My Bibliography

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Holton SE, Mitchem M, Chalian H, Pipavath S, Morrell ED, Bhatraju PK, Hamerman JA, Speake C, Malhotra U, Wurfel MM, Ziegler SE, Mikacenic C. Mediators of monocyte chemotaxis and matrix remodeling are associated with mortality and pulmonary fibroproliferation in patients with severe COVID-19. PLoS One. 2024;19(8):e0285638. doi: 10.1371/journal.pone.0285638. eCollection 2024. PubMed PMID: 39106254; PubMed Central PMCID: PMC11302896.

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Morrell ED, Holton SE, Wiedeman A, Kosamo S, Mitchem MA, Dmyterko V, Franklin Z, Garay A, Stanaway IB, Liu T, Sathe NA, Mabrey FL, Stapleton RD, Malhotra U, Speake C, Hamerman JA, Pipavath S, Evans L, Bhatraju PK, Long SA, Wurfel MM, Mikacenic C. PD-L1 and PD-1 Are Associated with Clinical Outcomes and Alveolar Immune Cell Activation in ARDS. Am J Respir Cell Mol Biol. 2024 Jul 1;. doi: 10.1165/rcmb.2024-0201OC. [Epub ahead of print] PubMed PMID: 38950166.

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Wu EY, Singh NP, Choi K, Zakeri M, Vincent M, Churchill GA, Ackert-Bicknell CL, Patro R, Love MI. SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty. Genome Biol. 2023 Jul 12;24(1):165. doi: 10.1186/s13059-023-03003-x. PubMed PMID: 37438847; PubMed Central PMCID: PMC10337143.

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Carter JA, Matta B, Battaglia J, Somerville C, Harris BD, LaPan M, Atwal GS, Barnes BJ. Identification of pan-cancer/testis genes and validation of therapeutic targeting in triple-negative breast cancer: Lin28a- and Siglece-based vaccination induces anti-tumor immunity and inhibits metastasis. bioRxiv. 2023 May 10;. doi: 10.1101/2023.05.09.539617. PubMed PMID: 37214884; PubMed Central PMCID: PMC10197572.

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Gastonguay MS, Keele GR, Churchill GA. The trouble with triples: Examining the impact of measurement error in mediation analysis. Genetics. 2023 May 4;224(1). doi: 10.1093/genetics/iyad045. PubMed PMID: 36932658; PubMed Central PMCID: PMC10158839.

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Canny SP, Orozco SL, Thulin NK, Hamerman JA. Immune Mechanisms in Inflammatory Anemia. Annu Rev Immunol. 2023 Apr 26;41:405-429. doi: 10.1146/annurev-immunol-101320-125839. Epub 2023 Feb 7. Review. PubMed PMID: 36750316; PubMed Central PMCID: PMC10367595.

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Romano L, Seu KG, Papoin J, Muench DE, Konstantinidis D, Olsson A, Schlum K, Chetal K, Chasis JA, Mohandas N, Barnes BJ, Zheng Y, Grimes HL, Salomonis N, Blanc L, Kalfa TA. Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis. Blood. 2022 Oct 6;140(14):1621-1634. doi: 10.1182/blood.2022015724. PubMed PMID: 35862735; PubMed Central PMCID: PMC9707396.

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Matta B, Battaglia J, Barnes BJ. Detection of neutrophil extracellular traps in patient plasma: method development and validation in systemic lupus erythematosus and healthy donors that carry IRF5 genetic risk. Front Immunol. 2022;13:951254. doi: 10.3389/fimmu.2022.951254. eCollection 2022. PubMed PMID: 35958624; PubMed Central PMCID: PMC9360330.

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Quail DF, Amulic B, Aziz M, Barnes BJ, Eruslanov E, Fridlender ZG, Goodridge HS, Granot Z, Hidalgo A, Huttenlocher A, Kaplan MJ, Malanchi I, Merghoub T, Meylan E, Mittal V, Pittet MJ, Rubio-Ponce A, Udalova IA, van den Berg TK, Wagner DD, Wang P, Zychlinsky A, de Visser KE, Egeblad M, Kubes P. Neutrophil phenotypes and functions in cancer: A consensus statement. J Exp Med. 2022 Jun 6;219(6). doi: 10.1084/jem.20220011. Epub 2022 May 6. Review. PubMed PMID: 35522219; PubMed Central PMCID: PMC9086501.

