A probe-density-based analysis method for array CGH data: simulation, normalization and centralization. - Hung-I Harry Chen; Fang-Han Hsu; Yuan Jiang; Mong-Hsun Tsai; Pan-Chyr Yang; Paul S. Meltzer; Eric Y. Chuang; Yidong Chen 002 (Bioinform., 2008)

Mapping miRNA Regulation to Functional Gene Sets. - Yidong Chen 002; Hung-I Harry Chen; Yufei Huang 001 (IJCBS, 2009)

Constructing a compound mode-of-action network for personalized drug effectiveness prediction. - Chifeng Ma; Hung-I Harry Chen; Yufei Huang 001; Yidong Chen 002 (BCB, 2010)

A computational framework for predicting drug Mode-of-Action. - Chifeng Ma; Hung-I Harry Chen; Yufei Huang 001; Yidong Chen 002 (BIBM Workshops, 2010)

Gene sets enrichment analysis of miRNA expression profile. - Tzu-Hung Hsiao; Hung-I Harry Chen; Patricia C. Sanchez-Diaz; Jaclyn Y. Hung; Yidong Chen 002; Yufei Huang 001 (BIBM Workshops, 2011)

S-score: A novel scoring method of gene signatures for molecular classification. - Hung-I Harry Chen; Tzu-Hung Hsiao; Yidong Chen 002; Charles Keller (GENSiPS, 2011)

Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model. - Jia Meng 001; Hung-I Chen 001; Jianqiu Zhang 002; Yidong Chen 002; Yufei Huang 001 (ICASSP, 2011)

Using gene sets to identify putative drugs for breast cancer. - Tzu-Hung Hsiao; Hung-I Harry Chen; Yidong Chen 002; Yu-Heng Chen; Eric Y. Chuang (BIBM, 2012)

Identification of functional genomic regions with copy number alteration in liver cancer. - Tzu-Hung Hsiao; Hung-I Harry Chen; Yidong Chen 002 (GENSiPS, 2012)

BRCA-Monet: a breast cancer specific drug treatment mode-of-action network for treatment effective prediction using large scale microarray database. - Chifeng Ma; Hung-I Harry Chen; Mario Flores; Yufei Huang 001; Yidong Chen 002 (BMC Syst. Biol., 2013)

Identification of genomic functional hotspots with copy number alteration in liver cancer. - Tzu-Hung Hsiao; Hung-I Harry Chen; Stephanie Roessler; Xin Wei Wang 001; Yidong Chen 002 (EURASIP J. Bioinform. Syst. Biol., 2013)

A novel significance score for gene selection and ranking. - Yufei Xiao; Tzu-Hung Hsiao; Uthra Suresh; Hung-I Harry Chen; Xiaowu Wu; Steven E. Wolf; Yidong Chen 002 (Bioinform., 2014)

Predicting drug response of tumors from integrated genomic profiles by deep neural networks. - Yu-Chiao Chiu; Hung-I Harry Chen; Tinghe Zhang; Songyao Zhang; Aparna Gorthi; Li-Ju Wang; Yufei Huang 001; Yidong Chen 002 (CoRR, 2018)

GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization. - Hung-I Harry Chen; Yu-Chiao Chiu; Tinghe Zhang; Songyao Zhang; Yufei Huang 001; Yidong Chen 002 (CoRR, 2018)

Deep learning of pharmacogenomics resources: moving towards precision oncology. - Yu-Chiao Chiu; Hung-I Harry Chen; Aparna Gorthi; Milad Mostavi; Siyuan Zheng; Yufei Huang 001; Yidong Chen 002 (Briefings Bioinform., 2020)