Gene regulatory networks in lactation: identification of global principles using bioinformatics. - Danielle G. Lemay; Margaret C. Neville; Michael Rudolph 004; Katherine S. Pollard; J. Bruce German (BMC Syst. Biol., 2007)

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. - Danielle G. Lemay; William F. Martin; Angie S. Hinrichs; Monique Rijnkels; J. Bruce German; Ian Korf; Katherine S. Pollard (BMC Bioinform., 2012)

SAMSA: a comprehensive metatranscriptome analysis pipeline. - Samuel T. Westreich; Ian Korf; David A. Mills; Danielle G. Lemay (BMC Bioinform., 2016)

SAMSA2: a standalone metatranscriptome analysis pipeline. - Samuel T. Westreich; Michelle L. Treiber; David A. Mills; Ian Korf; Danielle G. Lemay (BMC Bioinform., 2018)

Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. - Michelle L. Treiber; Diana H. Taft; Ian Korf; David A. Mills; Danielle G. Lemay (BMC Bioinform., 2020)

Harnessing AI to Transform Agriculture and Inform Agricultural Research. - Debra P. C. Peters; Adam R. Rivers; Jerry L. Hatfield; Danielle G. Lemay; Simon Liu; Bruno Basso (IT Prof., 2020)

Multimodal AI to Improve Agriculture. - Cynthia Sims Parr; Danielle G. Lemay; Christopher L. Owen; M. Jennifer Woodward-Greene; Jiayang Sun (IT Prof., 2021)

Special report: AI Institute for next generation food systems (AIFS). - Ilias Tagkopoulos; Stephen F. Brown; Xin Liu 002; Qing Zhao; Tarek I. Zohdi; J. Mason Earles; Nitin Nitin; Daniel E. Runcie; Danielle G. Lemay; Aaron D. Smith; Pamela C. Ronald; Hao Feng; et al. (Comput. Electron. Agric., 2022)

The AIFS Institute: Building a better food system through AI. - Ilias Tagkopoulos; J. Mason Earles; Danielle G. Lemay; Xin Liu 002; Nitin Nitin; Aaron D. Smith; Tarek I. Zohdi; Stephen F. Brown (AI Mag., 2024)

Interpreting Inflammation Prediction Model via Tag-based Cohort Explanation. - Fanyu Meng; Jules Larke; Xin Liu 002; Zhaodan Kong; Xin Chen; Danielle G. Lemay; Ilias Tagkopoulos (CoRR, 2024)