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Dulmovits BM, Tang Y, Papoin J, He M, Li J, Yang H, Addorisio ME, Kennedy L, Khan M, Brindley E, Ashley RJ, Ackert-Bicknell C, Hale J, Kurita R, Nakamura Y, Diamond B, Barnes BJ, Hermine O, Gallagher PG, Steiner LA, Lipton JM, Taylor N, Mohandas N, Andersson U, Al-Abed Y, Tracey KJ, Blanc L. HMGB1-mediated restriction of EPO signaling contributes to anemia of inflammation. Blood. 2022 May 26;139(21):3181-3193. doi: 10.1182/blood.2021012048. PubMed PMID: 35040907; PubMed Central PMCID: PMC9136881.

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Winkler A, Sun W, De S, Jiao A, Sharif MN, Symanowicz PT, Athale S, Shin JH, Wang J, Jacobson BA, Ramsey SJ, Dower K, Andreyeva T, Liu H, Hegen M, Homer BL, Brodfuehrer J, Tilley M, Gilbert SA, Danto SI, Beebe JJ, Barnes BJ, Pascual V, Lin LL, Kilty I, Fleming M, Rao VR. The Interleukin-1 Receptor-Associated Kinase 4 Inhibitor PF-06650833 Blocks Inflammation in Preclinical Models of Rheumatic Disease and in Humans Enrolled in a Randomized Clinical Trial. Arthritis Rheumatol. 2021 Dec;73(12):2206-2218. doi: 10.1002/art.41953. Epub 2021 Nov 1. PubMed PMID: 34423919; PubMed Central PMCID: PMC8671219.

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Orozco SL, Canny SP, Hamerman JA. Signals governing monocyte differentiation during inflammation. Curr Opin Immunol. 2021 Dec;73:16-24. doi: 10.1016/j.coi.2021.07.007. Epub 2021 Aug 16. Review. PubMed PMID: 34411882; PubMed Central PMCID: PMC8648978.

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Lu A, Wu S, Niu J, Cui M, Chen M, Clapp WL, Barnes BJ, Meng G. Aim2 Couples With Ube2i for Sumoylation-Mediated Repression of Interferon Signatures in Systemic Lupus Erythematosus. Arthritis Rheumatol. 2021 Aug;73(8):1467-1477. doi: 10.1002/art.41677. Epub 2021 Jul 7. PubMed PMID: 33559374; PubMed Central PMCID: PMC8324518.

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Sherman CD, Barnes BJ. Intracellular IRF5 Dimerization Assay. Bio Protoc. 2021 May 20;11(10):e4021. doi: 10.21769/BioProtoc.4021. eCollection 2021 May 20. PubMed PMID: 34150928; PubMed Central PMCID: PMC8187113.

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Hurley HJ, Dewald H, Rothkopf ZS, Singh S, Jenkins F, Deb P, De S, Barnes BJ, Fitzgerald-Bocarsly P. Frontline Science: AMPK regulates metabolic reprogramming necessary for interferon production in human plasmacytoid dendritic cells. J Leukoc Biol. 2021 Feb;109(2):299-308. doi: 10.1002/JLB.3HI0220-130. Epub 2020 Jul 8. PubMed PMID: 32640499.

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Song S, De S, Nelson V, Chopra S, LaPan M, Kampta K, Sun S, He M, Thompson CD, Li D, Shih T, Tan N, Al-Abed Y, Capitle E, Aranow C, Mackay M, Clapp WL, Barnes BJ. Inhibition of IRF5 hyperactivation protects from lupus onset and severity. J Clin Invest. 2020 Dec 1;130(12):6700-6717. doi: 10.1172/JCI120288. PubMed PMID: 32897883; PubMed Central PMCID: PMC7685739.

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Rasha F, Mims BM, Castro-Piedras I, Barnes BJ, Grisham MB, Rahman RL, Pruitt K. The Versatility of Sirtuin-1 in Endocrinology and Immunology. Front Cell Dev Biol. 2020;8:589016. doi: 10.3389/fcell.2020.589016. eCollection 2020. Review. PubMed PMID: 33330467; PubMed Central PMCID: PMC7717970.

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Acharya M, Raso F, Sagadiev S, Gilbertson E, Kadavy L, Li QZ, Yan M, Stuart LM, Hamerman JA, Lacy-Hulbert A. B Cell αv Integrins Regulate TLR-Driven Autoimmunity. J Immunol. 2020 Oct 1;205(7):1810-1818. doi: 10.4049/jimmunol.1901056. Epub 2020 Aug 28. PubMed PMID: 32859730; PubMed Central PMCID: PMC7504890.

