My Bibliography

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Paez R, Rowe DJ, Deppen SA, Grogan EL, Kaizer A, Bornhop DJ, Kussrow AK, Barón AE, Maldonado F, Kammer MN. Assessing the clinical utility of biomarkers using the intervention probability curve (IPC). Cancer Biomark. 2023 Oct 28;. doi: 10.3233/CBM-230054. [Epub ahead of print] PubMed PMID: 38073376; PubMed Central PMCID: PMC11055936.

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New ML, Hirsch EA, Feser WJ, Malkoski SP, Garg K, Miller YE, Baron AE. Differences in VA and Non-VA Pulmonary Nodules: All Evaluations Are not Created Equal. Clin Lung Cancer. 2023 Jul;24(5):407-414. doi: 10.1016/j.cllc.2023.02.006. Epub 2023 Mar 4. PubMed PMID: 37012147; PubMed Central PMCID: PMC10293033.

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Hart M, Anderson-Mellies A, Beltrami A, Gilani A, Green AL. Population-based analysis of CNS tumor diagnoses, treatment, and survival in congenital and infant age groups. J Neurooncol. 2022 Apr;157(2):333-344. doi: 10.1007/s11060-022-03967-z. Epub 2022 Feb 17. PubMed PMID: 35175546; PubMed Central PMCID: PMC10249758.

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Schubert L, Le AT, Estrada-Bernal A, Doak AE, Yoo M, Ferrara SE, Goodspeed A, Kinose F, Rix U, Tan AC, Doebele RC. Novel Human-Derived RET Fusion NSCLC Cell Lines Have Heterogeneous Responses to RET Inhibitors and Differential Regulation of Downstream Signaling. Mol Pharmacol. 2021 Jun;99(6):435-447. doi: 10.1124/molpharm.120.000207. Epub 2021 Apr 1. PubMed PMID: 33795352; PubMed Central PMCID: PMC11033948.

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Roberts JT, Porman AM, Johnson AM. Identification of m(6)A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline. RNA. 2021 Apr;27(4):527-541. doi: 10.1261/rna.078543.120. Epub 2020 Dec 29. PubMed PMID: 33376190; PubMed Central PMCID: PMC7962486.

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Estrada-Bernal A, Le AT, Doak AE, Tirunagaru VG, Silva S, Bull MR, Smaill JB, Patterson AV, Kim C, Liu SV, Doebele RC. Tarloxotinib Is a Hypoxia-Activated Pan-HER Kinase Inhibitor Active Against a Broad Range of HER-Family Oncogenes. Clin Cancer Res. 2021 Mar 1;27(5):1463-1475. doi: 10.1158/1078-0432.CCR-20-3555. Epub 2020 Dec 22. PubMed PMID: 33355298; PubMed Central PMCID: PMC7926264.

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Dimou A, Grewe P, Sidney J, Sette A, Norman PJ, Doebele RC. HLA Class I Binding of Mutant EGFR Peptides in NSCLC Is Associated With Improved Survival. J Thorac Oncol. 2021 Jan;16(1):104-112. doi: 10.1016/j.jtho.2020.08.023. Epub 2020 Sep 11. PubMed PMID: 32927123; PubMed Central PMCID: PMC7797166.

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Jordan KR, Sikora MJ, Slansky JE, Minic A, Richer JK, Moroney MR, Hu J, Wolsky RJ, Watson ZL, Yamamoto TM, Costello JC, Clauset A, Behbakht K, Kumar TR, Bitler BG. The Capacity of the Ovarian Cancer Tumor Microenvironment to Integrate Inflammation Signaling Conveys a Shorter Disease-free Interval. Clin Cancer Res. 2020 Dec 1;26(23):6362-6373. doi: 10.1158/1078-0432.CCR-20-1762. Epub 2020 Sep 14. PubMed PMID: 32928797; PubMed Central PMCID: PMC7923250.

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Joshi M, Kim J, D'Alessandro A, Monk E, Bruce K, Elajaili H, Nozik-Grayck E, Goodspeed A, Costello JC, Schlaepfer IR. CPT1A Over-Expression Increases Reactive Oxygen Species in the Mitochondria and Promotes Antioxidant Defenses in Prostate Cancer. Cancers (Basel). 2020 Nov 18;12(11). doi: 10.3390/cancers12113431. PubMed PMID: 33218188; PubMed Central PMCID: PMC7709014.

