My Bibliography

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Li S, Wang Z, Nguyen P, Wang Y, Zhao Y, Wang Y, Chen Y, Huang H, Wang X, Zhang Y, Huang Y, Pattarayan D, Zhang M, Liu Y, Li S, Yang D. MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis. Sci Adv. 2026 Apr 24;12(17):eaeb5147. doi: 10.1126/sciadv.aeb5147. Epub 2026 Apr 24. PubMed PMID: 42030388; PubMed Central PMCID: PMC13108557.

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Wang Y, Zhao Y, Hu J, Wang Z, Pattarayan D, Li S, Zhang Y, Wang X, Wang Y, Xie W, Zhang M, Yang D. CRISPR activation screens identify oncogenic lncRNAs that are susceptible to CDK4/6 inhibitor treatment. Nat Commun. 2026 Apr 9;. doi: 10.1038/s41467-026-70816-2. [Epub ahead of print] PubMed PMID: 41957359.

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Xi Y, Liu L, Kim JW, Zhang M, Wang X, Abdirassil A, Xu M, Ren S, Wang Q, Yang D, Xu P, Xie W. Targeting ADAR1-mediated RNA editing inhibits hepatic stellate cell activation and liver fibrosis by enhancing HSC-intrinsic innate immunity. Gut. 2026 Jan 19;. doi: 10.1136/gutjnl-2025-335942. [Epub ahead of print] PubMed PMID: 41554631; PubMed Central PMCID: PMC12910384.

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Aceto A, Wang Y, Yang D. An Integrative Drug-Induced Transcriptomic Analysis Identifies Novel MYC Antagonists and Potential Synergistic Drug Combinations. Mol Carcinog. 2025 Dec;64(12):2052-2062. doi: 10.1002/mc.70044. Epub 2025 Sep 30. PubMed PMID: 41025936; PubMed Central PMCID: PMC12639535.

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Xu P, Xi Y, Kim JW, Zhang M, Gao C, Wang Y, Xu M, Wang X, Ren S, Yang D, Wang Q, Xie W. A loss-of-function human ADAR variant activates innate immune response and promotes bowel inflammation. Nat Commun. 2025 Sep 29;16(1):8560. doi: 10.1038/s41467-025-63554-4. PubMed PMID: 41022715; PubMed Central PMCID: PMC12480066.

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Pattarayan D, Wang Y, Wang Z, Li S, Wang X, Chen Y, Wang Y, Chen CY, Bhuniya A, Yadav GS, Xie W, Kammula US, Li S, Zhang M, Yang D. The lncRNA EPIC1 suppresses dsRNA-induced type I IFN signaling and is a therapeutic target to enhance TNBC response to PD-1 inhibition. Sci Signal. 2025 Aug 12;18(899):eadr9131. doi: 10.1126/scisignal.adr9131. Epub 2025 Aug 12. PubMed PMID: 40794843; PubMed Central PMCID: PMC12640557.

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Wang X, Wang Z, Li S, Pattarayan D, Wang Y, Zhai J, Zhang Y, Wang H, Xu M, Zhu J, Wang J, Ma X, Mani S, Xie W, Zhang M, Yang D. Cytoplasmic PXR regulates glucose metabolism by binding mRNAs and modulating their stability. Nat Struct Mol Biol. 2025 Nov;32(11):2144-2157. doi: 10.1038/s41594-025-01614-5. Epub 2025 Aug 12. PubMed PMID: 40797049; PubMed Central PMCID: PMC12781130.

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Wang J, Young G, Zhang M, Salvatore SR, Qin FY, Cai X, Xu M, Ke M, Liu L, Kim JW, Xu P, Yang B, Ren S, Feng Y, Yang D, Ma X, Schopfer FJ, Xie W. Inhibition of sulfotransferase SULT2B1 prevents obesity and insulin resistance by regulating energy expenditure and intestinal lipid absorption. J Biol Chem. 2025 Jul;301(7):110327. doi: 10.1016/j.jbc.2025.110327. Epub 2025 May 31. PubMed PMID: 40456448; PubMed Central PMCID: PMC12268192.

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Li S, Wang Z, Wang X, Wang Y, Pattarayan D, Zhang Y, Nguyen P, Bhuniya A, Chen Y, Huang H, Huang Y, Wang L, Wang J, Li S, Zhang M, Liu Y, Lee N, Yang D. Integrative characterization of MYC RNA-binding function. Cell Genom. 2025 Jul 9;5(7):100878. doi: 10.1016/j.xgen.2025.100878. Epub 2025 May 15. PubMed PMID: 40378850; PubMed Central PMCID: PMC12278643.

