Rich probabilistic models for gene expression. - Eran Segal; Benjamin Taskar; Audrey P. Gasch; Nir Friedman; Daphne Koller (ISMB (Supplement of Bioinformatics), 2001)

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks. - Sushmita Roy; Stephen Lagree; Zhonggang Hou; James A. Thomson; Ron M. Stewart; Audrey P. Gasch (PLoS Comput. Biol., 2013)

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. - Matthew E. MacGilvray; Evgenia Shishkova; Deborah Chasman; Michael Place; Anthony Gitter; Joshua J. Coon; Audrey P. Gasch (PLoS Comput. Biol., 2018)

Context-Specific Nested Effects Models. - Yuriy Sverchkov; Yi-Hsuan Ho; Audrey P. Gasch; Mark Craven (J. Comput. Biol., 2020)