Corresponding *Equal contribution

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  • Noureen Nighat, Zhenqing Ye, Yidong Chen, Xiaojing Wang, Siyuan Zheng. 2021. Benchmarking supervised signature-scoring methods for single-cell RNA sequencing data in cancer. bioRxiv. Under review.







  • Kim H*, Zheng S*, Amini SS, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Muller F, Hu J, Sloan AE, Cohen ML, Van Meir EG, Scarpace L, Laird PW, Weinstein JN, Lander ES, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS, Verhaak RG. 2015. Whole genome and multi-sector sequencing of primary and post-treatment glioblastoma illustrates patterns of tumor evolution. Genome Res. 2015 Mar;25(3):316-27. doi: 10.1101/gr.180612.114. Epub 2015 Feb 3.
    • “Breaking Advances”, Cancer Res, 2015;75:1159-1160.
    • “Highlights from the literature”, Neuro-Oncology, 2015;17(6):773-775.


  • Torres-García W*, Zheng S*, Sivachenko A*, Vegesna R, Wang Q, Yao R, Berger MF, Weinstein JN, Getz G, Verhaak RG. 2014. PRADA: Pipeline for RNA Sequencing Data Analysis. Bioinformatics. 2014 Apr 1.
  • Zheng S, Kim H, Verhaak RG. Silent mutations make some noise. Cell. 2014 Mar 13;156(6):1129-31. doi: 10.1016/j.cell.2014.02.037.Preview.
  • Guan X*, Vengoechea J*, Zheng S*, Sloan AE, Chen Y, Brat DJ, O’Neill BP, de Groot J, Yust-Katz S, Yung WK, Cohen ML, Aldape KD, Rosenfeld S, Verhaak RG, Barnholtz-Sloan JS. 2014. Association between glioblastoma molecular subtypes and lower grade gliomas. PLoS One. 2014 Mar 10;9(3):e91216. doi: 10.1371/journal.pone.0091216.


  • Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W, Ezhilarasan R, Wang S, McKenna A, Chin L, Brennan CW, Yung WK, Weinstein JN, Aldape KD, Sulman EP, Chen K, Koul D, Verhaak RG. 2013. A survey of intragenic breakpoints in GBM identifies a distinct subset associated with poor survival. Genes Dev. 2013 Jul 1;27(13):1462-72.
    • Commentary, Zheng et al.Cell Cycle. 2013 Oct 21;12(24).


  • Zheng S, Chheda MG, Verhaak RG. 2012. Studying a Complex Tumor—Potential and Pitfalls. Cancer J. 2012 Jan-Feb;18(1):107-14.  Review
  • Zheng S, Zhao Z. 2012. DNA methylation profiling distinguishes three clusters of breast cancer cell lines. Chem Biodivers. 2012 May;9(5):848-56. doi: 10.1002/cbdv.201100354.
  • Zheng S, Zhao Z. 2012. GenRev: exploring gene relevance in molecular networks. Genomics. 2012 Mar;99(3):183-8. doi: 10.1016/j.ygeno.2011.12.005. Epub 2011 Dec 29.


  • Sun Y*, Zheng S*, Torossian A, Speirs CK, Schleicher S, Giacalone NJ, Carbone DP, Zhao Z, Lu B. Genetic profiling of lung cancer stem-like cells reveals IGF-1 signaling pathway as a promising target to improve treatment response. International Journal of Radiation Oncology, Biology, Physics. 2011 Dec 22.
  • Zheng S, Tansey WP, Hiebert SW, Zhao Z. Integrative network analysis identifies key genes and pathways in the progression of Hepatitis C virus induced hepatocellular carcinoma. BMC Med Genomics. 2011 Aug 8;4(1):62.
  • Jia P*, Zheng S*, Long J, Zheng W, Zhao Z. dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics. (2010) doi: 10.1093/bioinformatics/btq615.
  • Hao P*, Zheng S*, Ping J, Tu K, Gieger C, Wang-Sattler R, Zhong Y, Li Y. Human gene expression sensitivity according to large scale meta-analysis. BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S56.
  • Zheng S, Sheng J, Wang C, Wang X, Yu Y, Li Y, Michie A, Dai J, Zhong Y, Hao P, Liu L, Li Y. MPSQ: a web tool for protein-state searching. Bioinformatics. 2008 Oct 15;24(20):2412-3.