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Huang H, Mu Y, Huang Y, Ji B, Wang Y, Chen CY, Chen Y, Luo Z, Li S, Zhang Z, Wang L, Conway JF, Yang D, Wang J, Sun J, Li S. Rational development of gemcitabine-based nanoplatform for targeting SERPINB9/Granzyme B axis to overcome chemo-immune-resistance. Nat Commun. 2025 May 5;16(1):4176. doi: 10.1038/s41467-025-59490-y. PubMed PMID: 40325025; PubMed Central PMCID: PMC12053578.

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Zhu Y, Wang Y, Hoshitsuki K, Yang D, Kokai L, Ma X, Xie W, Fernandez CA. Induction of Cyp2e1 contributes to asparaginase-induced hepatocyte sensitization to lipotoxicity. Acta Pharm Sin B. 2025 Feb;15(2):963-972. doi: 10.1016/j.apsb.2024.11.002. Epub 2024 Nov 7. PubMed PMID: 40177540; PubMed Central PMCID: PMC11959929.

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Huang H, Ji B, Huang Y, Li S, Luo Z, Chen S, Li S, Chen Y, Bain DJ, Sun J, Yang D, Burns TF, Wang J, Li S. Advanced hierarchical computational modeling-based rational development of platinum (II) nanocomplex to improve lung cancer therapy. Adv Funct Mater. 2025 Feb 12;35(7). doi: 10.1002/adfm.202411334. Epub 2024 Sep 27. PubMed PMID: 40452781; PubMed Central PMCID: PMC12124824.

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Tung HC, Kim JW, Zhu J, Li S, Yan J, Liu Q, Koo I, Koshkin SA, Hao F, Zhong G, Xu M, Wang Z, Wang J, Huang Y, Xi Y, Cai X, Xu P, Ren S, Higashiyama T, Gonzalez FJ, Li S, Isoherranen N, Yang D, Ma X, Patterson AD, Xie W. Inhibition of heme-thiolate monooxygenase CYP1B1 prevents hepatic stellate cell activation and liver fibrosis by accumulating trehalose. Sci Transl Med. 2024 Sep 25;16(766):eadk8446. doi: 10.1126/scitranslmed.adk8446. Epub 2024 Sep 25. PubMed PMID: 39321267; PubMed Central PMCID: PMC12084873.

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Zhao Y, Park JY, Yang D, Zhang M. A computational framework to in silico screen for drug-induced hepatocellular toxicity. Toxicol Sci. 2024 Sep 1;201(1):14-25. doi: 10.1093/toxsci/kfae078. PubMed PMID: 38902949; PubMed Central PMCID: PMC11347774.

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Wang Y, Pattarayan D, Huang H, Zhao Y, Li S, Wang Y, Zhang M, Li S, Yang D. Systematic investigation of chemo-immunotherapy synergism to shift anti-PD-1 resistance in cancer. Nat Commun. 2024 Apr 12;15(1):3178. doi: 10.1038/s41467-024-47433-y. PubMed PMID: 38609378; PubMed Central PMCID: PMC11015024.

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Wilkinson AN, Chen R, Coleborn E, Neilson T, Le K, Bhavsar C, Wang Y, Atluri S, Irgam G, Wong K, Yang D, Steptoe R, Wu SY. Let-7i enhances anti-tumour immunity and suppresses ovarian tumour growth. Cancer Immunol Immunother. 2024 Mar 30;73(5):80. doi: 10.1007/s00262-024-03674-w. PubMed PMID: 38554167; PubMed Central PMCID: PMC10981620.

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Luo Z, Huang Y, Batra N, Chen Y, Huang H, Wang Y, Zhang Z, Li S, Chen CY, Wang Z, Sun J, Wang QJ, Yang D, Lu B, Conway JF, Li LY, Yu AM, Li S. Inhibition of iRhom1 by CD44-targeting nanocarrier for improved cancer immunochemotherapy. Nat Commun. 2024 Jan 4;15(1):255. doi: 10.1038/s41467-023-44572-6. PubMed PMID: 38177179; PubMed Central PMCID: PMC10766965.

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Zihui Fang, Yue Wang, Zehua Wang, Meishu Xu, Songrong Ren, Da Yang, Mei Hong, Wen Xie. Data from ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway. 2023 March. DOI: 10.1158/0008-5472.c.6512301.v1.

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Zihui Fang, Yue Wang, Zehua Wang, Meishu Xu, Songrong Ren, Da Yang, Mei Hong, Wen Xie. Data from ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway. 2023 March. DOI: 10.1158/0008-5472.c.6512301.