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Boyle TA, Khalil FK, Mino-Kenudson M, Sica GL, Moreira AL, Sholl LM, Knight MZ, Zhang L, Saller J, Varella-Garcia M, Berry LD, Chen H, Ellison KE, Rivard CJ, Kugler K, Wistuba II, Fujimoto J, Kwiatkowski DJ, Bunn PA, Kris MG, Haura EB, Hirsch FR. Round Robin Evaluation of MET Protein Expression in Lung Adenocarcinomas Improves Interobserver Concordance. Appl Immunohistochem Mol Morphol. 2020 Oct;28(9):669-677. doi: 10.1097/PAI.0000000000000810. PubMed PMID: 31876606; PubMed Central PMCID: PMC7242128.

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Kern JA, Kim J, Foster DG, Mishra R, Gardner EE, Poirier JT, Rivard C, Yu H, Finigan JH, Dowlati A, Rudin CM, Tan AC. Role of mTOR As an Essential Kinase in SCLC. J Thorac Oncol. 2020 Sep;15(9):1522-1534. doi: 10.1016/j.jtho.2020.05.026. Epub 2020 Jun 26. PubMed PMID: 32599072; PubMed Central PMCID: PMC7483946.

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Simons EA, Smith DE, Gao D, Camidge DR. Variation in Toxicity Reporting Methods for Early Phase Lung Cancer Treatment Trials at Oncology Conferences. J Thorac Oncol. 2020 Sep;15(9):1425-1433. doi: 10.1016/j.jtho.2020.04.020. Epub 2020 Apr 27. PubMed PMID: 32353598; PubMed Central PMCID: PMC7667578.

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Zhang H, Brown RD, Stenmark KR, Hu CJ. RNA-Binding Proteins in Pulmonary Hypertension. Int J Mol Sci. 2020 May 26;21(11). doi: 10.3390/ijms21113757. Review. PubMed PMID: 32466553; PubMed Central PMCID: PMC7312837.

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Patil T, Mushtaq R, Marsh S, Azelby C, Pujara M, Davies KD, Aisner DL, Purcell WT, Schenk EL, Pacheco JM, Bunn PA, Camidge DR, Doebele RC. Clinicopathologic Characteristics, Treatment Outcomes, and Acquired Resistance Patterns of Atypical EGFR Mutations and HER2 Alterations in Stage IV Non-Small-Cell Lung Cancer. Clin Lung Cancer. 2020 May;21(3):e191-e204. doi: 10.1016/j.cllc.2019.11.008. Epub 2019 Nov 21. PubMed PMID: 31859066; PubMed Central PMCID: PMC7442280.

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Johnson AM, Bullock BL, Neuwelt AJ, Poczobutt JM, Kaspar RE, Li HY, Kwak JW, Hopp K, Weiser-Evans MCM, Heasley LE, Schenk EL, Clambey ET, Nemenoff RA. Cancer Cell-Intrinsic Expression of MHC Class II Regulates the Immune Microenvironment and Response to Anti-PD-1 Therapy in Lung Adenocarcinoma. J Immunol. 2020 Apr 15;204(8):2295-2307. doi: 10.4049/jimmunol.1900778. Epub 2020 Mar 16. PubMed PMID: 32179637; PubMed Central PMCID: PMC7472648.

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Patil T, Pacheco JM, Dimou A, Purcell WT, Rossi C, Bunn PA, Doebele RC, Camidge DR, Ferrigno L. Cecal Volvulus as a Rare Complication of Osimertinib Dosed at 160 mg in Patients With EGFR-Mutant Non-small Cell Lung Cancer. Front Oncol. 2020;10:510. doi: 10.3389/fonc.2020.00510. eCollection 2020. PubMed PMID: 32351892; PubMed Central PMCID: PMC7174901.

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Warsavage T Jr, Xing F, Barón AE, Feser WJ, Hirsch E, Miller YE, Malkoski S, Wolf HJ, Wilson DO, Ghosh D. Quantifying the incremental value of deep learning: Application to lung nodule detection. PLoS One. 2020;15(4):e0231468. doi: 10.1371/journal.pone.0231468. eCollection 2020. PubMed PMID: 32287288; PubMed Central PMCID: PMC7156089.

