Publication – Zheng Lab

^†Corresponding ^*Equal contribution

See publications on PubMed (name highlighted) or PubMed (full list).

Juechen Yang^*, Qilin Li^*, Nighat Noureen, Yanbing Fang, Raushan Kurmasheva, Peter Houghton, Xiaojing Wang^†, Siyuan Zheng^†. PCAT: An integrated portal for genomic and preclinical testing data of pediatric cancer patient-derived xenograft models. Preprint. bioRxiv.
Nighat Noureen, Shaofang Wu, Yingli Lyu, Juechen Yang, WK Alfred Yung, Jonathan Gelfond, Xiaojing Wang, Dimpy Koul, Andrew Ludlow, Siyuan Zheng^†. Inferring Telomerase Enzymatic Activity from Expression Data. Preprint. bioRxiv. Under Review.

Zheng S^†, Kristin Alfaro-Munoz, Wei Wei, Xiaojing Wang, Fang Wang, Agda Karina Eterovic, Kenna M. Shaw, Funda Meric-Bernstam, Gregory N. Fuller, Ken Chen, Roel G.W. Verhaak, Gordon B. Mills, Alfred W.K. Yung, Shiao-Pei Weathers, John F. de Groot. Prospective Clinical Sequencing of Adult Glioma. Molecular Cancer Therapeutics. 2019 Mar 29. pii: molcanther.1122.2018. doi: 10.1158/1535-7163.
- Highlight of the issue

Hu X, Wang Q, Tang M, Barthel FP, Amin S, Yoshihara K, Lang FM, Martinez-Ledesma E, Lee SH, Zheng S^†, Verhaak RG^†. TumorFusions: an integrative resource for cancer-associated transcript fusions. Nucleic Acids Res. 2018 Jan 4;46(D1):D1144-D1149. doi: 10.1093/nar/gkx1018.

Zheng S^†. Benchmarking: contexts and details matter. Genome Biology. 2017 Jul 5;18(1):129. doi: 10.1186/s13059-017-1258-3.
Barthel FP, Wei W, Tang M, Martinez-Ledesma E, Hu X, Amin S, Akdemir K, Seth S, Song X, Wang Q, Lichtenberg T, Hu J, Zhang J, Zheng S^†, Verhaak RG^†. Systematic Analysis of Telomere Length and Somatic Alterations in 31 Cancer Types. Nat Genet. 2017 Jan 30. doi: 10.1038/ng.3781.
- Science Daily: Unraveling the mystery of why cancer cells survive and thrive https://www.sciencedaily.com/releases/2017/01/170130110914.htm

Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, Robertson AG, Raphael BJ, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MC, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA, The Cancer Genome Atlas Research Network, Hammer GD, Giordano TJ, Verhaak RG. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell, 2016; 29 (5): 723 DOI: 10.1016/j.ccell.2016.04.002
- Science Daily: Study shows possible ‘key’ to improved therapy for adrenocortical carcinoma https://www.sciencedaily.com/releases/2016/05/160509132455.htm
- Nature Reviews Endocrinology: The genetics of adrenocortical carcinoma revealed http://www.nature.com/nrendo/journal/vaop/ncurrent/full/nrendo.2016.89.html

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. 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. 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. 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. 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. Studying a Complex Tumor—Potential and Pitfalls. Cancer J. 2012 Jan-Feb;18(1):107-14. Review
Zheng S, Zhao Z. 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. 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.
- F1000Prime Recommendation (http://m.f1000.com/prime/6469956)
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.