Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites. - Timothy E. Reddy; Charles DeLisi; Boris E. Shakhnovich (PLoS Comput. Biol., 2007)

High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. - William H. Majoros; Michael Campbell; Carson Holt; Erin K. DeNardo; Doreen Ware; Andrew S. Allen; Mark Yandell; Timothy E. Reddy (Bioinform., 2017)

Predicting gene structure changes resulting from genetic variants via exon definition features. - William H. Majoros; Carson Holt; Michael Campbell; Doreen Ware; Mark Yandell; Timothy E. Reddy (Bioinform., 2018)

Clustering gene expression time series data using an infinite Gaussian process mixture model. - Ian C. McDowell; Dinesh Manandhar; Christopher M. Vockley; Amy K. Schmid; Timothy E. Reddy; Barbara E. Engelhardt (PLoS Comput. Biol., 2018)

Bayesian estimation of genetic regulatory effects in high-throughput reporter assays. - William H. Majoros; Young-Sook Kim; Alejandro Barrera; Fan Li; Xingyan Wang; Sarah J. Cunningham; Graham D. Johnson; Cong Guo; William L. Lowe; Denise M. Scholtens; M. Geoffrey Hayes; Timothy E. Reddy; et al. (Bioinform., 2020)

Causal network inference from gene transcriptional time-series response to glucocorticoids. - Jonathan Lu; Bianca Dumitrascu; Ian C. McDowell; Brian Jo; Alejandro Barrera; Linda K. Hong; Sarah M. Leichter; Timothy E. Reddy; Barbara E. Engelhardt (PLoS Comput. Biol., 2021)