 into p50 in a translation-independent manner. EMBO J. (2006) doi:10.1038/sj.emboj.7601081.
49. Grant, B. J., Rodrigues, A. P. C., ElSawy, K. M., McCammon, J. A. & Caves, L.S. D. Bio3d: An R package for the comparative analysis of protein structures.Bioinformatics (2006) doi:10.1093/bioinformatics/btl461.
50. You, M. et al. Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19. Nat. Cell Biol. 23, 620–630 (2021).
51. Granja, J. M. et al. Author Correction: ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis (Nature Genetics, (2021), 53, 3, (403-411), 10.1038/s41588-021-00790-6). Nat. Genet. 53, 935 (2021).
52. van Dijk, D. et al. Recovering Gene Interactions from Single-Cell Data Using Data Diffusion. Cell 174, 716-729.e27 (2018).
53. Waltman, L. & Van Eck, N. J. A smart local moving algorithm for large-scale modularity-based community detection. Eur. Phys. J. B 86, (2013).
54. Goentoro, L., Shoval, O., Kirschner, M. W. & Alon, U. The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation. Mol.Cell (2009) doi:10.1016/j.molcel.2009.11.018.
55. Fagerlund, R. et al. Anatomy of a negative feedback loop: The case of IκB. J. R. Soc. Interface (2015) doi:10.1098/rsif.2015.0262.
56. Nam, S. & Lim, J. S. Essential role of interferon regulatory factor 4 (IRF4) in immune cell development. Archives of Pharmacal Research (2016) doi:10.1007/s12272-016-0854-1.
57. Gomard, T. et al. An NF-κB-dependent role for JunB in the induction of proinflammatory cytokines in LPS-activated bone marrow-derived dendritic cells. PLoS One (2010) doi:10.1371/journal.pone.0009585.
58. Bauer, J. et al. Lymphotoxin, NF-κB, and cancer: The dark side of cytokines.Dig. Dis. (2012) doi:10.1159/000341690.
59. Baud, V. & Collares, D. Post-Translational Modifications of RelB NF-κB Subunit and Associated Functions. Cells (2016) doi:10.3390/cells5020022.
60. Alon, U. Network motifs: Theory and experimental approaches. Nat. Rev. Genet.8, 450–461 (2007).
61. Ma, H. W. et al. An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res. 32, 6643–6649 (2004).
62. Mangan, S. & Alon, U. Structure and function of the feed-forward loop network motif. Proc. Natl. Acad. Sci. U. S. A. 100, 11980–11985 (2003).
63. Mangan, S., Itzkovitz, S., Zaslaver, A. & Alon, U. The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J. Mol. Biol. 356, 1073–1081 (2006).
64. Tan, T. T. et al. Key roles of BIM-driven apoptosis in epithelial tumors and rational chemotherapy. Cancer Cell (2005) doi:10.1016/j.ccr.2005.02.008.
65. Sundqvist, A. et al. JUNB governs a feed-forward network of TGFβ signaling that aggravates breast cancer invasion. Nucleic Acids Res. (2018) doi:10.1093/nar/gkx1190.
66. Lee, J. H. et al. A20 promotes metastasis of aggressive basal-like breast cancers through multi-monoubiquitylation of Snail1. Nat. Cell Biol. (2017) doi:10.1038/ncb3609.
67. Yoon, C. I. et al. High A20 expression negatively impacts survival in patients with breast cancer. PLoS One (2019) doi:10.1371/journal.pone.0221721.
68. Balkwill, F. TNF-α in promotion and progression of cancer. Cancer and Metastasis Reviews (2006) doi:10.1007/s10555-006-9005-3.
69. Van Antwerp, D. J., Martin, S. J., Kafri, T., Green, D. R. & Verma, I. M. Suppression of TNF-α-induced apoptosis by NF-κB. Science (80-. ). (1996) doi:10.1126/science.274.5288.787.
70. Knüpfer, H. & Preiß, R. Significance of interleukin-6 (IL-6) in breast cancer (review). Breast Cancer Research and Treatment (2007) doi:10.1007/s10549- 006-9328-3.
71. van Horssen, R., ten Hagen, T. L. M. & Eggermont, A. M. M. TNF‐α in Cancer Treatment: Molecular Insights, Antitumor Effects, and Clinical Utility. Oncologist (2006) doi:10.1634/theoncologist.11-4-397.
72. Säemann, M. D. et al. Anti‐inflammatory effects of sodium butyrate on human monocytes: potent inhibition of IL‐12 and up‐regulation of IL‐10 production. FASEB J. (2000) doi:10.1096/fj.00-0359fje.
73. Yoshimoto, T. et al. Regulation of antitumor immune responses by the IL-12family cytokines, IL-12, IL-23, and IL-27. Clinical and Developmental Immunology (2010) doi:10.1155/2010/832454.
74. Song, K. D., Kim, D. J., Lee, J. E., Yun, C. H. & Lee, W. K. KLF10,transforming growth factor-β-inducible early gene 1, acts as a tumor suppressor.Biochem. Biophys. Res. Commun. (2012) doi:10.1016/j.bbrc.2012.02.032.
75. Hume, D. A., Irvine, K. M. & Pridans, C. The Mononuclear Phagocyte System: The Relationship between Monocytes and Macrophages. Trends Immunol. 40, 98–112 (2019).
76. Dewey, W. C., Ling, C. C. & Meyn, R. E. Radiation-induced apoptosis: Relevance to radiotherapy. Int. J. Radiat. Oncol. Biol. Phys. (1995) doi:10.1016/0360-3016(95)00214-8.