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Zihui Fang, Yue Wang, Zehua Wang, Meishu Xu, Songrong Ren, Da Yang, Mei Hong, Wen Xie. Supplementary Data from ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway. 2023 March. DOI: 10.1158/0008-5472.22426317.v1.

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Zihui Fang, Yue Wang, Zehua Wang, Meishu Xu, Songrong Ren, Da Yang, Mei Hong, Wen Xie. Supplementary Data from ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway. 2023 March. DOI: 10.1158/0008-5472.22426320.v1.

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Zihui Fang, Yue Wang, Zehua Wang, Meishu Xu, Songrong Ren, Da Yang, Mei Hong, Wen Xie. Supplementary Data from ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway. 2023 March. DOI: 10.1158/0008-5472.22426323.v1.

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Zihui Fang, Yue Wang, Zehua Wang, Meishu Xu, Songrong Ren, Da Yang, Mei Hong, Wen Xie. Supplementary Data from ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway. 2023 March. DOI: 10.1158/0008-5472.22426320.

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Zihui Fang, Yue Wang, Zehua Wang, Meishu Xu, Songrong Ren, Da Yang, Mei Hong, Wen Xie. Supplementary Data from ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway. 2023 March. DOI: 10.1158/0008-5472.22426323.

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Zihui Fang, Yue Wang, Zehua Wang, Meishu Xu, Songrong Ren, Da Yang, Mei Hong, Wen Xie. Supplementary Data from ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway. 2023 March. DOI: 10.1158/0008-5472.22426317.

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Xu P, Xi Y, Kim JW, Zhu J, Zhang M, Xu M, Ren S, Yang D, Ma X, Xie W. Sulfation of chondroitin and bile acids converges to antagonize Wnt/β-catenin signaling and inhibit APC deficiency-induced gut tumorigenesis. Acta Pharm Sin B. 2024 Mar;14(3):1241-1256. doi: 10.1016/j.apsb.2023.12.006. Epub 2023 Dec 16. PubMed PMID: 38487006; PubMed Central PMCID: PMC10935170.

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Wang Y, Pattarayan D, Huang H, Zhao Y, Li S, Wang Y, Zhang M, Li S, Yang D. Systematic investigation of chemo-immunotherapy synergism to shift anti-PD-1 resistance in cancer. Res Sq. 2023 Sep 14;. doi: 10.21203/rs.3.rs-3290264/v1. PubMed PMID: 37790509; PubMed Central PMCID: PMC10543256.

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Chen R, Coleborn E, Bhavsar C, Wang Y, Alim L, Wilkinson AN, Tran MA, Irgam G, Atluri S, Wong K, Shim JJ, Adityan S, Lee JS, Overwijk WW, Steptoe R, Yang D, Wu SY. miR-146a inhibits ovarian tumor growth in vivo via targeting immunosuppressive neutrophils and enhancing CD8(+) T cell infiltration. Mol Ther Oncolytics. 2023 Dec 19;31:100725. doi: 10.1016/j.omto.2023.09.001. eCollection 2023 Dec 19. PubMed PMID: 37781339; PubMed Central PMCID: PMC10539880.

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Cai X, Li S, Zeng X, Xu M, Wang Z, Singhi AD, Tang D, Li S, Yates NA, Yang D, Xie W. Inhibition of the SLC35B2-TPST2 Axis of Tyrosine Sulfation Attenuates the Growth and Metastasis of Pancreatic Ductal Adenocarcinom. Cell Mol Gastroenterol Hepatol. 2023;16(3):473-495. doi: 10.1016/j.jcmgh.2023.05.003. Epub 2023 May 14. PubMed PMID: 37192689; PubMed Central PMCID: PMC10393550.

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Wang J, Zhang Z, Guan J, Tung HC, Xie J, Huang H, Chen Y, Xu M, Ren S, Li S, Zhang M, Yang D, Xie W. Hepatocyte estrogen sulfotransferase inhibition protects female mice from concanavalin A-induced T cell-mediated hepatitis independent of estrogens. J Biol Chem. 2023 Mar;299(3):103026. doi: 10.1016/j.jbc.2023.103026. Epub 2023 Feb 15. PubMed PMID: 36796516; PubMed Central PMCID: PMC10027562.

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Wan Z, Huang H, West RE 3rd, Zhang M, Zhang B, Cai X, Zhang Z, Luo Z, Chen Y, Zhang Y, Xie W, Yang D, Nolin TD, Wang J, Li S, Sun J. Overcoming pancreatic cancer immune resistance by codelivery of CCR2 antagonist using a STING-activating gemcitabine-based nanocarrier. Mater Today (Kidlington). 2023 Jan-Feb;62:33-50. doi: 10.1016/j.mattod.2022.11.008. Epub 2022 Dec 8. PubMed PMID: 38239407; PubMed Central PMCID: PMC10795849.

