Publications

Selected refereed articles

  1. 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, Accepted (#: corresponding author).
  2. Wang Z, Yang B, Zhang M, Guo W, Wu Z, Jia L, Wang Y, 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. PMID: 29622465 (#: corresponding author).
  3. 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. 2017 Jan 17. pii: bbw142. doi: 10.1093/bib/bbw142. PMID: 28096076 (#: corresponding author)
  4. Zhang M, Liu G, Xue F, Edwards R, Sood A, Zhang, W, Yang D#, Copy number deletion of RAD50 as a 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. (#: corresponding author)
  5. Zhao W, Chen B, Guo X, Wang R, Chang Z, Dong Y, Song K, Wang W, Qi L, Gu Y, Wang C, Yang D#, Guo Z#, A rank-based transcriptional signature for predicting relapse risk of stage II colorectal cancer identified with proper data sources. Oncotarget. 2016 Mar 7. doi: 10.18632/oncotarget.7956 (#: corresponding author)
  6. Li X, Cai H, Zheng W, Tong M, Li H, Ao L, Li J, Hong G, Li M, Guan Q, Yang S, Yang D#, Lin X#, Guo Z#. An individualized prognostic signature for gastric cancer patients treated with 5-Fluorouracil-based chemotherapy and distinct multi-omics characteristics of prognostic groups. Oncotarget. 2016 Jan 30. doi: 10.18632/oncotarget.7087 (#: corresponding author)
  7. Rupaimoole R, Ivan C, Yang D, Gharpure KM, Wu SY, Pecot CV, Previs RA, Nagaraja AS, Armaiz-Pena GN, McGuire M, Pradeep S, Mangala LS, Rodriguez-Aguayo C, Huang L, Bar-Eli M, Zhang W, Lopez-Berestein G, Calin GA, Sood AK. Hypoxia-upregulated microRNA-630 targets Dicer, leading to increased tumor progression. 2016 Jan 4. doi: 10.1038/onc.2015.492.
  8. Liu G, Yang D, Rupaimoole R, Pecot CV, Sun Y, Mangala LS, Li X, Ji P, Cogdell D, Hu L, Wang Y, Rodriguez-Aguayo C, Lopez-Berestein G, Shmulevich I, De Cecco L, Chen K, Mezzanzanica D, Xue F, Sood AK, Zhang W. Augmentation of response to chemotherapy by microRNA-506 through synthetic lethality in serous ovarian cancers. J Natl Cancer Inst. 2015 107 (7): djv108 doi: 10.1093/jnci/djv108
  9. Chen K*, Yang D*, Li X*, Sun B, Song F, Cao W, Brat D, Gao Z, Li H, Liang H, Zhao Y, Zheng H, Li M, Buckner J, Patterson S, Ye X, Reinhard C, Bhathena A, Joshi D, Mischel P, Croce C, Wang Y, Kaimal S, Li H, Lu X, Pan Y, Chang H, Ba S, Luo L, Cavenee W, 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. (*:equal contributions)
  10. 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 miR-200 family” Clin Cancer Res 2014 Feb 15;20(4):878-89 (*:equal contributions)
  11. 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. Featured on the cover.
  12. Pecot C, Rupaimoole R*, Yang D*, Akbani R*, Ivan C, Lu C, Wu S, Han H, Shah M, Rodriguez-Aguayo C, Bottsford-Miller J, Liu Y, Kim S, Unruh A, Gonzalez-Villasana V, Huang L, Zand B, Moreno-Smith M, Mangala L, Taylor M, Dalton H, Sehgal V, Wen Y, Kang Y, Baggerly K, Lee J, Ram P, Ravoori M, Kundra V, Zhang X, Ali-Fehmi A, Gonzalez-Angulo A, Massion P, Calin G, Lopez-Berestein G, Zhang W, Sood A “Tumor Angiogenesis Regulation by the miR-200 Family.” Nat Commun. 2013 Sep 10;4:2427. (*:equal contributions)
  13. Yang D, Khan S, Sun Y, Hess K, Shmulevich I, Sood A and Zhang W. “Association between BRCA2 but not BRCA1 Mutations and Beneficial Survival, Chemotherapy Sensitivity, and Gene Mutator Phenotype in Patients with Ovarian Cancer.” JAMA. 2011 Oct 12;306(14):1557-65. Highlighted by JAMA, Nature Reviews Cancer, Nature Reviews Clinical Oncology, NCI Cancer Bulletin, LA Times, Bloomberg, and U.S. News etc.
  14. Yang J*, Yang D*, Sun Y, Cogdell D, Hu L, Li H, Pang Y, Du X, Yang Y, Zhang J, Wang G, Trent J, Chen K, Sun B, Hao X, Zhang W. Genetic amplification of the vascular endothelial growth factor (VEGF) pathway genes, including VEGFA, in human osteosarcoma. Cancer. 2011 Nov 1;117(21):4925-38. (*:equal contributions)

