A programmable VLSI architecture for 2-D discrete wavelet transform. - Chien-Yu Chen 001; Zhong-Lan Yang; Tu-Chih Wang; Liang-Gee Chen (ISCAS, 2000)

A Study on the Hierarchical Data Clustering Algorithm Based on Gravity Theory. - Yen-Jen Oyang; Chien-Yu Chen 001; Tsui-Wei Yang (PKDD, 2001)

Quantity and Due Date Quoting Available to Promise. - Chien-Yu Chen 001; Zhen-Ying Zhao; Michael O. Ball (Inf. Syst. Frontiers, 2001)

A Programmable Parallel VLSI Architecture for 2-D Discrete Wavelet Transform. - Chien-Yu Chen 001; Zhong-Lan Yang; Tu-Chih Wang; Liang-Gee Chen (J. VLSI Signal Process., 2001)

Analysis and summarization of correlations in data cubes. - Chien-Yu Chen 001; Shien-Ching Hwang; Yen-Jen Oyang (Data Mining and Knowledge Discovery: Theory, Tools, and Technology, 2002)

An Incremental Hierarchical Data Clustering Algorithm Based on Gravity Theory. - Chien-Yu Chen 001; Shien-Ching Hwang; Yen-Jen Oyang (PAKDD, 2002)

Design of an incremental clustering package for protein function and family analysis. - Chien-Yu Chen 001; Hsueh-Fen Juan; Po-Jen Hsiao; Shui-Tein Chen; Hsiang-Wen Tseng; Yen-Jen Oyang (ISMSE, 2003)

Expediting protein structural analysis with an efficient kernel density estimation algorithm. - Yen-Jen Oyang; Darby Tien-Hao Chang; Chien-Yu Chen 001; Shien-Ching Hwang (ISMSE, 2003)

Expediting model selection for Support Vector Machines based on data reduction. - Yu-Yen Ou; Chien-Yu Chen 001; Shien-Ching Hwang; Yen-Jen Oyang (SMC, 2003)

Material compatibility constraints for make-to-order production planning. - Michael O. Ball; Chien-Yu Chen 001; Zhen-Ying Zhao (Oper. Res. Lett., 2003)

Geometric Reed-Solomon codes of length 64 and 65 over F8. - Chien-Yu Chen 001; Iwan M. Duursma (IEEE Trans. Inf. Theory, 2003)

An Efficient Mechanism for Prediction of Protein-Ligand Interactions Based on Analysis of Protein Tertiary Substructures. - Darby Tien-Hao Chang; Chien-Yu Chen 001; Yen-Jen Oyang; Hsueh-Fen Juan; Hsuan-Cheng Huang (BIBE, 2004)

The Combination of Kaiser Window and Moving Average for the Low-Pass Filtering of the Remote ECG Signals. - Ying-Wen Bai; Wen-Yang Chu; Chien-Yu Chen 001; Yi-Ting Lee; Yi-Ching Tsai; Cheng-Hung Tsai (CBMS, 2004)

Incremental generation of summarized clustering hierarchy for protein family analysis. - Chien-Yu Chen 001; Yen-Jen Oyang; Hsueh-Fen Juan (Bioinform., 2004)

Image Reconstruction With Improved Super-Resolution Algorithm. - Chien-Yu Chen 001; Yu-Chuan Kuo; Chiou-Shann Fuh (Int. J. Pattern Recognit. Artif. Intell., 2004)

ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures. - Darby Tien-Hao Chang; Chien-Yu Chen 001; Wen-Chin Chung; Yen-Jen Oyang; Hsueh-Fen Juan; Hsuan-Cheng Huang (Nucleic Acids Res., 2004)

Genetic algorithms and silhouette measures applied to microarray data classification. - Tsun-Chen Lin; Ru-Sheng Liu; Shu-Yuan Chen; Chen-Chung Liu; Chien-Yu Chen 001 (APBC, 2005)

Prediction of Outer Membrane Proteins by Support Vector Machines Using Combinations of Gapped Amino Acid Pair Compositions. - Ssu-Hua Huang; Ru-Sheng Liu; Chien-Yu Chen 001; Ya-Ting Chao; Shu-Yuan Chen (BIBE, 2005)

A novel radial basis function network classifier with centers set by hierarchical clustering. - Yu-Yen Ou; Yen-Jen Oyang; Chien-Yu Chen 001 (IJCNN, 2005)

Data classification with a relaxed model of variable kernel density estimation. - Yen-Jen Oyang; Yu-Yen Ou; Shien-Ching Hwang; Chien-Yu Chen 001; Darby Tien-Hao Chang (IJCNN, 2005)