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Nassar KW, Tan AC. The mutational landscape of mucosal melanoma. Semin Cancer Biol. 2020 Apr;61:139-148. doi: 10.1016/j.semcancer.2019.09.013. Epub 2019 Oct 23. Review. PubMed PMID: 31655118; PubMed Central PMCID: PMC7078020.

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Neuwelt AJ, Kimball AK, Johnson AM, Arnold BW, Bullock BL, Kaspar RE, Kleczko EK, Kwak JW, Wu MH, Heasley LE, Doebele RC, Li HY, Nemenoff RA, Clambey ET. Cancer cell-intrinsic expression of MHC II in lung cancer cell lines is actively restricted by MEK/ERK signaling and epigenetic mechanisms. J Immunother Cancer. 2020 Apr;8(1). doi: 10.1136/jitc-2019-000441. PubMed PMID: 32312906; PubMed Central PMCID: PMC7204826.

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Joshi SR, Kitagawa A, Jacob C, Hashimoto R, Dhagia V, Ramesh A, Zheng C, Zhang H, Jordan A, Waddell I, Leopold J, Hu CJ, McMurtry IF, D'Alessandro A, Stenmark KR, Gupte SA. Hypoxic activation of glucose-6-phosphate dehydrogenase controls the expression of genes involved in the pathogenesis of pulmonary hypertension through the regulation of DNA methylation. Am J Physiol Lung Cell Mol Physiol. 2020 Apr 1;318(4):L773-L786. doi: 10.1152/ajplung.00001.2020. Epub 2020 Mar 11. PubMed PMID: 32159369; PubMed Central PMCID: PMC7191486.

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Yang Y, Gao R, Tang Y, Antic SL, Deppen S, Huo Y, Sandler KL, Massion PP, Landman BA. Internal-transfer Weighting of Multi-task Learning for Lung Cancer Detection. Proc SPIE Int Soc Opt Eng. 2020;11313. doi: 10.1117/12.2548755. Epub 2020 Mar 10. PubMed PMID: 34040274; PubMed Central PMCID: PMC8148030.

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Gao R, Li L, Tang Y, Antic SL, Paulson AB, Huo Y, Sandler KL, Massion PP, Landman BA. Deep Multi-task Prediction of Lung Cancer and Cancer-free Progression from Censored Heterogenous Clinical Imaging. Proc SPIE Int Soc Opt Eng. 2020;11313. doi: 10.1117/12.2548464. Epub 2020 Mar 10. PubMed PMID: 34040276; PubMed Central PMCID: PMC8148074.

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Borgers JSW, Tobin RP, Vorwald VM, Smith JM, Davis DM, Kimball AK, Clambey ET, Couts KL, McWilliams JA, Jordan KR, Torphy RJ, Schulick R, McCarter MD. High-Dimensional Analysis of Postsplenectomy Peripheral Immune Cell Changes. Immunohorizons. 2020 Feb 18;4(2):82-92. doi: 10.4049/immunohorizons.1900089. PubMed PMID: 32071067; PubMed Central PMCID: PMC7476217.

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Hu CJ, Poth JM, Zhang H, Flockton A, Laux A, Kumar S, McKeon B, Mouradian G, Li M, Riddle S, Pugliese SC, Brown RD, Wallace EM, Graham BB, Frid MG, Stenmark KR. Suppression of HIF2 signalling attenuates the initiation of hypoxia-induced pulmonary hypertension. Eur Respir J. 2019 Dec;54(6). doi: 10.1183/13993003.00378-2019. Print 2019 Dec. PubMed PMID: 31515405; PubMed Central PMCID: PMC6911916.

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Ramzan AA, Bitler BG, Hicks D, Barner K, Qamar L, Behbakht K, Powell T, Jansson T, Wilson H. Adiponectin receptor agonist AdipoRon induces apoptotic cell death and suppresses proliferation in human ovarian cancer cells. Mol Cell Biochem. 2019 Nov;461(1-2):37-46. doi: 10.1007/s11010-019-03586-9. Epub 2019 Jul 10. PubMed PMID: 31292831; PubMed Central PMCID: PMC7490954.

