Selected recent publications
- An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors
Tao Wang, Rong Lu, Payal Kapur, Bijay S. Jaiswal, Raquibul Hannan, Ze Zhang, Ivan Pedrosa, Jason J. Luke, He Zhang, Leonard D. Goldstein, Qurratulain Yousuf, Yi-Feng Gu, Tiffani McKenzie, Allison Joyce, Min S. Kim, Xinlei Wang, Danni Luo, Oreoluwa Onabolu, Christina Stevens, Zhiqun Xie, Mingyi Chen, Alexander Filatenkov, Jose Torrealba, Xin Luo, Wenbin Guo, Jingxuan He, Eric Stawiski, Zora Modrusan, Steffen Durinck, Somasekar Seshagiri, James Brugarolas Cancer Discovery. 2018
This paper created the DisHet model to dissect cellular components found in heterogeneous tumors, and provided the eTME gene signatures for profiling tumor immune cell infiltrations. DisHet and eTME uncovered missing links between tumor cells, the tumor microenvironment, systemic manifestations of inflammation, and poor prognosis.
- Probability of phenotypically detectable protein damage by predicted deleterious mutations: analysis of ENU-induced mutations in the Mutagenetix database
Tao Wang, Chun Hui Bu, Sara Hildebrand, Gaoxiang Jia, Owen Siggs, Stephen Lyon, David Pratt, Lindsay Scott, Jamie Russell, Sara Ludwig, Anne Murray, Eva Marie Moresco. Nature Communications. 2017
Programs such as PolyPhen-2 (PP2) provide scores of relative severity of damage caused by missense mutations. Here, we estimate actual probabilities that putative null or missense alleles would cause phenotypically detectable protein damage, which could lead to many interesting and useful applications.
- Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data.
Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC; Prostate Cancer Challenge DREAM Community. Lancet Oncology . 2016
We organized the Prostate Dream Challenge where we leveraged open-source clinical trial data to develop prognostic models for precision medicine.
- Real-time resolution of point mutations that cause phenovariance in mice.
Wang T, Zhan X, Bu CH, Lyon S, Pratt D, Hildebrand S, Choi JH, Zhang Z, Zeng M, Wang KW, Turer E, Chen Z, Zhang D, Yue T, Wang Y, Shi H, Wang J, Sun L, SoRelle J, McAlpine W, Hutchins N, Zhan X, Fina M, Gobert R, Quan J, Kreutzer M, Arnett S, Hawkins K, Leach A, Tate C, Daniel C, Reyna C, Prince L, Davis S, Purrington J, Bearden R, Weatherly J, White D, Russell J, Sun Q, Tang M, Li X, Scott L, Moresco EM, McInerney GM, Karlsson Hedestam GB, Xie Y, Beutler B. Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):E440-9. doi: 10.1073/pnas.1423216112. Epub 2015 Jan 20. PMID:25605905
- Design and bioinformatics analysis of genome-wide CLIP experiments.
Wang T, Xiao G, Chu Y, Zhang MQ, Corey DR, Xie Y. Nucleic Acids Res. 2015 Jun 23;43(11):5263-74. doi: 10.1093/nar/gkv439. Epub 2015 May 9. Review. PMID:25958398
Full publication list
Available through Google Scholar.