77. Rübe, C. E. et al. Modulation of radiation-induced tumour necrosis factor α(TNF-α) expression in the lung tissue by pentoxifylline. Radiother. Oncol. (2002) doi:10.1016/S0167-8140(02)00077-4.
78. Burow, M. E. et al. Differences in susceptibility to tumor necrosis factor α- induced apoptosis among MCF-7 breast cancer cell variants. Cancer Res. (1998).
79. Bar-Even, A. et al. Noise in protein expression scales with natural protein abundance. Nat. Genet. 38, 636–643 (2006).
80. Cheong, R., Rhee, A., Wang, C. J., Nemenman, I. & Levchenko, A. Information transduction capacity of noisy biochemical signaling networks. Science (80-. ). 334, 354–358 (2011).
81. Ross, H.E., and Murray, D.J. E.H. Weber on the Tactile Senses (East Sussex, UK: Erlbaum Taylor & Francis) doi: https://doi.org/10.4324/9781315782089 (1996).
82. Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005).
83. Krejčí, A., Bernard, F., Housden, B., Collins, S. & Bray, S. J. Erratum: Direct response to notch activation: Signaling crosstalk and incoherent logic (Science Signaling (2009) 2 (er3)). Sci. Signal. 2, 1–15 (2009).
84. Swiers, G., Patient, R. & Loose, M. Genetic regulatory networks programming hematopoietic stem cells and erythroid lineage specification. Dev. Biol. 294, 525–540 (2006).
85. Tyler, J. K. & Kadonaga, J. T. The “Dark Side” of Chromatin Remodeling. Cell(1999) doi:10.1016/s0092-8674(00)81530-5.
86. Di Croce, L. & Helin, K. Transcriptional regulation by Polycomb group proteins.Nature Structural and Molecular Biology (2013) doi:10.1038/nsmb.2669.
87. Bornelöv, S. et al. The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression. Mol. Cell (2018) doi:10.1016/j.molcel.2018.06.003.
88. Morey, L. et al. MBD3, a Component of the NuRD Complex, Facilitates Chromatin Alteration and Deposition of Epigenetic Marks. Mol. Cell. Biol. (2008) doi:10.1128/mcb.00467-08.
89. Reynolds, N. et al. NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression. EMBOJ. (2012) doi:10.1038/emboj.2011.431.
90. Bantignies, F. & Cavalli, G. Polycomb group proteins: Repression in 3D. Trends in Genetics (2011) doi:10.1016/j.tig.2011.06.008.
91. Ribeiro-Silva, C., Vermeulen, W. & Lans, H. SWI/SNF: Complex complexes in genome stability and cancer. DNA Repair (2019) doi:10.1016/j.dnarep.2019.03.007.
92. Galardi, S., Mercatelli, N., Farace, M. G. & Ciafrè, S. A. NF-κkB and c-Jun induce the expression of the oncogenic miR-221 and miR-222 in prostate carcinoma and glioblastoma cells. Nucleic Acids Res. (2011) doi:10.1093/nar/gkr006.
93. Messner, B., Stütz, A. M., Albrecht, B., Peiritsch, S. & Woisetschläger, M. Cooperation of binding sites for STAT6 and NF kappa B/rel in the IL-4-induced up-regulation of the human IgE germline promoter. J. Immunol. (1997).
94. Planeta, C. S., Lepsch, L. B., Alves, R. & Scavone, C. Influence of the dopaminergic system, CREB, and transcription factor-κB on cocaine neurotoxicity. Brazilian Journal of Medical and Biological Research (2013) doi:10.1590/1414-431X20133379.
95. Toledano, M. B. & Leonard, W. J. Modulation of transcription factor NF-κB binding activity by oxidation-reduction in vitro. Proc. Natl. Acad. Sci. U. S. A. (1991) doi:10.1073/pnas.88.10.4328.
96. DeFelice, M. M. et al. NF-B signaling dynamics is controlled by a dose-sensing autoregulatory loop. Sci. Signal. (2019) doi:10.1126/scisignal.aau3568.
97. Lewin, S. R., Lambert, P., Deacon, N. J., Mills, J. & Crowe, S. M. Constitutive expression of p50 homodimer in freshly isolated human monocytes decreases with in vitro and in vivo differentiation: a possible mechanism influencing human immunodeficiency virus replication in monocytes and mature macrophages. J. Virol. (1997) doi:10.1128/jvi.71.3.2114-2119.1997.
98. Najem, M. Y., Couturaud, F. & Lemarié, C. A. Cytokine and chemokine regulation of venous thromboembolism. J. Thromb. Haemost. 18, 1009–1019 (2020).
99. Beyaert, R. et al. The p38/RK mitogen-activated protein kinase pathway regulates interleukin-6 synthesis in response to tumour necrosis factor. EMBO J. 15, 1914–1923 (1996).
100. Tomida, T., Takekawa, M. & Saito, H. Oscillation of p38 activity controls efficient pro-inflammatory gene expression. Nat. Commun. 6, 4–6 (2015).
101. Wagner, E. F. & Nebreda, Á. R. Signal integration by JNK and p38 MAPK pathways in cancer development. Nat. Rev. Cancer 9, 537–549 (2009).
102. Vaziri-harami, R. & Delkash, P. Can L -carnitine reduce post-COVID-19 fatigue ? Ann. Med. Surg. 73, (2022).
103. Roselli, M. et al. TNF-α gene promoter polymorphisms and risk of venous thromboembolism in gastrointestinal cancer patients undergoing chemotherapy. Ann. Oncol. 24, 2571–2575 (2013).
104. Breitbart, W. et al. Depression , cytokines , and pancreatic cancer.Psychooncology. 345, 339–345 (2014).