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Doebele RC. Acquired Resistance Is Oncogene and Drug Agnostic. Cancer Cell. 2019 Oct 14;36(4):347-349. doi: 10.1016/j.ccell.2019.09.011. Review. PubMed PMID: 31614114; PubMed Central PMCID: PMC7437928.

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Gao R, Huo Y, Bao S, Tang Y, Antic SL, Epstein ES, Balar AB, Deppen S, Paulson AB, Sandler KL, Massion PP, Landman BA. Distanced LSTM: Time-Distanced Gates in Long Short-Term Memory Models for Lung Cancer Detection. Mach Learn Med Imaging. 2019 Oct;11861:310-318. doi: 10.1007/978-3-030-32692-0_36. Epub 2019 Oct 10. PubMed PMID: 34040283; PubMed Central PMCID: PMC8148226.

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Yamamoto TM, McMellen A, Watson ZL, Aguilera J, Ferguson R, Nurmemmedov E, Thakar T, Moldovan GL, Kim H, Cittelly DM, Joglar AM, Brennecke EP, Wilson H, Behbakht K, Sikora MJ, Bitler BG. Activation of Wnt signaling promotes olaparib resistant ovarian cancer. Mol Carcinog. 2019 Oct;58(10):1770-1782. doi: 10.1002/mc.23064. Epub 2019 Jun 10. PubMed PMID: 31219654; PubMed Central PMCID: PMC7537108.

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Bullock BL, Kimball AK, Poczobutt JM, Neuwelt AJ, Li HY, Johnson AM, Kwak JW, Kleczko EK, Kaspar RE, Wagner EK, Hopp K, Schenk EL, Weiser-Evans MC, Clambey ET, Nemenoff RA. Tumor-intrinsic response to IFNγ shapes the tumor microenvironment and anti-PD-1 response in NSCLC. Life Sci Alliance. 2019 Jun;2(3). doi: 10.26508/lsa.201900328. Print 2019 Jun. PubMed PMID: 31133614; PubMed Central PMCID: PMC6537751.

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El Osta B, Behera M, Kim S, Berry LD, Sica G, Pillai RN, Owonikoko TK, Kris MG, Johnson BE, Kwiatkowski DJ, Sholl LM, Aisner DL, Bunn PA, Khuri FR, Ramalingam SS. Characteristics and Outcomes of Patients With Metastatic KRAS-Mutant Lung Adenocarcinomas: The Lung Cancer Mutation Consortium Experience. J Thorac Oncol. 2019 May;14(5):876-889. doi: 10.1016/j.jtho.2019.01.020. Epub 2019 Feb 5. PubMed PMID: 30735816; PubMed Central PMCID: PMC8108452.

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Camidge DR, Davies KD. MET Copy Number as a Secondary Driver of Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor Resistance in EGFR-Mutant Non-Small-Cell Lung Cancer. J Clin Oncol. 2019 Apr 10;37(11):855-857. doi: 10.1200/JCO.19.00033. Epub 2019 Feb 27. PubMed PMID: 30811294; PubMed Central PMCID: PMC6455716.

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Kessler BE, Mishall KM, Kellett MD, Clark EG, Pugazhenthi U, Pozdeyev N, Kim J, Tan AC, Schweppe RE. Resistance to Src inhibition alters the BRAF-mutant tumor secretome to promote an invasive phenotype and therapeutic escape through a FAK>p130Cas>c-Jun signaling axis. Oncogene. 2019 Apr;38(14):2565-2579. doi: 10.1038/s41388-018-0617-1. Epub 2018 Dec 10. PubMed PMID: 30531837; PubMed Central PMCID: PMC6450711.

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Pacheco JM, Gao D, Smith D, Purcell T, Hancock M, Bunn P, Robin T, Liu A, Karam S, Gaspar L, Kavanagh B, Rusthoven C, Aisner D, Doebele R, Camidge DR. Natural History and Factors Associated with Overall Survival in Stage IV ALK-Rearranged Non-Small Cell Lung Cancer. J Thorac Oncol. 2019 Apr;14(4):691-700. doi: 10.1016/j.jtho.2018.12.014. Epub 2018 Dec 30. PubMed PMID: 30599201; PubMed Central PMCID: PMC7310567.

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Cherry PD, Peach SE, Hesselberth JR. Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response. Elife. 2019 Mar 15;8. doi: 10.7554/eLife.42262. PubMed PMID: 30874502; PubMed Central PMCID: PMC6456296.

