hp-DPI: Helicobacter pylori Database of Protein Interactomes-embracing experimental and inferred interactions. - Chung-Yen Lin; Chia-Ling Chen; Chi-Shiang Cho; Li-Ming Wang; Chia-Ming Chang; Pao-Yang Chen; Chen-Zen Lo; Chao A. Hsiung (Bioinform., 2005)

Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology. - Chung-Yen Lin; Shu-Hwa Chen; Chi-Shiang Cho; Chia-Ling Chen; Fan-Kai Lin; Chieh Hua Lin; Pao-Yang Chen; Chen-Zen Lo; Chao A. Hsiung (BMC Bioinform., 2006)

A statistical approach using network structure in the prediction of protein characteristics. - Pao-Yang Chen; Charlotte M. Deane; Gesine Reinert (Bioinform., 2007)

Predicting and Validating Protein Interactions Using Network Structure. - Pao-Yang Chen; Charlotte M. Deane; Gesine Reinert (PLoS Comput. Biol., 2008)

BS Seeker: precise mapping for bisulfite sequencing. - Pao-Yang Chen; Shawn Cokus; Matteo Pellegrini (BMC Bioinform., 2010)

Deciphering chemotaxis pathways using cross species comparisons. - Rebecca Hamer; Pao-Yang Chen; Judith P. Armitage; Gesine Reinert; Charlotte M. Deane (BMC Syst. Biol., 2010)

BS-Seeker3: ultrafast pipeline for bisulfite sequencing. - Kevin Yu Yuan Huang; Yan-Jiun Huang; Pao-Yang Chen (BMC Bioinform., 2018)

BSImp: Imputing Partially Observed Methylation Patterns for Evaluating Methylation Heterogeneity. - Ya-Ting Sabrina Chang; Ming-Ren Yen; Pao-Yang Chen (Frontiers Bioinform., 2022)