Biomarker Identification by Knowledge-Driven Multi-Level ICA and Motif Analysis. - Li Chen 018; Chen Wang 001; Ie-Ming Shih; Tian-Li Wang; Zhen Zhang; Yue Joseph Wang; Robert Clarke; Eric P. Hoffman; Jianhua Xuan (ICMLA, 2007)

Knowledge-guided multi-scale independent component analysis for biomarker identification. - Li Chen 018; Jianhua Xuan; Chen Wang 001; Ie-Ming Shih; Yue Joseph Wang; Zhen Zhang; Eric P. Hoffman; Robert Clarke (BMC Bioinform., 2008)

Analyzing DNA Copy Number Changes Using Fused Margin Regression. - Yuanjian Feng; Guoqiang Yu; Tian-Li Wang; Ie-Ming Shih; Yue Joseph Wang (BIBM, 2009)

Accurate Estimation of Genomic Deletions and Normal Cell Contamination by Bayesian Analysis of Mixtures. - Guoqiang Yu; Bai Zhang; Jianfeng Xu; Ie-Ming Shih; Yue Joseph Wang (BIBM, 2009)

Biomarker identification by knowledge-driven multilevel ICA and motif analysis. - Li Chen 018; Jianhua Xuan; Chen Wang 001; Yue Joseph Wang; Ie-Ming Shih; Tian-Li Wang; Zhen Zhang; Robert Clarke; Eric P. Hoffman (Int. J. Data Min. Bioinform., 2009)

Analysing DNA copy number changes using Fused Margin Regression. - Yuanjian Feng; Guoqiang Yu; Tian-Li Wang; Ie-Ming Shih; Yue Joseph Wang (Int. J. Funct. Informatics Pers. Medicine, 2010)

Matched Gene Selection and Committee Classifier for Molecular Classification of Heterogeneous Diseases. - Guoqiang Yu; Yuanjian Feng; David J. Miller 001; Jianhua Xuan; Eric P. Hoffman; Robert Clarke; Ben Davidson; Ie-Ming Shih; Yue Joseph Wang (J. Mach. Learn. Res., 2010)

Knowledge-guided differential dependency network learning for detecting structural changes in biological networks. - Ye Tian; Bai Zhang; Ie-Ming Shih; Yue Joseph Wang (BCB, 2011)

GIST: A Gibbs sampler to identify intracellular signal transduction pathways. - Jinghua Gu; Chen Wang 001; Ie-Ming Shih; Tian-Li Wang; Yue Wang 021; Robert Clarke; Jianhua Xuan (EMBC, 2011)

PUGSVM: a caBIGTM analytical tool for multiclass gene selection and predictive classification. - Guoqiang Yu; Huai Li; Sook Shin Ha; Ie-Ming Shih; Robert Clarke; Eric P. Hoffman; Subha Madhavan; Jianhua Xuan; Yue Joseph Wang (Bioinform., 2011)

BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data. - Guoqiang Yu; Bai Zhang; G. Steven Bova; Jianfeng Xu; Ie-Ming Shih; Yue Joseph Wang (Bioinform., 2011)

DDN: a caBIG® analytical tool for differential network analysis. - 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 (Bioinform., 2011)

Detecting aberrant signal transduction pathways from high-throughput data using GIST algorithm. - Jinghua Gu; Jianhua Xuan; Chen Wang 001; Li Chen 018; Tian-Li Wang; Ie-Ming Shih (CIBCB, 2012)

Accurate identification of significant aberrations in contaminated cancer genome. - Xuchu Hou; Guoqiang Yu; Xiguo Yuan; Bai Zhang; Ie-Ming Shih; Zhen Zhang; Robert Clarke; Subha Madhavan (GENSiPS, 2012)

Integrative Network Analysis to Identify Aberrant Pathway Networks in Ovarian Cancer. - Li Chen 018; Jianhua Xuan; Jinghua Gu; Yue Wang 021; Zhen Zhang; Tian-Li Wang; Ie-Ming Shih (Pacific Symposium on Biocomputing, 2012)

Regulatory component analysis: A semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge. - Chen Wang 001; Jianhua Xuan; Ie-Ming Shih; Robert Clarke; Yue Joseph Wang (Signal Process., 2012)

AISAIC: a software suite for accurate identification of significant aberrations in cancers. - 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 (Bioinform., 2014)

Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks. - Ye Tian; Bai Zhang; Eric P. Hoffman; Robert Clarke; Zhen Zhang; Ie-Ming Shih; Jianhua Xuan; David M. Herrington; Yue Joseph Wang (BMC Syst. Biol., 2014)

Integration of Network Biology and Imaging to Study Cancer Phenotypes and Responses. - 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 005; et al. (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring. - Ye Tian; Bai Zhang; Eric P. Hoffman; Robert Clarke; Zhen Zhang; Ie-Ming Shih; Jianhua Xuan; David M. Herrington; Yue Joseph Wang (Bioinform., 2015)

UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples. - Niya Wang; Ting Gong; Robert Clarke; Lulu Chen; Ie-Ming Shih; Zhen Zhang; Douglas A. Levine; Jianhua Xuan; Yue Joseph Wang (Bioinform., 2015)

Biologically inspired survival analysis based on integrating gene expression as mediator with genomic variants. - Ibrahim Youssef; Robert Clarke; Ie-Ming Shih; Yue Joseph Wang; Guoqiang Yu (Comput. Biol. Medicine, 2016)