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Wojcik KY, Escobedo LA, Wysong A, Heck JE, Ritz B, Hamilton AS, Milam J, Cockburn MG. High Birth Weight, Early UV Exposure, and Melanoma Risk in Children, Adolescents, and Young Adults. Epidemiology. 2019 Mar;30(2):278-284. doi: 10.1097/EDE.0000000000000963. PubMed PMID: 30499783; PubMed Central PMCID: PMC6435257.

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Hu CJ, Zhang H, Laux A, Pullamsetti SS, Stenmark KR. Mechanisms contributing to persistently activated cell phenotypes in pulmonary hypertension. J Physiol. 2019 Feb;597(4):1103-1119. doi: 10.1113/JP275857. Epub 2018 Aug 7. Review. PubMed PMID: 29920674; PubMed Central PMCID: PMC6375873.

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Marwan AI, Shabeka U, Reisz JA, Zheng C, Serkova NJ, Dobrinskikh E. Unique Heterogeneous Topological Pattern of the Metabolic Landscape in Rabbit Fetal Lungs following Tracheal Occlusion. Fetal Diagn Ther. 2019;45(3):145-154. doi: 10.1159/000487752. Epub 2018 Apr 18. PubMed PMID: 29669344; PubMed Central PMCID: PMC6314905.

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Ng TL, Yu H, Smith DE, Boyle TA, York ER, Leedy S, Gao D, Aisner DL, Van Bokhoven A, Heasley LE, Hirsch FR, Camidge DR. Preselection of Lung Cancer Cases Using FGFR1 mRNA and Gene Copy Number for Treatment With Ponatinib. Clin Lung Cancer. 2019 Jan;20(1):e39-e51. doi: 10.1016/j.cllc.2018.09.001. Epub 2018 Sep 7. PubMed PMID: 30297175; PubMed Central PMCID: PMC6339510.

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Gibson ES, Woolfrey KM, Li H, Hogan PG, Nemenoff RA, Heasley LE, Dell'Acqua ML. Subcellular Localization and Activity of the Mitogen-Activated Protein Kinase Kinase 7 (MKK7) γ Isoform are Regulated through Binding to the Phosphatase Calcineurin. Mol Pharmacol. 2019 Jan;95(1):20-32. doi: 10.1124/mol.118.113159. Epub 2018 Nov 7. PubMed PMID: 30404891; PubMed Central PMCID: PMC6277928.

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Yu H, Chen Z, Ballman KV, Watson MA, Govindan R, Lanc I, Beer DG, Bueno R, Chirieac LR, Chui MH, Chen G, Franklin WA, Gandara DR, Genova C, Brovsky KA, Joshi MM, Merrick DT, Richards WG, Rivard CJ, Harpole DH, Tsao MS, van Bokhoven A, Shepherd FA, Hirsch FR. Correlation of PD-L1 Expression with Tumor Mutation Burden and Gene Signatures for Prognosis in Early-Stage Squamous Cell Lung Carcinoma. J Thorac Oncol. 2019 Jan;14(1):25-36. doi: 10.1016/j.jtho.2018.09.006. Epub 2018 Sep 22. PubMed PMID: 30253973; PubMed Central PMCID: PMC6309634.

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Patil T, Smith DE, Bunn PA, Aisner DL, Le AT, Hancock M, Purcell WT, Bowles DW, Camidge DR, Doebele RC. The Incidence of Brain Metastases in Stage IV ROS1-Rearranged Non-Small Cell Lung Cancer and Rate of Central Nervous System Progression on Crizotinib. J Thorac Oncol. 2018 Nov;13(11):1717-1726. doi: 10.1016/j.jtho.2018.07.001. Epub 2018 Jul 5. PubMed PMID: 29981925; PubMed Central PMCID: PMC6204290.

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Suda K, Kim J, Murakami I, Rozeboom L, Shimoji M, Shimizu S, Rivard CJ, Mitsudomi T, Tan AC, Hirsch FR. Innate Genetic Evolution of Lung Cancers and Spatial Heterogeneity: Analysis of Treatment-Naïve Lesions. J Thorac Oncol. 2018 Oct;13(10):1496-1507. doi: 10.1016/j.jtho.2018.05.039. Epub 2018 Jun 19. PubMed PMID: 29933065; PubMed Central PMCID: PMC6153034.

