Publications

Selected refereed articles (Full publication list on PubMed.)

  1. 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
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. Deng X, Li S, Kong F, Ruan H, Xu X, Zhang X, Wu Z, Zhang L, Xu Y, Yuan H, Peng H, Yang D, Guan M. Long noncoding RNA PiHL regulates p53 protein stability through GRWD1/RPL11/MDM2 axis in colorectal cancer. Theranostics. 2020;10(1):265-280. doi: 10.7150/thno.36045. eCollection 2020. PubMed PMID: 31903119; PubMed Central PMCID: PMC6929633.
  12. Yan J, Tung HC, Li S, Niu Y, Garbacz WG, Lu P, Bi Y, Li Y, He J, Xu M, Ren S, Monga SP, Schwabe RF, Yang D, Xie W. Aryl Hydrocarbon Receptor Signaling Prevents Activation of Hepatic Stellate Cells and Liver Fibrogenesis in Mice. Gastroenterology. 2019 Sep;157(3):793-806.e14. doi: 10.1053/j.gastro.2019.05.066. Epub 2019 Jun 3. PubMed PMID: 31170413; PubMed Central PMCID: PMC6707837.
  13. Wang Y, Wang Z, Xu J, Li J, Li S, Zhang M, Yang D. Systematic identification of non-coding pharmacogenomic landscape in cancer. Nat Commun. 2018 Aug 9;9(1):3192. doi: 10.1038/s41467-018-05495-9. PubMed PMID: 30093685; PubMed Central PMCID: PMC6085336.
  14. Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S, Xie W, Yang D. lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. Cancer Cell. 2018 Apr 9;33(4):706-720.e9. doi: 10.1016/j.ccell.2018.03.006. Epub 2018 Apr 2. PubMed PMID: 29622465; PubMed Central PMCID: PMC6143179.
  15. Wang Y, Fang Z, Hong M, Yang D, Xie W. Long-noncoding RNAs (lncRNAs) in drug metabolism and disposition, implications in cancer chemo-resistance. Acta Pharm Sin B. 2020 Jan;10(1):105-112. doi: 10.1016/j.apsb.2019.09.011. Epub 2019 Oct 19. Review. PubMed PMID: 31993309; PubMed Central PMCID: PMC6976993.
  16. Gu Y, Wang R, Han Y, Zhou W, Zhao Z, Chen T, Zhang Y, Peng F, Liang H, Qi L, Zhao W, Yang D, Guo Z. A landscape of synthetic viable interactions in cancer. Brief Bioinform. 2018 Jul 20;19(4):644-655. doi: 10.1093/bib/bbw142. PubMed PMID: 28096076.
  17. Zhang M, Liu G, Xue F, Edwards R, Sood AK, Zhang W, Yang D. Copy number deletion of RAD50 as predictive marker of BRCAness and PARP inhibitor response in BRCA wild type ovarian cancer. Gynecol Oncol. 2016 Apr;141(1):57-64. doi: 10.1016/j.ygyno.2016.01.004. PubMed PMID: 27016230; PubMed Central PMCID: PMC4967351.
  18. Chen K, Yang D, Li X, Sun B, Song F, Cao W, Brat DJ, Gao Z, Li H, Liang H, Zhao Y, Zheng H, Li M, Buckner J, Patterson SD, Ye X, Reinhard C, Bhathena A, Joshi D, Mischel PS, Croce CM, Wang YM, Raghavakaimal S, Li H, Lu X, Pan Y, Chang H, Ba S, Luo L, Cavenee WK, Zhang W, Hao X. Mutational landscape of gastric adenocarcinoma in Chinese: implications for prognosis and therapy. Proc Natl Acad Sci U S A. 2015 Jan 27;112(4):1107-12. doi: 10.1073/pnas.1422640112. Epub 2015 Jan 12. PubMed PMID: 25583476; PubMed Central PMCID: PMC4313862.
  19. Song F, Yang D, Liu B, Guo Y, Zheng H, Li L, Wang T, Yu J, Zhao Y, Niu R, Liang H, Winkler H, Zhang W, Hao X, Chen K. Integrated microRNA network analyses identify a poor-prognosis subtype of gastric cancer characterized by the miR-200 family. Clin Cancer Res. 2014 Feb 15;20(4):878-89. doi: 10.1158/1078-0432.CCR-13-1844. Epub 2013 Dec 18. PubMed PMID: 24352645.
  20. Yang D, Sun Y, Hu L, Zheng H, Ji P, Pecot CV, Zhao Y, Reynolds S, Cheng H, Rupaimoole R, Cogdell D, Nykter M, Broaddus R, Rodriguez-Aguayo C, Lopez-Berestein G, Liu J, Shmulevich I, Sood AK, Chen K, Zhang W. Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer. Cancer Cell. 2013 Feb 11;23(2):186-99. doi: 10.1016/j.ccr.2012.12.020. PubMed PMID: 23410973; PubMed Central PMCID: PMC3603369.
  21. Pecot CV, Rupaimoole R, Yang D, Akbani R, Ivan C, Lu C, Wu S, Han HD, Shah MY, Rodriguez-Aguayo C, Bottsford-Miller J, Liu Y, Kim SB, Unruh A, Gonzalez-Villasana V, Huang L, Zand B, Moreno-Smith M, Mangala LS, Taylor M, Dalton HJ, Sehgal V, Wen Y, Kang Y, Baggerly KA, Lee JS, Ram PT, Ravoori MK, Kundra V, Zhang X, Ali-Fehmi R, Gonzalez-Angulo AM, Massion PP, Calin GA, Lopez-Berestein G, Zhang W, Sood AK. Tumour angiogenesis regulation by the miR-200 family. Nat Commun. 2013;4:2427. doi: 10.1038/ncomms3427. PubMed PMID: 24018975; PubMed Central PMCID: PMC3904438.
  22. Liu G, Yang D, Sun Y, Shmulevich I, Xue F, Sood AK, Zhang W. Differing clinical impact of BRCA1 and BRCA2 mutations in serous ovarian cancer. Pharmacogenomics. 2012 Oct;13(13):1523-35. doi: 10.2217/pgs.12.137. Review. PubMed PMID: 23057551; PubMed Central PMCID: PMC3603383.
  23. Yang D, Khan S, Sun Y, Hess K, Shmulevich I, Sood AK, Zhang W. Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer. JAMA. 2011 Oct 12;306(14):1557-65. doi: 10.1001/jama.2011.1456. PubMed PMID: 21990299; PubMed Central PMCID: PMC4159096.
  24. Yang D, Li Y, Xiao H, Liu Q, Zhang M, Zhu J, Ma W, Yao C, Wang J, Wang D, Guo Z, Yang B. Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories. Bioinformatics. 2008 Jan 15;24(2):265-71. doi: 10.1093/bioinformatics/btm558. Epub 2007 Nov 15. PubMed PMID: 18006543.