Robust Identification of Large Genetic Networks. - Diego di Bernardo; Timothy S. Gardner; James J. Collins (Pacific Symposium on Biocomputing, 2004)

Inferring Regulatory Interactions between Transcriptional Factors and Genes by Propagating Known Regulatory Links. - Qian Zhong; Riccardo Boscolo; Timothy S. Gardner; Vwani P. Roychowdhury (CIBCB, 2007)

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context. - Jeremiah J. Faith; Andrew J. Olson; Timothy S. Gardner; Ravi Sachidanandam (BMC Bioinform., 2007)

Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia. - Elissa J. Cosgrove; Yingchun Zhou; Timothy S. Gardner; Eric D. Kolaczyk (Bioinform., 2008)

Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. - Jeremiah J. Faith; Michael E. Driscoll; Vincent A. Fusaro; Elissa J. Cosgrove; Boris Hayete; Frank S. Juhn; Stephen J. Schneider; Timothy S. Gardner (Nucleic Acids Res., 2008)

On the Choice and Number of Microarrays for Transcriptional Regulatory Network Inference. - Elissa J. Cosgrove; Timothy S. Gardner; Eric D. Kolaczyk (BMC Bioinform., 2010)

Rewriting yeast central carbon metabolism for industrial isoprenoid production. - Adam L. Meadows; Kristy M. Hawkins; Yoseph Tsegaye; Eugene Antipov; Youngnyun Kim; Lauren Raetz; Robert H. Dahl; Anna Tai; Tina Mahatdejkul-Meadows; Lan Xu; Lishan Zhao; Madhukar S. Dasika; et al. (Nat., 2016)