Construction of a reference gene association network from multiple profiling data: application to data analysis. - Duygu Ucar; Isaac Neuhaus; Petra Ross-MacDonald; Charles Tilford; Srinivasan Parthasarathy 001; Nathan O. Siemers; Rui-Ru Ji (Bioinform., 2007)

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. - Curtis Huttenhower; Avi I. Flamholz; Jessica N. Landis; Sauhard Sahi; Chad L. Myers; Kellen L. Olszewski; Matthew A. Hibbs; Nathan O. Siemers; Olga G. Troyanskaya; Hilary A. Coller (BMC Bioinform., 2007)

Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities. - Rui-Ru Ji; Heshani de Silva; Yisheng Jin; Robert E. Bruccoleri; Jian Cao; Aiqing He; Wenjun Huang; Paul S. Kayne; Isaac Neuhaus; Karl-Heinz Ott; Becky Penhallow; Mark I. Cockett; et al. (PLoS Comput. Biol., 2009)

SDRS - an algorithm for analyzing large-scale dose-response data. - Rui-Ru Ji; Nathan O. Siemers; Ming Lei; Liang Schweizer; Robert E. Bruccoleri (Bioinform., 2011)