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2010 – 2019
- 2016
[j14]Ibrahim Youssef
, Robert Clarke, Ie-Ming Shih, Yue Joseph Wang, Guoqiang Yu:
Biologically inspired survival analysis based on integrating gene expression as mediator with genomic variants. Comput. Biol. Medicine 77: 231-239 (2016)- 2015
- [j13]Niya Wang, Ting Gong, Robert Clarke, Lulu Chen, Ie-Ming Shih, Zhen Zhang, Douglas A. Levine, Jianhua Xuan, Yue Joseph Wang:
UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples. Bioinform. 31(1): 137-139 (2015) - [j12]Ye Tian, Bai Zhang, Eric P. Hoffman, Robert Clarke, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M. Herrington, Yue Joseph Wang:
KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring. Bioinform. 31(2): 287-289 (2015) - 2014
- [j11]Bai Zhang, Xuchu Hou, Xiguo Yuan, Ie-Ming Shih, Zhen Zhang, Robert Clarke, Roger R. Wang, Yi Fu, Subha Madhavan, Yue Joseph Wang, Guoqiang Yu:
AISAIC: a software suite for accurate identification of significant aberrations in cancers. Bioinform. 30(3): 431-433 (2014) - [j10]Ye Tian, Bai Zhang, Eric P. Hoffman, Robert Clarke, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M. Herrington, Yue Joseph Wang:
Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks. BMC Syst. Biol. 8: 87 (2014) - [j9]Ye Tian, Sean S. Wang, Zhen Zhang, Olga C. Rodriguez, Emanuel Petricoin III, Ie-Ming Shih, Daniel Chan, Maria Avantaggiati, Guoqiang Yu, Shaozhen Ye, Robert Clarke, Chao Wang, Bai Zhang, Yue Joseph Wang, Chris Albanese:
Integration of Network Biology and Imaging to Study Cancer Phenotypes and Responses. IEEE ACM Trans. Comput. Biol. Bioinform. 11(6): 1009-1019 (2014) - 2012
- [j8]Chen Wang, Jianhua Xuan, Ie-Ming Shih, Robert Clarke, Yue Joseph Wang:
Regulatory component analysis: A semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge. Signal Process. 92(8): 1902-1915 (2012) - [c8]Jinghua Gu, Jianhua Xuan, Chen Wang, Li Chen, Tian-Li Wang, Ie-Ming Shih:
Detecting aberrant signal transduction pathways from high-throughput data using GIST algorithm. CIBCB 2012: 267-274 - [c7]Xuchu Hou, Guoqiang Yu, Xiguo Yuan, Bai Zhang, Ie-Ming Shih, Zhen Zhang, Robert Clarke, Subha Madhavan:
Accurate identification of significant aberrations in contaminated cancer genome. GENSiPS 2012: 74-77 - [c6]Li Chen, Jianhua Xuan, Jinghua Gu, Yue Wang, Zhen Zhang, Tian-Li Wang, Ie-Ming Shih:
Integrative Network Analysis to Identify Aberrant Pathway Networks in Ovarian Cancer. Pacific Symposium on Biocomputing 2012: 31-42 - 2011
- [j7]Guoqiang Yu, Huai Li, Sook S. Ha, Ie-Ming Shih, Robert Clarke, Eric P. Hoffman, Subha Madhavan, Jianhua Xuan, Yue Joseph Wang:
PUGSVM: a caBIGTM analytical tool for multiclass gene selection and predictive classification. Bioinform. 27(5): 736-738 (2011) - [j6]Bai Zhang, Ye Tian, Lu Jin, Huai Li, Ie-Ming Shih, Subha Madhavan, Robert Clarke, Eric P. Hoffman, Jianhua Xuan, Leena Hilakivi-Clarke, Yue Joseph Wang:
DDN: a caBIG® analytical tool for differential network analysis. Bioinform. 27(7): 1036-1038 (2011) - [j5]Guoqiang Yu, Bai Zhang, G. Steven Bova, Jianfeng Xu, Ie-Ming Shih, Yue Joseph Wang:
BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data. Bioinform. 27(11): 1473-1480 (2011) - [c5]Ye Tian, Bai Zhang, Ie-Ming Shih, Yue Joseph Wang:
Knowledge-guided differential dependency network learning for detecting structural changes in biological networks. BCB 2011: 254-263 - [c4]Jinghua Gu, Chen Wang, Ie-Ming Shih, Tian-Li Wang, Yue Wang, Robert Clarke, Jianhua Xuan:
GIST: A Gibbs sampler to identify intracellular signal transduction pathways. EMBC 2011: 2434-2437 - 2010
- [j4]Yuanjian Feng, Guoqiang Yu, Tian-Li Wang, Ie-Ming Shih, Yue Joseph Wang:
Analysing DNA copy number changes using Fused Margin Regression. Int. J. Funct. Informatics Pers. Medicine 3(1): 3-15 (2010) - [j3]Guoqiang Yu, Yuanjian Feng, David J. Miller, Jianhua Xuan, Eric P. Hoffman, Robert Clarke, Ben Davidson, Ie-Ming Shih, Yue Joseph Wang:
Matched Gene Selection and Committee Classifier for Molecular Classification of Heterogeneous Diseases. J. Mach. Learn. Res. 11: 2141-2167 (2010)
2000 – 2009
- 2009
- [j2]Li Chen, Jianhua Xuan, Chen Wang, Yue Joseph Wang, Ie-Ming Shih, Tian-Li Wang, Zhen Zhang, Robert Clarke, Eric P. Hoffman:
Biomarker identification by knowledge-driven multilevel ICA and motif analysis. Int. J. Data Min. Bioinform. 3(4): 365-381 (2009) - [c3]Guoqiang Yu, Bai Zhang, Jianfeng Xu, Ie-Ming Shih, Yue Joseph Wang:
Accurate Estimation of Genomic Deletions and Normal Cell Contamination by Bayesian Analysis of Mixtures. BIBM 2009: 332-337 - [c2]Yuanjian Feng, Guoqiang Yu, Tian-Li Wang, Ie-Ming Shih, Yue Joseph Wang:
Analyzing DNA Copy Number Changes Using Fused Margin Regression. BIBM 2009: 388-391 - 2008
- [j1]Li Chen, Jianhua Xuan, Chen Wang, Ie-Ming Shih, Yue Joseph Wang, Zhen Zhang, Eric P. Hoffman, Robert Clarke:
Knowledge-guided multi-scale independent component analysis for biomarker identification. BMC Bioinform. 9 (2008) - 2007
- [c1]Li Chen, Chen Wang, Ie-Ming Shih, Tian-Li Wang, Zhen Zhang, Yue Joseph Wang, Robert Clarke, Eric P. Hoffman, Jianhua Xuan:
Biomarker Identification by Knowledge-Driven Multi-Level ICA and Motif Analysis. ICMLA 2007: 560-566
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