Modeling competing endogenous RNA regulatory networks in glioblastoma multiforme. - Yu-Chiao Chiu; Eric Y. Chuang; Tzu-Hung Hsiao; Yidong Chen 002 (BIBM, 2013)

Characterization of conditions for competing endogenous RNA regulation in GBM. - Yu-Chiao Chiu; Eric Y. Chuang; Tzu-Hung Hsiao; Yidong Chen 002 (GENSiPS, 2013)

Gene Regulation, Modulation, and Their Applications in Gene Expression Data Analysis. - Mario Flores; Tzu-Hung Hsiao; Yu-Chiao Chiu; Eric Y. Chuang; Yufei Huang 001; Yidong Chen 002 (Adv. Bioinformatics, 2013)

Note-Taking for 3D Curricular Contents using Markerless Augmented Reality. - Mau-Tsuen Yang; Yu-Chiao Chiu (Interact. Comput., 2014)

Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme. - Yu-Chiao Chiu; Kai-Wen Liang; Tzu-Hung Hsiao; Yidong Chen 002; Eric Y. Chuang (BIBM, 2015)

Patho-finder - A fast and accurate program for pathogen identification through RNA-seq. - Chin-Ting Wu; Tzu-Hung Hsiao; Yu-Chiao Chiu; Yu-Ching Hsu; Eric Y. Chuang; Yidong Chen 002 (BIBM, 2015)

A simple gene set-based method accurately predicts the synergy of drug pairs. - Yu-Ching Hsu; Yu-Chiao Chiu; Yidong Chen 002; Tzu-Hung Hsiao; Eric Y. Chuang (BMC Syst. Biol., 2016)

Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival. - Yu-Chiao Chiu; Li-Ju Wang; Tzu-Pin Lu; Tzu-Hung Hsiao; Eric Y. Chuang; Yidong Chen 002 (BMC Bioinform., 2017)

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)

Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme. - Yu-Chiao Chiu; Tzu-Hung Hsiao; Li-Ju Wang; Yidong Chen 002; Eric Y. Chuang (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Convolutional neural network models for cancer type prediction based on gene expression. - Milad Mostavi; Yu-Chiao Chiu; Yufei Huang 001; Yidong Chen 002 (CoRR, 2019)

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)

CancerSiamese: one-shot learning for predicting primary and metastatic tumor types unseen during model training. - Milad Mostavi; Yu-Chiao Chiu; Yidong Chen 002; Yufei Huang 001 (BMC Bioinform., 2021)

Deep learning tackles single-cell analysis - a survey of deep learning for scRNA-seq analysis. - Mario Flores; Zhentao Liu; Tinghe Zhang; Md Musaddaqui Hasib; Yu-Chiao Chiu; Zhenqing Ye; Karla Paniagua; Sumin Jo; Jianqiu Zhang 002; Shou-Jiang Gao; Yu-Fang Jin; Yidong Chen 002; et al. (Briefings Bioinform., 2022)

MetaphorPrompt - An Analogical Reasoning Approach for Extracting Causal Links from Biological Text. - Parth Patel; Yu-Chiao Chiu; Yufei Huang 001; Jianqiu Zhang 002 (BCB, 2024)

ReguloGPT: Harnessing GPT for End-to-End Knowledge Graph Construction of Molecular Regulatory Pathways. - Xidong Wu; Sumin Jo; Yiming Zeng 014; Arun Das 001; Tinghe Zhang; Parth Patel; Yuanjing Wei; Lei Li; Shou-Jiang Gao; Jianqiu Zhang 002; Dexter Pratt; Yu-Chiao Chiu; et al. (BHI, 2024)

Predicting drug response through tumor deconvolution by cancer cell lines. - Yu-Ching Hsu; Yu-Chiao Chiu; Tzu-Pin Lu; Tzu-Hung Hsiao; Yidong Chen 002 (Patterns, 2024)

shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning. - Li-Ju Wang; Michael Ning; Tapsya Nayak; Michael J. Kasper; Satdarshan P. Monga; Yufei Huang 001; Yidong Chen 002; Yu-Chiao Chiu (Patterns, 2024)

Systems approach for congruence and selection of cancer models towards precision medicine. - Jian Zou; Osama Shah; Yu-Chiao Chiu; Tianzhou Ma; Jennifer M. Atkinson; Steffi Oesterreich; Adrian V. Lee; George C. Tseng (PLoS Comput. Biol., 2024)