Model-based method for transcription factor target identification with limited data. - Antti Honkela; Charles Girardot; Eleanor Hilary Gustafson; Ya-Hsin Liu; Eileen E. M. Furlong; Neil D. Lawrence; Magnus Rattray (Proc. Natl. Acad. Sci. USA, 2010)

Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State. - Bartek Wilczynski; Ya-Hsin Liu; Zhen Xuan Yeo; Eileen E. M. Furlong (PLoS Comput. Biol., 2012)

PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. - Chi-Nga Chow; Tzong-Yi Lee; Yu-Cheng Hung; Guan-Zhen Li; Kuan-Chieh Tseng; Ya-Hsin Liu; Po-Li Kuo; Han-Qin Zheng; Wen-Chi Chang (Nucleic Acids Res., 2019)