A new measure of the robustness of biochemical networks. - Bor-Sen Chen; Yu-Chao Wang; Wei-Sheng Wu; Wen-Hsiung Li (Bioinform., 2005)

Robust Filtering Circuit Design for Gene Networks under Intrinsic and Extrinsic Molecular Noises. - Bor-Sen Chen; Wei-Sheng Wu (SMC, 2006)

Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. - Wei-Sheng Wu; Wen-Hsiung Li; Bor-Sen Chen (BMC Bioinform., 2006)

Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. - Wei-Sheng Wu; Wen-Hsiung Li; Bor-Sen Chen (BMC Bioinform., 2007)

Systematic identification of yeast cell cycle transcription factors using multiple data sources. - Wei-Sheng Wu; Wen-Hsiung Li (BMC Bioinform., 2008)

YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. - Darby Tien-Hao Chang; Cheng-Yi Huang; Chi-Yeh Wu; Wei-Sheng Wu (Nucleic Acids Res., 2011)

Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. - Tzu-Hsien Yang; Wei-Sheng Wu (BMC Syst. Biol., 2012)

Fuzzy Logic Applications in Control Theory and Systems Biology. - Sendren Sheng-Dong Xu; Hao Ying 001; Pablo Carbonell; Ching-Hung Lee; Wei-Sheng Wu (Adv. Fuzzy Syst., 2013)

Missing value imputation for microarray data: a comprehensive comparison study and a web tool. - Chia-Chun Chiu; Shih-Yao Chan; Chung-Ching Wang; Wei-Sheng Wu (BMC Syst. Biol., 2013)

Shrinkage regression-based methods for microarray missing value imputation. - Hsiuying Wang; Chia-Chun Chiu; Yi-Ching Wu; Wei-Sheng Wu (BMC Syst. Biol., 2013)

Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. - Tzu-Hsien Yang; Wei-Sheng Wu (BMC Syst. Biol., 2013)

IMDE: An easy-to-use web server for missing data estimation. - Chia-Chun Chiu; Wei-Sheng Wu (ICCA, 2014)

YTRP: a repository for yeast transcriptional regulatory pathways. - Tzu-Hsien Yang; Chung-Ching Wang; Yu-Chao Wang; Wei-Sheng Wu (Database J. Biol. Databases Curation, 2014)

iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation. - Tzu-Hsien Yang; Hong-Tsun Chang; Eric S. L. Hsiao; Juo-Ling Sun; Chung-Ching Wang; Hsin-Yi Wu; Pao-Chi Liao; Wei-Sheng Wu (BMC Bioinform., 2014)

A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. - Fu-Jou Lai; Hong-Tsun Chang; Yueh-Min Huang; Wei-Sheng Wu (BMC Syst. Biol., 2014)

Identifying cooperative transcription factors in yeast using multiple data sources. - Fu-Jou Lai; Mei-Huei Jhu; Chia-Chun Chiu; Yueh-Min Huang; Wei-Sheng Wu (BMC Syst. Biol., 2014)

A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae. - Wei-Sheng Wu; Ming-Liang Wei; Chia-Ming Yeh; Darby Tien-Hao Chang (BMC Syst. Biol., 2014)

cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila. - Tzu-Hsien Yang; Chung-Ching Wang; Po-Cheng Hung; Wei-Sheng Wu (BMC Syst. Biol., 2014)

Topologically associating domains are stable units of replication-timing regulation Open. - Benjamin D. Pope; Tyrone Ryba; Vishnu Dileep; Feng Yue; Wei-Sheng Wu; Olgert Denas; Daniel L. Vera; Yanli Wang; R. Scott Hansen; Theresa K. Canfield; Robert E. Thurman; Yong Cheng; et al. (Nat., 2014)

PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast. - Fu-Jou Lai; Hong-Tsun Chang; Wei-Sheng Wu (BMC Bioinform., 2015)