Other refereed articles

  1. Banerjee Mustafi S, Chakraborty PK, Naz S, Dwivedi SK, Street M, Basak R, Yang D, Ding K, Mukherjee P, Bhattacharya R. MDR1 mediated chemoresistance: BMI1 and TIP60 in action. Biochim Biophys Acta. 2016 Aug;1859(8):983-93. doi: 10.1016/j.bbagrm.2016.06.002. Epub 2016 Jun 22. PubMed PMID: 27295567; PubMed Central PMCID: PMC4958591.
  2. Wu SY, Rupaimoole R, Shen F, Pradeep S, Pecot CV, Ivan C, Nagaraja AS, Gharpure KM, Pham E, Hatakeyama H, McGuire MH, Haemmerle M, Vidal-Anaya V, Olsen C, Rodriguez-Aguayo C, Filant J, Ehsanipour EA, Herbrich SM, Maiti SN, Huang L, Kim JH, Zhang X, Han HD, Armaiz-Pena GN, Seviour EG, Tucker S, Zhang M, Yang D, Cooper LJ, Ali-Fehmi R, Bar-Eli M, Lee JS, Ram PT, Baggerly KA, Lopez-Berestein G, Hung MC, Sood AK. A miR-192-EGR1-HOXB9 regulatory network controls the angiogenic switch in cancer. Nat Commun. 2016 Apr 4;7:11169. doi: 10.1038/ncomms11169.
  3. The Cancer Genome Atlas Research Network (include Yang D), Genomic Classification of Cutaneous Melanoma. Cell. 2015 Volume 161, Issue 7, 18 June 2015, Pages 1681–1696
  4. The Cancer Genome Atlas Research Network (include Yang D), Comprehensive, Integrative Genomic Analysis of Diffuse Lower Grade Gliomas. N Engl J Med. 2015; 372:2481-2498 June 25, 2015, DOI: 10.1056/NEJMoa1402121
  5. Du X*, Yang J*, Yang D*, Tian W, Zhu Z. The genetic basis for inactivation of Wnt pathway in human osteosarcoma. BMC Cancer. 2014 Jun 18;14:450. *:equal contributions
  6. The Cancer Genome Atlas Research Network (include Yang D), Comprehensive Molecular Characterization of Gastric Adenocarcinoma. Nature. 2014 Sep 11;513(7517):202-9. doi: 10.1038/nature13480. Epub 2014 Jul 23.
  7. Guo F, Cogdell D, Hu L, Yang D, Sood AK, Xue F, Zhang W. “miR-101 suppresses the epithelial-to-mesenchymal transition by targeting ZEB1 and ZEB2 in ovarian carcinoma.” Oncol Rep. 2014 May;31(5):2021-8.
  8. Guo F, Parker Kerrigan BC, Yang D, Hu L, Shmulevich I, Sood AK, Xue F, Zhang W. Post-transcriptional regulatory network of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions. J Hematol Oncol. 2014 Mar 5;7(1):19.
  9. Liu G, Sun Y, Ji P, Li X, Cogdell D, Yang D, Kerrigan B, Shmulevich I, Chen K, Sood A, Xue F, and Zhang W. MiR-506 Suppresses Proliferation and Induces Senescence by Directly Targeting the CDK4/6-FOXM1 Axis in Ovarian Cancer. J Pathol. 2014 Mar 6. Doi: 10.1002/path.4348.
  10. Patel L, Parker B, Yang D, Zhang W. Translational genomics in cancer research: converting profiles into personalized cancer medicine. Cancer Biol Med. 2013 Dec;10(4):214-220
  11. Zheng H, Zhang L, Zhao Y, Yang D, Song F, Wen Y, Hao Q, Hu Z, Zhang W, Chen K. Plasma miRNAs as diagnostic and prognostic biomarkers for ovarian cancer. PloS One. 2013 Nov 1;8(11)
  12. The Cancer Genome Atlas Research Network (include Yang D), John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander & Joshua M Stuart “The Cancer Genome Atlas Pan-Cancer analysis project” Nat Genet. 2013 Sep 26;45(10):1113-20.
  13. Zhang Y, Xia J, Zhang Y, Qin Y, Yang D, Qi L, Zhao W, Wang C, Guo Z. Pitfalls in experimental designs for characterizing the transcriptional, methylation and copy number changes of oncogenes and tumor suppressor genes. PloS One. 2013;8(3):e58163.
  14. Chen X, Zhang J, Cheng W, Chang DY, Huang J, Wang X, Jia L, Rosen DG, Zhang W, Yang D, Gershenson DM, Sood AK, Bast RC Jr, Liu J. CA-125 level as a prognostic indicator in type I and type II epithelial ovarian cancer. Int J Gynecol Cancer. 2013 Jun;23(5):815-22.
  15. 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.
  16. The Cancer Genome Atlas Research Network (include Yang D), “Comprehensive Molecular Characterization of Human Colon and Rectal tumors.” Nature. 2012 Jul 18;487(7407):330-7.
