sORF finder: a program package to identify small open reading frames with high coding potential. - Kousuke Hanada; Kenji Akiyama; Tetsuya Sakurai; Tetsuro Toyoda; Kazuo Shinozaki; Shin-Han Shiu (Bioinform., 2010)

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast. - Zing Tsung-Yeh Tsai; Shin-Han Shiu; Huai-Kuang Tsai (PLoS Comput. Biol., 2015)

Utility and Limitations of Using Gene Expression Data to Identify Functional Associations. - Sahra Uygun; Cheng Peng; Melissa D. Lehti-Shiu; Robert L. Last; Shin-Han Shiu (PLoS Comput. Biol., 2016)

Editorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and Genetics. - Aalt D. J. van Dijk; Shin-Han Shiu; Dick de Ridder (Frontiers Artif. Intell., 2022)