POWER: PhylOgenetic WEb Repeater - an integrated and user-optimized framework for biomolecular phylogenetic analysis. - Chung-Yen Lin; Fan-Kai Lin; Chieh Hua Lin; Li-Wei Lai; Hsiu-Jun Hsu; Shu-Hwa Chen; Chao A. Hsiung (Nucleic Acids Res., 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)

The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays. - Shu-Hwa Chen; Chen-Zen Lo; Ming-Chi Tsai; Chao A. Hsiung; Chung-Yen Lin (BMC Bioinform., 2008)

Hubba: hub objects analyzer - a framework of interactome hubs identification for network biology. - Chung-Yen Lin; Chia-Hao Chin; Hsin-Hung Wu; Shu-Hwa Chen; Chin-Wen Ho; Ming-Tat Ko (Nucleic Acids Res., 2008)

A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles. - Chia-Hao Chin; Shu-Hwa Chen; Chin-Wen Ho; Ming-Tat Ko; Chung-Yen Lin (BMC Bioinform., 2010)

cytoHubba: identifying hub objects and sub-networks from complex interactome. - Chia-Hao Chin; Shu-Hwa Chen; Hsin-Hung Wu; Chin-Wen Ho; Ming-Tat Ko; Chung-Yen Lin (BMC Syst. Biol., 2014)

A gene profiling deconvolution approach to estimating immune cell composition from complex tissues. - Shu-Hwa Chen; Wen-Yu Kuo; Sheng-Yao Su; Wei-Chun Chung; Jen-Ming Ho; Henry Horng-Shing Lu; Chung-Yen Lin (BMC Bioinform., 2018)

MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification. - Chun-Chieh Liao; Po-Ying Fu; Chih-Wei Huang; Chia-Hsien Chuang; Yun Yen; Chung-Yen Lin; Shu-Hwa Chen (Bioinform., 2022)