Analysis and summarization of correlations in data cubes and its application in microarray data analysis. - Chien-Yu Chen 001; Shien-Ching Hwang; Yen-Jen Oyang (Intell. Data Anal., 2005)

A statistics-based approach to control the quality of subclusters in incremental gravitational clustering. - Chien-Yu Chen 001; Shien-Ching Hwang; Yen-Jen Oyang (Pattern Recognit., 2005)

Data classification with radial basis function networks based on a novel kernel density estimation algorithm. - Yen-Jen Oyang; Shien-Ching Hwang; Yu-Yen Ou; Chien-Yu Chen 001; Zhi-Wei Chen (IEEE Trans. Neural Networks, 2005)

Efficient Discovery of Structural Motifs from Protein Sequences with Combination of Flexible Intra- and Inter-block Gap Constraints. - Chen-Ming Hsu; Chien-Yu Chen 001; Ching-Chi Hsu; Baw-Jhiune Liu (PAKDD, 2006)

Protein disorder prediction by condensed PSSM considering propensity for order or disorder. - Chung-Tsai Su; Chien-Yu Chen 001; Yu-Yen Ou (BMC Bioinform., 2006)

MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences. - Chen-Ming Hsu; Chien-Yu Chen 001; Baw-Jhiune Liu (Nucleic Acids Res., 2006)

Exploiting homogeneity in protein sequence clusters for construction of protein family hierarchies. - Chien-Yu Chen 001; Wen-Chin Chung; Chung-Tsai Su (Pattern Recognit., 2006)

Pattern classification in DNA microarray data of multiple tumor types. - Tsun-Chen Lin; Ru-Sheng Liu; Chien-Yu Chen 001; Ya-Ting Chao; Shu-Yuan Chen (Pattern Recognit., 2006)

Enhancing Protein Disorder Detection by Refined Secondary Structure Prediction. - Chung-Tsai Su; Tong-Ming Hsu; Chien-Yu Chen 001; Yu-Yen Ou; Yen-Jen Oyang (BIRD, 2007)

Prediction of Protein Secondary Structures with a Novel Kernel Density Estimator. - Yen-Jen Oyang; Darby Tien-Hao Chang; Yu-Yen Ou; Hao-Geng Hung; Chien-Yu Chen 001 (MLMTA, 2007)

Identification of hot regions in protein-protein interactions by sequential pattern mining. - Chen-Ming Hsu; Chien-Yu Chen 001; Baw-Jhiune Liu; Chih-Chang Huang; Min-Hung Laio; Chien-Chieh Lin; Tzung-Lin Wu (BMC Bioinform., 2007)

iPDA: integrated protein disorder analyzer. - Chung-Tsai Su; Chien-Yu Chen 001; Chen-Ming Hsu (Nucleic Acids Res., 2007)

Cross-generation and cross-laboratory predictions of Affymetrix microarrays by rank-based methods. - Hsi-Che Liu; Chien-Yu Chen 001; Yu-Ting Liu; Cheng-Bang Chu; Der-Cherng Liang; Lee-Yung Shih; Chih-Jen Lin (J. Biomed. Informatics, 2008)

E1DS: catalytic site prediction based on 1D signatures of concurrent conservation. - Ting-Ying Chien; Darby Tien-Hao Chang; Chien-Yu Chen 001; Yi-Zhong Weng; Chen-Ming Hsu (Nucleic Acids Res., 2008)

Statistical identification of gene association by CID in application of constructing ER regulatory network. - Li-Yu Daisy Liu; Chien-Yu Chen 001; Mei-Ju May Chen; Ming-Shian Tsai; Cho-Han S. Lee; Tzu L. Phang; Li-Yun Chang; Wen-Hung Kuo; Hsiao-Lin Hwa; Huang-Chun Lien; Shih-Ming Jung; Yi-Shing Lin; et al. (BMC Bioinform., 2009)

seeMotif: exploring and visualizing sequence motifs in 3D structures. - Darby Tien-Hao Chang; Ting-Ying Chien; Chien-Yu Chen 001 (Nucleic Acids Res., 2009)

Sequence composition analysis on arsenic-binding proteins in human cells. - Yi-An Tung; Yu-Ying Chang; Rong-Nan Huang; Chien-Yu Chen 001 (BIBM Workshops, 2010)

Predicting DNA-binding locations and orientation on proteins using knowledge-based learning of geometric properties. - Chien-Chih Wang; Chien-Yu Chen 001 (BIBM, 2010)