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Wang Y, Zhao Y, Guo W, Yadav GS, Bhaskarla C, Wang Z, Wang X, Li S, Wang Y, Chen Y, Pattarayan D, Xie W, Li S, Lu B, Kammula US, Zhang M, Yang D. Genome-wide gain-of-function screening characterized lncRNA regulators for tumor immune response. Sci Adv. 2022 Dec 9;8(49):eadd0005. doi: 10.1126/sciadv.add0005. Epub 2022 Dec 7. PubMed PMID: 36475797; PubMed Central PMCID: PMC9728976.

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Zhao Y, Zhang M, Yang D. Bioinformatics approaches to analyzing CRISPR screen data: from dropout screens to single-cell CRISPR screens. Quant Biol. 2022 Dec;10(4):307-320. PubMed PMID: 36937794; PubMed Central PMCID: PMC10019185.

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Bhuniya A, Pattarayan D, Yang D. Lentiviral vector transduction provides nonspecific immunogenicity for syngeneic tumor models. Mol Carcinog. 2022 Dec;61(12):1073-1081. doi: 10.1002/mc.23467. Epub 2022 Sep 26. PubMed PMID: 36161729; PubMed Central PMCID: PMC9643670.

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Zhao Y, Wang Y, Yang D, Suh K, Zhang M. A Computational Framework to Characterize the Cancer Drug Induced Effect on Aging Using Transcriptomic Data. Front Pharmacol. 2022;13:906429. doi: 10.3389/fphar.2022.906429. eCollection 2022. PubMed PMID: 35847024; PubMed Central PMCID: PMC9277350.

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Xie Y, Sun R, Gao L, Guan J, Wang J, Bell A, Zhu J, Zhang M, Xu M, Lu P, Cai X, Ren S, Xu P, Monga SP, Ma X, Yang D, Liu Y, Lu B, Xie W. Chronic Activation of LXRα Sensitizes Mice to Hepatocellular Carcinoma. Hepatol Commun. 2022 May;6(5):1123-1139. doi: 10.1002/hep4.1880. Epub 2022 Jan 3. PubMed PMID: 34981658; PubMed Central PMCID: PMC9035576.

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Wan Z, Sun R, Liu YW, Li S, Sun J, Li J, Zhu J, Moharil P, Zhang B, Ren P, Ren G, Zhang M, Ma X, Dai S, Yang D, Lu B, Li S. Targeting metabotropic glutamate receptor 4 for cancer immunotherapy. Sci Adv. 2021 Dec 10;7(50):eabj4226. doi: 10.1126/sciadv.abj4226. Epub 2021 Dec 10. PubMed PMID: 34890233; PubMed Central PMCID: PMC8664261.

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Xi Y, Li Y, Xu P, Li S, Liu Z, Tung HC, Cai X, Wang J, Huang H, Wang M, Xu M, Ren S, Li S, Zhang M, Lee YJ, Huang L, Yang D, He J, Huang Z, Xie W. The anti-fibrotic drug pirfenidone inhibits liver fibrosis by targeting the small oxidoreductase glutaredoxin-1. Sci Adv. 2021 Sep 3;7(36):eabg9241. doi: 10.1126/sciadv.abg9241. Epub 2021 Sep 1. PubMed PMID: 34516906; PubMed Central PMCID: PMC8442864.

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Zhang M, Yang D, Gold B. Origins of nonsense mutations in human tumor suppressor genes. Mutat Res. 2021 Jul-Dec;823:111761. doi: 10.1016/j.mrfmmm.2021.111761. Epub 2021 Aug 16. PubMed PMID: 34461460.

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Liu B, Zhou M, Li X, Zhang X, Wang Q, Liu L, Yang M, Yang D, Guo Y, Zhang Q, Zheng H, Wang Q, Li L, Chu X, Wang W, Li H, Song F, Pan Y, Zhang W, Chen K. Interrogation of gender disparity uncovers androgen receptor as the transcriptional activator for oncogenic miR-125b in gastric cancer. Cell Death Dis. 2021 May 4;12(5):441. doi: 10.1038/s41419-021-03727-3. PubMed PMID: 33947843; PubMed Central PMCID: PMC8096848.