CoopTFD: a repository for predicted yeast cooperative transcription factor pairs. - Wei-Sheng Wu; Fu-Jou Lai; Bor-Wen Tu; Darby Tien-Hao Chang (Database J. Biol. Databases Curation, 2016)

YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules. - Wei-Sheng Wu; Pin-Han Chen; Tsung-Te Chen; Yan Yuan Tseng (Database J. Biol. Databases Curation, 2017)

MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm. - Wei-Sheng Wu; Meng-Jhun Jhou (BMC Bioinform., 2017)

HRPDviewer: human ribosome profiling data viewer. - Wei-Sheng Wu; Yu-Xuan Jiang 001; Jer-Wei Chang; Yu-Han Chu; Yi-Hao Chiu; Yi-Hong Tsao; Torbjörn E. M. Nordling; Yan Yuan Tseng; Joseph T. Tseng (Database J. Biol. Databases Curation, 2018)

YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast. - Wei-Sheng Wu; Hao-Ping Tu; Yu-Han Chu; Torbjörn E. M. Nordling; Yan Yuan Tseng; Hung-Jiun Liaw (Database J. Biol. Databases Curation, 2018)

pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans. - Wei-Sheng Wu; Wei-Che Huang; Jordan S. Brown; Donglei Zhang; Xiaoyan Song; Hao Chen; Shikui Tu; Zhiping Weng; Heng-Chi Lee (Nucleic Acids Res., 2018)

piRTarBase: a database of piRNA targeting sites and their roles in gene regulation. - Wei-Sheng Wu; Jordan S. Brown; Tsung-Te Chen; Yu-Han Chu; Wei-Che Huang; Shikui Tu; Heng-Chi Lee (Nucleic Acids Res., 2019)

YQFC: a web tool to compare quantitative biological features between two yeast gene lists. - Wei-Sheng Wu; Lai-Ji Wang; Han-Chen Yen; Yan Yuan Tseng (Database J. Biol. Databases Curation, 2020)

A tool for analyzing and visualizing ribo-seq data at the isoform level. - Wei-Sheng Wu; Yi-Hong Tsao; Sheng-Cian Shiue; Ting-Yu Chen; Yan Yuan Tseng; Joseph T. Tseng (BMC Bioinform., 2021)

Identifying piRNA targets on mRNAs in C. elegans using a deep multi-head attention network. - Tzu-Hsien Yang; Sheng-Cian Shiue; Kuan-Yu Chen; Yan Yuan Tseng; Wei-Sheng Wu (BMC Bioinform., 2021)

YMLA: A comparative platform to carry out functional enrichment analysis for multiple gene lists in yeast. - Tzu-Hsien Yang; Chia-Wei Hsu; Yan-Xiang Wang; Chien-Hung Yu; Jagat Rathod; Yan-Yuan Tseng; Wei-Sheng Wu (Comput. Biol. Medicine, 2022)

BAPCP: A comprehensive and user-friendly web tool for identifying biomarkers from protein microarray technologies. - Tzu-Hsien Yang; Guan-Da Syu; Chien-Sheng Chen; Guan-Ru Chen; Song-En Jhong; Po-Heng Lin; Pei-Chun Lin; Yun-Cih Wang; Pramod Shah; Yan-Yuan Tseng; Wei-Sheng Wu (Comput. Methods Programs Biomed., 2024)

Identifying Human miRNA Target Sites via Learning the Interaction Patterns between miRNA and mRNA Segments. - Tzu-Hsien Yang; Jhih-Cheng Chen; Yuan-Han Lee; Shang-Yi Lu; Sheng-Hang Wu; Fang-Yuan Chang; Yan-Cheng Huang; Mei-Hsien Lee; Yan-Yuan Tseng; Wei-Sheng Wu (J. Chem. Inf. Model., 2024)

mirTarCLASH: a comprehensive miRNA target database based on chimeric read-based experiments. - Tzu-Hsien Yang; Xiang-Wei Li; Yuan-Han Lee; Shang-Yi Lu; Wei-Sheng Wu; Heng-Chi Lee (Database J. Biol. Databases Curation, 2025)