FIRE: functional inference of genetic variants that regulate gene expression. - Nilah M. Ioannidis; Joe R. Davis; Marianne K. DeGorter; Nicholas B. Larson; Shannon K. McDonnell; Amy J. French; Alexis J. Battle; Trevor J. Hastie; Stephen N. Thibodeau; Stephen B. Montgomery; Carlos D. Bustamante; Weiva Sieh; et al. (Bioinform., 2017)

Predicting target genes of non-coding regulatory variants with IRT. - Zhenqin Wu; Nilah M. Ioannidis; James Zou 001; Russell Schwartz (Bioinform., 2020)

Generation of structure-guided pMHC-I libraries using Diffusion Models. - Sergio Mares; Ariel Espinoza Weinberger; Nilah M. Ioannidis (CoRR, 2025)