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Xu P, Xi Y, Zhu J, Zhang M, Luka Z, Stolz DB, Cai X, Xie Y, Xu M, Ren S, Huang Z, Yang D, York JD, Ma X, Xie W. Intestinal Sulfation Is Essential to Protect Against Colitis and Colonic Carcinogenesis. Gastroenterology. 2021 Jul;161(1):271-286.e11. doi: 10.1053/j.gastro.2021.03.048. Epub 2021 Apr 2. PubMed PMID: 33819483; PubMed Central PMCID: PMC8238844.

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Wang X, Yang D. The regulation of RNA metabolism in hormone signaling and breast cancer. Mol Cell Endocrinol. 2021 Jun 1;529:111221. doi: 10.1016/j.mce.2021.111221. Epub 2021 Mar 10. Review. PubMed PMID: 33711334; PubMed Central PMCID: PMC8262629.

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Guo W, Wang Y, Yang M, Wang Z, Wang Y, Chaurasia S, Wu Z, Zhang M, Yadav GS, Rathod S, Concha-Benavente F, Fernandez C, Li S, Xie W, Ferris RL, Kammula US, Lu B, Yang D. LincRNA-immunity landscape analysis identifies EPIC1 as a regulator of tumor immune evasion and immunotherapy resistance. Sci Adv. 2021 Feb;7(7). doi: 10.1126/sciadv.abb3555. Print 2021 Feb. PubMed PMID: 33568470; PubMed Central PMCID: PMC7875530.

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Dwivedi SKD, Rao G, Dey A, Buechel M, Zhang Y, Zhang M, Yang D, Mukherjee P, Bhattacharya R. Targeting the TGFβ pathway in uterine carcinosarcoma. Cell Stress. 2020 Aug 25;4(11):252-260. doi: 10.15698/cst2020.11.234. PubMed PMID: 33150300; PubMed Central PMCID: PMC7590842.

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Fang Z, Wang Y, Wang Z, Xu M, Ren S, Yang D, Hong M, Xie W. ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway. Cancer Res. 2020 Oct 15;80(20):4399-4413. doi: 10.1158/0008-5472.CAN-20-1031. Epub 2020 Aug 21. PubMed PMID: 32826278; PubMed Central PMCID: PMC7572695.

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Wang Y, Zhang M, Wang Z, Guo W, Yang D. MYC-binding lncRNA EPIC1 promotes AKT-mTORC1 signaling and rapamycin resistance in breast and ovarian cancer. Mol Carcinog. 2020 Oct;59(10):1188-1198. doi: 10.1002/mc.23248. Epub 2020 Aug 18. PubMed PMID: 32810332; PubMed Central PMCID: PMC7882146.

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Gao L, Li B, Wang J, Shen D, Yang M, Sun R, Tung HC, Xu M, Ren S, Zhang M, Yang D, Lu B, Wang H, Liu Y, Xie W. Activation of Liver X Receptor α Sensitizes Mice to T-Cell Mediated Hepatitis. Hepatol Commun. 2020 Nov;4(11):1664-1679. doi: 10.1002/hep4.1584. eCollection 2020 Nov. PubMed PMID: 33163836; PubMed Central PMCID: PMC7603537.

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Xiong X, Rao G, Roy RV, Zhang Y, Means N, Dey A, Tsaliki M, Saha S, Bhattacharyya S, Dhar Dwivedi SK, Rao CV, McCormick DJ, Dhanasekaran D, Ding K, Gillies E, Zhang M, Yang D, Bhattacharya R, Mukherjee P. Ubiquitin-binding associated protein 2 regulates KRAS activation and macropinocytosis in pancreatic cancer. FASEB J. 2020 Sep;34(9):12024-12039. doi: 10.1096/fj.201902826RR. Epub 2020 Jul 21. PubMed PMID: 32692445; PubMed Central PMCID: PMC7808438.

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Li T, Zhang C, Zhao G, Zhang X, Hao M, Hassan S, Zhang M, Zheng H, Yang D, Liu L, Mehraein-Ghomi F, Bai X, Chen K, Zhang W, Yang J. Data analysis of PD-1 antibody in the treatment of melanoma patients. Data Brief. 2020 Jun;30:105523. doi: 10.1016/j.dib.2020.105523. eCollection 2020 Jun. PubMed PMID: 32322636; PubMed Central PMCID: PMC7168734.

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Wu Z, Li S, Tang X, Wang Y, Guo W, Cao G, Chen K, Zhang M, Guan M, Yang D. Copy Number Amplification of DNA Damage Repair Pathways Potentiates Therapeutic Resistance in Cancer. Theranostics. 2020;10(9):3939-3951. doi: 10.7150/thno.39341. eCollection 2020. PubMed PMID: 32226530; PubMed Central PMCID: PMC7086350.