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Weber AG, Chau AS, Egeblad M, Barnes BJ, Janowitz T. Nebulized in-line endotracheal dornase alfa and albuterol administered to mechanically ventilated COVID-19 patients: a case series. Mol Med. 2020 Sep 29;26(1):91. doi: 10.1186/s10020-020-00215-w. PubMed PMID: 32993479; PubMed Central PMCID: PMC7522910.

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Taylor MD, Brewer MR, Nedeljkovic-Kurepa A, Yang Y, Reddy KS, Abraham MN, Barnes BJ, Deutschman CS. CD4 T Follicular Helper Cells Prevent Depletion of Follicular B Cells in Response to Cecal Ligation and Puncture. Front Immunol. 2020;11:1946. doi: 10.3389/fimmu.2020.01946. eCollection 2020. PubMed PMID: 32903485; PubMed Central PMCID: PMC7434988.

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Matta B, Barnes BJ. Coordination between innate immune cells, type I IFNs and IRF5 drives SLE pathogenesis. Cytokine. 2020 Aug;132:154731. doi: 10.1016/j.cyto.2019.05.018. Epub 2019 May 23. Review. PubMed PMID: 31130331.

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Yan J, Pandey SP, Barnes BJ, Turner JR, Abraham C. T Cell-Intrinsic IRF5 Regulates T Cell Signaling, Migration, and Differentiation and Promotes Intestinal Inflammation. Cell Rep. 2020 Jun 30;31(13):107820. doi: 10.1016/j.celrep.2020.107820. PubMed PMID: 32610123; PubMed Central PMCID: PMC7409536.

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Zuo Y, Yalavarthi S, Shi H, Gockman K, Zuo M, Madison JA, Blair C, Weber A, Barnes BJ, Egeblad M, Woods RJ, Kanthi Y, Knight JS. Neutrophil extracellular traps in COVID-19. JCI Insight. 2020 Jun 4;5(11). doi: 10.1172/jci.insight.138999. PubMed PMID: 32329756; PubMed Central PMCID: PMC7308057.

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Brune Z, Rice MR, Barnes BJ. Potential T Cell-Intrinsic Regulatory Roles for IRF5 via Cytokine Modulation in T Helper Subset Differentiation and Function. Front Immunol. 2020;11:1143. doi: 10.3389/fimmu.2020.01143. eCollection 2020. Review. PubMed PMID: 32582209; PubMed Central PMCID: PMC7283537.

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Barnes BJ, Adrover JM, Baxter-Stoltzfus A, Borczuk A, Cools-Lartigue J, Crawford JM, Daßler-Plenker J, Guerci P, Huynh C, Knight JS, Loda M, Looney MR, McAllister F, Rayes R, Renaud S, Rousseau S, Salvatore S, Schwartz RE, Spicer JD, Yost CC, Weber A, Zuo Y, Egeblad M. Targeting potential drivers of COVID-19: Neutrophil extracellular traps. J Exp Med. 2020 Jun 1;217(6). doi: 10.1084/jem.20200652. PubMed PMID: 32302401; PubMed Central PMCID: PMC7161085.

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Barnes BJ, Somerville CC. Modulating Cytokine Production via Select Packaging and Secretion From Extracellular Vesicles. Front Immunol. 2020;11:1040. doi: 10.3389/fimmu.2020.01040. eCollection 2020. Review. PubMed PMID: 32547552; PubMed Central PMCID: PMC7272603.

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Banga J, Srinivasan D, Sun CC, Thompson CD, Milletti F, Huang KS, Hamilton S, Song S, Hoffman AF, Qin YG, Matta B, LaPan M, Guo Q, Lu G, Li D, Qian H, Bolin DR, Liang L, Wartchow C, Qiu J, Downing M, Narula S, Fotouhi N, DeMartino JA, Tan SL, Chen G, Barnes BJ. Inhibition of IRF5 cellular activity with cell-penetrating peptides that target homodimerization. Sci Adv. 2020 May;6(20):eaay1057. doi: 10.1126/sciadv.aay1057. eCollection 2020 May. PubMed PMID: 32440537; PubMed Central PMCID: PMC7228753.

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Weber AG, Chau AS, Egeblad M, Barnes BJ, Janowitz T. Nebulized in-line endotracheal dornase alfa and albuterol administered to mechanically ventilated COVID-19 patients: A case series. medRxiv. 2020 May 15;. doi: 10.1101/2020.05.13.20087734. PubMed PMID: 32511514; PubMed Central PMCID: PMC7273282.

