Determining context-defining windows: Pitch spelling using the spiral array. - Elaine Chew; Yun-Ching Chen (ISMIR, 2003)

Parsimony-spaced suffix trees for DNA sequences. - Yun-Ching Chen; Suh-Yin Lee (ISMSE, 2003)

Real-Time Pitch Spelling Using the Spiral Array. - Elaine Chew; Yun-Ching Chen (Comput. Music. J., 2005)

ZooDDD: a cross-species database for digital differential display analysis. - Yun-Ching Chen; Chung-Der Hsiao; Wen-Dar Lin; Chung-Ming Hu; Pung-Pung Hwang; Jan-Ming Ho (Bioinform., 2006)

GOBU: Toward an Integration Interface for Biological Objects. - Wen-Dar Lin; Yun-Ching Chen; Jan-Ming Ho; Chung-Der Hsiao (J. Inf. Sci. Eng., 2006)

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing. - Yun-Ching Chen; Christopher Douville; Cheng Wang; Noushin Niknafs; Grace H. T. Yeo; Violeta Beleva Guthrie; Hannah Carter; Peter D. Stenson; David N. Cooper; Biao Li; Sean D. Mooney; Rachel Karchin (PLoS Comput. Biol., 2014)

Significant associations between driver gene mutations and DNA methylation alterations across many cancer types. - Yun-Ching Chen; Valer Gotea; Gennady Margolin; Laura Elnitski (PLoS Comput. Biol., 2017)

Aberrant DNA methylation defines isoform usage in cancer, with functional implications. - Yun-Ching Chen; Laura Elnitski (PLoS Comput. Biol., 2019)