  17. Yang D, Ylipää A, Yang J, Hunt K, Pollock R, Trent J, Yli-Harja O, Shmulevich I, Nykter M, Zhang W. “An integrated study of aberrant gene copy number and gene expression in GIST and LMS”. Technol Cancer Res Treat. 2010 Apr;9(2):171-8
  18. Zheng H, Song F, Zhang L, Yang D, Ji P, Wang Y, Almeida M, Calin GA, Hao X, Wei Q, Zhang W, Chen K. Genetic variants at the miR-124 binding site on the cytoskeleton-organizing IQGAP1 gene confer differential predisposition to breast cancer. Int J Oncol. 2011 Apr;38(4):1153-61.
  19. Zhu J, Xiao H, Shen X, Wang J, Zou J, Zhang L, Yang D, Ma W, Yao C, Gong X, Zhang M, Zhang Y, Guo Z. “Viewing cancer genes from co-evolving gene modules.” Bioinformatics. 2010 Apr 1;26(7):919-24.
  20. Yang J, Yang D, Cogdell D, Du X, Hu L, Li H, Zheng H, Pang Y,Trent J, Chen K, Zhang W.. “APEX1 Gene Amplification and Its Protein Overexpression in Osteosarcoma: Correlation with Recurrence, Metastasis, and Survival”. Technol Cancer Res Treat. 2010 Apr;9(2):161-9.
  21. Wang Y, Yang D, Cogdell D, Hu L, Xue F, Broaddus R, Zhang W. “Genomic characterization of gene copy-number aberrations in endometrial carcinoma cell lines derived from endometrioid-type endometrial adenocarcinoma”. Technol Cancer Res Treat. 2010 Apr;9(2):179-89.
  22. Yang J, Cogdell D, Yang D, Hu L, Li H, Zheng H, Du X, Pang Y, Trent J, Chen K, Zhang W. “Deletion of the WWOX gene and frequent loss of its protein expression in human osteosarcoma” Cancer Lett. 2010 May 1;291(1):31-8.
  23. Gu Y*, Yang D*, Zou J, Ma W, Wu R, Zhao W, Zhang Y, Xiao H, Gong X, Zhang M, Zhu J, Guo Z. “Systematic interpretation of co-occurring mutation using large-scale mutation profile”. Molecular Cancer Therapeutics. 2010 Aug;9(8):2186-95. (*:equal contributions)
  24. Wang D, Wang C, Zhang L, Xiao H, Shen X, Ren L, Zhao W, Hong G, Zhang Y, Zhu J, Zhang M, Yang D, Ma W, Guo Z. “Evaluation of cDNA Microarray Data by Multiple Clones Mapping to the Same Transcript”. OMICS: A Journal of Integrative Biology. 2009, 13(6): 493-499.
  25. Ma W, Yang D, Guo X, Gu Y, Zhao W, Gong X, Zhang M, Zhu J, Guo Z. “Coordinated functions involving multiple-function disease genes: a study for cancer”. Genomics. 94: 02, 2009, P 94-100
  26. Zhang M, Yao C, Guo Z, Zou J, Zhang L, Xiao H, Wang D, Yang D, Gong X, Zhu J. “Apparently low reproducibility of true differential expression discoveries in microarray studies”. Bioinformatics. 2008, 24:18, p. 2057-63.
  27. Yang D, Li Y, Xiao H, Guo Z, Liu Q, Zhu J, Zhang M, Wang D, Yang B. “Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories”, Bioinformatics. 24: 2, p.265-71, 2008.
  28. Yang D, Li Q, Hao X, Li C, Lv Y, Wang D, Zhong G, Zhang M, Guo Z. “Studying molecular mechanisms of depression by a rat model based on gene expression profiles and gene functional modules”. Chinese Advanced Technology Letters, 2007, 17: 05.
  29. Guo Z, Li Y, Gong X, Yao C, Ma W, Wang D, Li Y, Zhu J, Zhang M, Yang D, Wang J, “Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network”, Bioinformatics. 2007, 23: 16 p. 2121-2128.
  30. Zhu J, Wang J, Guo Z, Zhang M, Yang D, Li Y, Wang D, Xiao G. “GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology”. BMC Genomics. 2007, Jan 24;8:30.
  31. Wang D, Lv Y, Guo Z, Li X, Li Y, Zhu J, Yang D, Xu J, Rao S, Yang B, “Effects of replacing the unreliable cDNA microarray measurements on the disease classification based on gene expression profiles and functional modules”. Bioinformatics. 2006, 22: 23, p. 2883-9.

Other publications

Zhang W, Yang D, and Sood A. BRCA1 and BRCA2 Mutations in Ovarian Cancer—Reply. JAMA 2012;307(4):360-361.