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New ML, White CM, McGonigle P, McArthur DG, Dwyer-Nield LD, Merrick DT, Keith RL, Tennis MA. Prostacyclin and EMT Pathway Markers for Monitoring Response to Lung Cancer Chemoprevention. Cancer Prev Res (Phila). 2018 Oct;11(10):643-654. doi: 10.1158/1940-6207.CAPR-18-0052. Epub 2018 Jul 25. PubMed PMID: 30045935; PubMed Central PMCID: PMC6170683.

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Gavin KM, Kohrt WM, Klemm DJ, Melanson EL. Modulation of Energy Expenditure by Estrogens and Exercise in Women. Exerc Sport Sci Rev. 2018 Oct;46(4):232-239. doi: 10.1249/JES.0000000000000160. Review. PubMed PMID: 30001272; PubMed Central PMCID: PMC6138559.

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Betker JL, Jones D, Childs CR, Helm KM, Terrell K, Nagel MA, Anchordoquy TJ. Nanoparticle uptake by circulating leukocytes: A major barrier to tumor delivery. J Control Release. 2018 Sep 28;286:85-93. doi: 10.1016/j.jconrel.2018.07.031. Epub 2018 Jul 17. PubMed PMID: 30030182; PubMed Central PMCID: PMC6936323.

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Gurule NJ, Heasley LE. Linking tyrosine kinase inhibitor-mediated inflammation with normal epithelial cell homeostasis and tumor therapeutic responses. Cancer Drug Resist. 2018;1:118-125. doi: 10.20517/cdr.2018.12. Epub 2018 Sep 19. PubMed PMID: 30656289; PubMed Central PMCID: PMC6333470.

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Mukherjee N, Strosnider A, Vagher B, Lambert KA, Slaven S, Robinson WA, Amato CM, Couts KL, Bemis JGT, Turner JA, Norris DA, Shellman YG. BH3 mimetics induce apoptosis independent of DRP-1 in melanoma. Cell Death Dis. 2018 Sep 5;9(9):907. doi: 10.1038/s41419-018-0932-z. PubMed PMID: 30185782; PubMed Central PMCID: PMC6125485.

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Ren S, Rivard CJ, Yu H, Genova C, Rozenboom L, Gao D, Hinz TK, Rikke BA, Wynes MW, Caldwell C, Agustoni F, Kenichi Suda, Jiang T, Zhou C, Heasley LE, Hirsch FR. A miRNA Panel Predicts Sensitivity of FGFR Inhibitor in Lung Cancer Cell Lines. Clin Lung Cancer. 2018 Sep;19(5):450-456. doi: 10.1016/j.cllc.2018.06.004. Epub 2018 Jun 28. PubMed PMID: 30146263; PubMed Central PMCID: PMC6339511.

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Merrick DT, Edwards MG, Franklin WA, Sugita M, Keith RL, Miller YE, Friedman MB, Dwyer-Nield LD, Tennis MA, O'Keefe MC, Donald EJ, Malloy JM, van Bokhoven A, Wilson S, Koch PJ, O'Shea C, Coldren C, Orlicky DJ, Lu X, Baron AE, Hickey G, Kennedy TC, Powell R, Heasley L, Bunn PA, Geraci M, Nemenoff RA. Altered Cell-Cycle Control, Inflammation, and Adhesion in High-Risk Persistent Bronchial Dysplasia. Cancer Res. 2018 Sep 1;78(17):4971-4983. doi: 10.1158/0008-5472.CAN-17-3822. Epub 2018 Jul 11. PubMed PMID: 29997230; PubMed Central PMCID: PMC6147150.

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Dodson RB, Powers KN, Gien J, Rozance PJ, Seedorf G, Astling D, Jones K, Crombleholme TM, Abman SH, Alvira CM. Intrauterine growth restriction decreases NF-κB signaling in fetal pulmonary artery endothelial cells of fetal sheep. Am J Physiol Lung Cell Mol Physiol. 2018 Sep 1;315(3):L348-L359. doi: 10.1152/ajplung.00052.2018. Epub 2018 May 3. PubMed PMID: 29722560; PubMed Central PMCID: PMC6172617.