WildSpan: mining structured motifs from protein sequences. - Chen-Ming Hsu; Chien-Yu Chen 001; Baw-Jhiune Liu (Algorithms Mol. Biol., 2011)

De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae. - Mei-Ju May Chen; Lih-Ching Chou; Tsung-Ting Hsieh; Ding-Dar Lee; Kai-Wei Liu; Chi-Yuan Yu; Yen-Jen Oyang; Huai-Kuang Tsai; Chien-Yu Chen 001 (Bioinform., 2012)

DBD2BS: connecting a DNA-binding protein with its binding sites. - Ting-Ying Chien; Chih-Kang Lin; Chih-Wei Lin; Yi-Zhong Weng; Chien-Yu Chen 001; Darby Tien-Hao Chang (Nucleic Acids Res., 2012)

PiDNA: predicting protein-DNA interactions with structural models. - Chih-Kang Lin; Chien-Yu Chen 001 (Nucleic Acids Res., 2013)

Advanced Ear Detection Algorithm Using Faster R-CNN, Refocus Filters, and the Gradient Map. - Chien-Yu Chen 001; Jian-Jiun Ding; Chen-Wei Huang (DSP, 2018)

Advanced Orientation Robust Face Detection Algorithm Using Prominent Features and Hybrid Learning Techniques. - Chien-Yu Chen 001; Jian-Jiun Ding; Hung-Wei Hsu; Yih-Cherng Lee (VCIP, 2018)

Predicting Pathogenic Non-coding Variants on Imbalanced Data Set using Cluster Ensemble Sampling. - Kai-Wen Chuang; Chien-Yu Chen 001 (BIBE, 2019)

Comprehensive Study of Keywords for Sequence-Based Automatic Annotation of Protein Functions. - Yu-Cheng Li; Mao-Jan Lin; Xiao-Xuan Huang; Chien-Yu Chen 001; Yi-Chang Lu (BIBE, 2020)

GenEpi: gene-based epistasis discovery using machine learning. - Yu-Chuan Chang; June-Tai Wu; Ming-Yi Hong 002; Yi-An Tung; Ping-Han Hsieh; Sook Wah Yee; Kathleen M. Giacomini; Yen-Jen Oyang; Chien-Yu Chen 001 (BMC Bioinform., 2020)

Evaluation of using WGS/WES to characterize ACMG actionable genes in genetic testing reports. - Wen-Tse Yang; Dong-Chi Wu; Jen-Feng Liu; Jin-Bon Hong; June-Tai Wu; Pei-Lung Chen; Chien-Yu Chen 001 (BIBM, 2021)

ezGeno: an automatic model selection package for genomic data analysis. - Jun-Liang Lin; Tsung-Ting Hsieh; Yi-An Tung; Xuan-Jun Chen; Yu-Chun Hsiao; Chia-Lin Yang; Tyng-Luh Liu; Chien-Yu Chen 001 (Bioinform., 2021)

DockCoV2: a drug database against SARS-CoV-2. - Ting-Fu Chen; Yu-Chuan Chang; Yi Hsiao; Ko-Han Lee; Yu-Chun Hsiao; Yu-Hsiang Lin; Yi-Chin Ethan Tu; Hsuan-Cheng Huang; Chien-Yu Chen 001; Hsueh-Fen Juan (Nucleic Acids Res., 2021)

pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature. - Peng-Hsuan Li; Ting-Fu Chen; Jheng-Ying Yu; Shang-Hung Shih; Chan-Hung Su; Yin-Hung Lin; Huai-Kuang Tsai; Hsueh-Fen Juan; Chien-Yu Chen 001; Jia-Hsin Huang (Nucleic Acids Res., 2022)

Evaluating the Performance of Protein Structure Prediction in Detecting Structural Changes of Pathogenic Nonsynonymous Single Nucleotide Variants. - Hong-Sheng Lai; Chien-Yu Chen 001 (BIOSTEC (1), 2024)

A large language model framework for literature-based disease-gene association prediction. - Peng-Hsuan Li; Yih-Yun Sun; Hsueh-Fen Juan; Chien-Yu Chen 001; Huai-Kuang Tsai; Jia-Hsin Huang (Briefings Bioinform., 2024)

CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data. - Ping-Han Hsieh; Ru-Xiu Hsiao; Katalin Ferenc; Anthony Mathelier; Rebekka Burkholz; Chien-Yu Chen 001; Geir Kjetil Sandve; Tatiana Belova; Marieke L. Kuijjer (CoRR, 2024)