Retrieval of 3D protein structures. - Shann-Ching Chen; Tsuhan Chen (ICIP (3), 2002)

Mining frequent patterns in protein structures: a study of protease families. - Shann-Ching Chen; Ivet Bahar (ISMB/ECCB (Supplement of Bioinformatics), 2004)

A Novel Graphical Model Approach to Segmenting Cell Images. - Shann-Ching Chen; Ting Zhao; Geoffrey J. Gordon; Robert F. Murphy (CIBCB, 2006)

A novel approximate inference approach to automated classification of protein subcellular location patterns in multi-cell images. - Shann-Ching Chen; Geoffrey J. Gordon; Robert F. Murphy (ISBI, 2006)

A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images. - Shann-Ching Chen; Robert F. Murphy (BMC Bioinform., 2006)

oGNM: online computation of structural dynamics using the Gaussian Network Model. - Lee-Wei Yang; A. J. Rader; Xiong Liu 001; Christopher Jon Jursa; Shann-Ching Chen; Hassan A. Karimi; Ivet Bahar (Nucleic Acids Res., 2006)

Automated image analysis of protein localization in budding yeast. - Shann-Ching Chen; Ting Zhao; Geoffrey J. Gordon; Robert F. Murphy (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Quantitative analysis of border cell migration. - Shann-Ching Chen; Gaudenz Danuser (ACSCC, 2008)

Graphical Models for Structured Classification, with an Application to Interpreting Images of Protein Subcellular Location Patterns. - Shann-Ching Chen; Geoffrey J. Gordon; Robert F. Murphy (J. Mach. Learn. Res., 2008)

A Practical Framework for ROI Detection in Medical Images - a case study for hip detection in anteroposterior pelvic radiographs. - Feng-Yu Liu; Chih-Chi Chen; Shann-Ching Chen; Chien-Hung Liao (CoRR, 2021)