Correcting log ratios for signal saturation in cDNA microarrays. - Lori E. Dodd; Edward L. Korn; Lisa M. McShane; G. V. R. Chandramouli; Eric Y. Chuang (Bioinform., 2004)

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)

Comparison of triple negative breast cancer between Asian and western data sets. - Lee H. Chen; Liang-Chuan Lai; Chuhsing Kate Hsiao; Pei-Chun Chen; Mong-Hsun Tsai; Wen-Hung Kuo; King-Jen Chang; Eric Y. Chuang (BIBM Workshops, 2010)

Projecting partial least square and principle component regression across microarray studies. - Chi-Cheng Huang; Heng-Hui Lien; Eric Y. Chuang; Shih-Hsin Tu; Ching-Shui Huang; Liang-Chuan Lai (BIBM Workshops, 2010)

Utilizing Cox regression model to assess the relations between predefined gene sets and the survival outcome of lung adenocarcinoma. - Jo-Yang Lu; Eric Y. Chuang; Chuhsing Kate Hsiao; Mong-Hsun Tsai; Liang-Chuan Lai; Pei-Chun Chen (BIBM, 2010)

Concurrent analysis of copy number variations and expression profiles to identify genes associated with tumorigenesis and survival outcome in lung adenocarcinoma. - Tzu-Pin Lu; Liang-Chuan Lai; Chuhsing Kate Hsiao; Pei-Chun Chen; Mong-Hsun Tsai; Eric Y. Chuang (BIBM, 2010)

DBCAT: Database of CpG Islands and Analytical Tools for Identifying Comprehensive Methylation Profiles in Cancer Cells. - Hsien-Chi Kuo; Po-Yu Lin; Ting-Chiun Chung; Chin-Mei Chao; Liang-Chuan Lai; Mong-Hsun Tsai; Eric Y. Chuang (J. Comput. Biol., 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)

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)

Identification of reproducible gene expression signatures in lung adenocarcinoma. - Tzu-Pin Lu; Eric Y. Chuang; James J. Chen (BMC Bioinform., 2013)

Concurrent analysis of copy number variation and gene expression: application in paired non-smoking female lung cancer patients. - Pei-Chun Chen; Tzu-Pin Lu; Jung-Chih Chang; Liang-Chuan Lai; Mong-Hsun Tsai; Chuhsing Kate Hsiao; Eric Y. Chuang (Int. J. Data Min. Bioinform., 2013)

Estrogen receptor status prediction by gene component regression: a comparative study. - Chi-Cheng Huang; Shih-Hsin Tu; Heng-Hui Lien; Jaan-Yeh Jeng; Jung-Sen Liu; Ching-Shui Huang; Liang-Chuan Lai; Eric Y. Chuang (Int. J. Data Min. Bioinform., 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)

iGC - an integrated analysis package of gene expression and copy number alteration. - Yi-Pin Lai; Liang-Bo Wang; Wei-An Wang; Liang-Chuan Lai; Mong-Hsun Tsai; Tzu-Pin Lu; Eric Y. Chuang (BMC Bioinform., 2017)

CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system. - Yi-Fang Lee; Chien-Yueh Lee; Liang-Chuan Lai; Mong-Hsun Tsai; Tzu-Pin Lu; Eric Y. Chuang (Database J. Biol. Databases Curation, 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)

VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases. - Chien-Yueh Lee; Amrita Chattopadhyay; Li-Mei Chiang; Jyh-Ming Jimmy Juang; Liang-Chuan Lai; Mong-Hsun Tsai; Tzu-Pin Lu; Eric Y. Chuang (Database J. Biol. Databases Curation, 2019)

anamiR: integrated analysis of MicroRNA and gene expression profiling. - Ti-Tai Wang; Chien-Yueh Lee; Liang-Chuan Lai; Mong-Hsun Tsai; Tzu-Pin Lu; Eric Y. Chuang (BMC Bioinform., 2019)

ATTRACTIVE - An Auto-Updating Database for Experimental Protocols in Regenerative Medicine. - Yuan-Mao Hung; Mong-Hsun Tsai; Liang-Chuan Lai; Eric Y. Chuang (IEEE Access, 2021)

High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data. - Nam Nhut Phan; Amrita Chattopadhyay; Tsui-Ting Lee; Hsiang-I Yin; Tzu-Pin Lu; Liang-Chuan Lai; Hsiao-Lin Hwa; Mong-Hsun Tsai; Eric Y. Chuang (Briefings Bioinform., 2021)

CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer. - Amrita Chattopadhyay; Zi Han Teoh; Chi-Yun Wu; Jyh-Ming Jimmy Juang; Liang-Chuan Lai; Mong-Hsun Tsai; Chia-Hsin Wu; Tzu-Pin Lu; Eric Y. Chuang (Database J. Biol. Databases Curation, 2021)

RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow. - Kuan-Hao Chao; Yi-Wen Hsiao; Yi-Fang Lee; Chien-Yueh Lee; Liang-Chuan Lai; Mong-Hsun Tsai; Tzu-Pin Lu; Eric Y. Chuang (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Join Classifier of Type and Index Mutation on Lung Cancer DNA Using Sequential Labeling Model. - Untari Novia Wisesty; Ayu Purwarianti; Adi Pancoro; Amrita Chattopadhyay; Nam Nhut Phan; Eric Y. Chuang; Tati Rajab Mengko (IEEE Access, 2022)

CLIN_SKAT: an R package to conduct association analysis using functionally relevant variants. - Amrita Chattopadhyay; Ching-Yu Shih; Yu-Chen Hsu; Jyh-Ming Jimmy Juang; Eric Y. Chuang; Tzu-Pin Lu (BMC Bioinform., 2022)

To compare the performance of prokaryotic taxonomy classifiers using curated 16S full-length rRNA sequences. - Yuan-Mao Hung; Wei-Ni Lyu; Ming-Lin Tsai; Chiang-Lin Liu; Liang-Chuan Lai; Mong-Hsun Tsai; Eric Y. Chuang (Comput. Biol. Medicine, 2022)

16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences. - Yu-Peng Hsieh; Yuan-Mao Hung; Mong-Hsun Tsai; Liang-Chuan Lai; Eric Y. Chuang (Frontiers Bioinform., 2022)

Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data. - Amrita Chattopadhyay; Chien-Yueh Lee; Ying-Cheng Shen; Kuan-Chen Lu; Tzu-Hung Hsiao; Ching-Heng Lin; Liang-Chuan Lai; Mong-Hsun Tsai; Tzu-Pin Lu; Eric Y. Chuang (J. Biomed. Informatics, 2023)

NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition. - Zhao-Qi Hu; Yuan-Mao Hung; Li-Han Chen; Liang-Chuan Lai; Min-Hsiung Pan; Eric Y. Chuang; Mong-Hsun Tsai (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)