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Zuo Y, Yalavarthi S, Shi H, Gockman K, Zuo M, Madison JA, Blair C, Weber A, Barnes BJ, Egeblad M, Woods RJ, Kanthi Y, Knight JS. Neutrophil extracellular traps (NETs) as markers of disease severity in COVID-19. medRxiv. 2020 Apr 14;. doi: 10.1101/2020.04.09.20059626. PubMed PMID: 32511633; PubMed Central PMCID: PMC7276989.

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Li D, Matta B, Song S, Nelson V, Diggins K, Simpfendorfer KR, Gregersen PK, Linsley P, Barnes BJ. IRF5 genetic risk variants drive myeloid-specific IRF5 hyperactivation and presymptomatic SLE. JCI Insight. 2020 Jan 30;5(2). doi: 10.1172/jci.insight.124020. PubMed PMID: 31877114; PubMed Central PMCID: PMC7098722.

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Liu T, Xiang A, Peng T, Doran AC, Tracey KJ, Barnes BJ, Tabas I, Son M, Diamond B. HMGB1-C1q complexes regulate macrophage function by switching between leukotriene and specialized proresolving mediator biosynthesis. Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23254-23263. doi: 10.1073/pnas.1907490116. Epub 2019 Sep 30. PubMed PMID: 31570601; PubMed Central PMCID: PMC6859319.

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Shih T, De S, Barnes BJ. RNAi Transfection Optimized in Primary Naïve B Cells for the Targeted Analysis of Human Plasma Cell Differentiation. Front Immunol. 2019;10:1652. doi: 10.3389/fimmu.2019.01652. eCollection 2019. PubMed PMID: 31396212; PubMed Central PMCID: PMC6664017.

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Barnes BJ. Genetic Versus Non-genetic Drivers of SLE: Implications of IRF5 Dysregulation in Both Roads Leading to SLE. Curr Rheumatol Rep. 2019 Jan 15;21(1):2. doi: 10.1007/s11926-019-0803-3. Review. PubMed PMID: 30645688.

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Akilesh HM, Buechler MB, Duggan JM, Hahn WO, Matta B, Sun X, Gessay G, Whalen E, Mason M, Presnell SR, Elkon KB, Lacy-Hulbert A, Barnes BJ, Pepper M, Hamerman JA. Chronic TLR7 and TLR9 signaling drives anemia via differentiation of specialized hemophagocytes. Science. 2019 Jan 11;363(6423). doi: 10.1126/science.aao5213. PubMed PMID: 30630901; PubMed Central PMCID: PMC6413693.

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Thompson CD, Matta B, Barnes BJ. Therapeutic Targeting of IRFs: Pathway-Dependence or Structure-Based?. Front Immunol. 2018;9:2622. doi: 10.3389/fimmu.2018.02622. eCollection 2018. Review. PubMed PMID: 30515152; PubMed Central PMCID: PMC6255967.

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Obr AE, Kumar S, Chang YJ, Bulatowicz JJ, Barnes BJ, Birge RB, Lazzarino DA, Gallagher E, LeRoith D, Wood TL. Insulin-like growth factor receptor signaling in breast tumor epithelium protects cells from endoplasmic reticulum stress and regulates the tumor microenvironment. Breast Cancer Res. 2018 Nov 20;20(1):138. doi: 10.1186/s13058-018-1063-2. PubMed PMID: 30458886; PubMed Central PMCID: PMC6245538.

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Korczeniewska J, Barnes BJ. Corrected and Republished from: The COP9 Signalosome Interacts with and Regulates Interferon Regulatory Factor 5 Protein Stability. Mol Cell Biol. 2018 Feb 1;38(3). doi: 10.1128/MCB.00493-17. Print 2018 Feb 1. PubMed PMID: 29339435; PubMed Central PMCID: PMC5770539.

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De S, Zhang B, Shih T, Singh S, Winkler A, Donnelly R, Barnes BJ. B Cell-Intrinsic Role for IRF5 in TLR9/BCR-Induced Human B Cell Activation, Proliferation, and Plasmablast Differentiation. Front Immunol. 2017;8:1938. doi: 10.3389/fimmu.2017.01938. eCollection 2017. PubMed PMID: 29367853; PubMed Central PMCID: PMC5768180.

