ETOPE: evolutionary test of predicted exons. - Anton Nekrutenko; Wen-Yu Chung; Wen-Hsiung Li (Nucleic Acids Res., 2003)

Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. - Hong-Chu Chen; Hsiao-Ching Lee; Tsai-Yun Lin; Wen-Hsiung Li; Bor-Sen Chen (Bioinform., 2004)

Patterns of Gene Deletion following Genome Duplication in Yeast. - Jake K. Byrnes; Wen-Hsiung Li (CSB Workshops, 2005)

Prediction of splice sites with dependency graphs and their expanded bayesian networks. - Te-Ming Chen; Chung-Chin Lu; Wen-Hsiung Li (Bioinform., 2005)

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

Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification. - Li-Hsieh Lin; Hsiao-Ching Lee; Wen-Hsiung Li; Bor-Sen Chen (BMC Bioinform., 2005)

On the Inference of Regulatory Elements, Circuits, and Modules. - Wen-Hsiung Li (APBC, 2006)

Method for identifying transcription factor binding sites in yeast. - Huai-Kuang Tsai; Grace Tzu-Wei Huang; Meng-Yuan Chou; Henry Horng-Shing Lu; Wen-Hsiung Li (Bioinform., 2006)

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

A systematic approach to detecting transcription factors in response to environmental stresses. - Li-Hsieh Lin; Hsiao-Ching Lee; Wen-Hsiung Li; Bor-Sen Chen (BMC Bioinform., 2007)

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)

MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. - Huai-Kuang Tsai; Meng-Yuan Chou; Ching Hua Shih; Grace Tzu-Wei Huang; Tien-Hsien Chang; Wen-Hsiung Li (Nucleic Acids Res., 2007)

On the Robust Circuit Design Schemes of Biochemical Networks: Steady-State Approach. - Bor-Sen Chen; Wan-Shian Wu; Yu-Chao Wang; Wen-Hsiung Li (IEEE Trans. Biomed. Circuits Syst., 2007)

Multidimensional scaling for large genomic data sets. - Jengnan Tzeng; Henry Horng-Shing Lu; Wen-Hsiung Li (BMC Bioinform., 2008)

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

SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns. - Yan Yuan Tseng; Craig Dupree; Z. Jeffrey Chen; Wen-Hsiung Li (Nucleic Acids Res., 2009)

fPOP: footprinting functional pockets of proteins by comparative spatial patterns. - Yan Yuan Tseng; Z. Jeffrey Chen; Wen-Hsiung Li (Nucleic Acids Res., 2010)

MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues. - Sung-Chou Li; Kuo-Wang Tsai; Hung-Wei Pan; Yung-Ming Jeng; Meng-Ru Ho; Wen-Hsiung Li (BMC Syst. Biol., 2012)

PSC: protein surface classification. - Yan Yuan Tseng; Wen-Hsiung Li (Nucleic Acids Res., 2012)

Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context. - Misook Ha; Soondo Hong; Wen-Hsiung Li (Bioinform., 2013)

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3, 000 Cancer Genomes across 9 Cancer Types. - Feixiong Cheng; Chuang Liu; Chen-Ching Lin; Junfei Zhao; Peilin Jia; Wen-Hsiung Li; Zhongming Zhao (PLoS Comput. Biol., 2015)