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Cevik O, Li D, Baljinnyam E, Manvar D, Pimenta EM, Waris G, Barnes BJ, Kaushik-Basu N. Interferon regulatory factor 5 (IRF5) suppresses hepatitis C virus (HCV) replication and HCV-associated hepatocellular carcinoma. J Biol Chem. 2017 Dec 29;292(52):21676-21689. doi: 10.1074/jbc.M117.792721. Epub 2017 Oct 27. PubMed PMID: 29079574; PubMed Central PMCID: PMC5766933.

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Matta B, Song S, Li D, Barnes BJ. Interferon regulatory factor signaling in autoimmune disease. Cytokine. 2017 Oct;98:15-26. doi: 10.1016/j.cyto.2017.02.006. Epub 2017 Mar 7. Review. PubMed PMID: 28283223; PubMed Central PMCID: PMC8033540.

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Li D, De S, Li D, Song S, Matta B, Barnes BJ. Specific detection of interferon regulatory factor 5 (IRF5): A case of antibody inequality. Sci Rep. 2016 Aug 2;6:31002. doi: 10.1038/srep31002. PubMed PMID: 27481535; PubMed Central PMCID: PMC4969615.

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Ishikawa C, Senba M, Barnes BJ, Mori N. Constitutive expression of IRF-5 in HTLV-1-infected T cells. Int J Oncol. 2015 Jul;47(1):361-9. doi: 10.3892/ijo.2015.3020. Epub 2015 May 22. PubMed PMID: 26004104.

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Pimenta EM, De S, Weiss R, Feng D, Hall K, Kilic S, Bhanot G, Ganesan S, Ran S, Barnes BJ. IRF5 is a novel regulator of CXCL13 expression in breast cancer that regulates CXCR5(+) B- and T-cell trafficking to tumor-conditioned media. Immunol Cell Biol. 2015 May-Jun;93(5):486-99. doi: 10.1038/icb.2014.110. Epub 2014 Dec 23. PubMed PMID: 25533286.

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Pimenta EM, Barnes BJ. A conserved region within interferon regulatory factor 5 controls breast cancer cell migration through a cytoplasmic and transcription-independent mechanism. Mol Cancer. 2015 Feb 4;14(1):32. doi: 10.1186/s12943-015-0305-5. PubMed PMID: 25649192; PubMed Central PMCID: PMC4326371.

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Lazzari E, Korczeniewska J, Ní Gabhann J, Smith S, Barnes BJ, Jefferies CA. TRIpartite motif 21 (TRIM21) differentially regulates the stability of interferon regulatory factor 5 (IRF5) isoforms. PLoS One. 2014;9(8):e103609. doi: 10.1371/journal.pone.0103609. eCollection 2014. PubMed PMID: 25084355; PubMed Central PMCID: PMC4118895.

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Bi X, Feng D, Korczeniewska J, Alper N, Hu G, Barnes BJ. Deletion of Irf5 protects hematopoietic stem cells from DNA damage-induced apoptosis and suppresses γ-irradiation-induced thymic lymphomagenesis. Oncogene. 2014 Jun 19;33(25):3288-97. doi: 10.1038/onc.2013.295. Epub 2013 Aug 5. PubMed PMID: 23912454.

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Pimenta EM, Barnes BJ. Role of Tertiary Lymphoid Structures (TLS) in Anti-Tumor Immunity: Potential Tumor-Induced Cytokines/Chemokines that Regulate TLS Formation in Epithelial-Derived Cancers. Cancers (Basel). 2014 Apr 23;6(2):969-97. doi: 10.3390/cancers6020969. PubMed PMID: 24762633; PubMed Central PMCID: PMC4074812.

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Barnes BJ. Editorial: are regulatory B10 cells a viable target for autoimmune diseases?. J Leukoc Biol. 2013 Oct;94(4):548-50. doi: 10.1189/jlb.0513267. PubMed PMID: 24082049.

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Feng D, Barnes BJ. Bioinformatics analysis of the factors controlling type I IFN gene expression in autoimmune disease and virus-induced immunity. Front Immunol. 2013;4:291. doi: 10.3389/fimmu.2013.00291. eCollection 2013. PubMed PMID: 24065968; PubMed Central PMCID: PMC3776951.

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Korczeniewska J, Barnes BJ. The COP9 signalosome interacts with and regulates interferon regulatory factor 5 protein stability. Mol Cell Biol. 2013 Mar;33(6):1124-38. doi: 10.1128/MCB.00802-12. Epub 2012 Dec 28. PubMed PMID: 23275442; PubMed Central PMCID: PMC3592028.