Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. - Yixin Zhao; Noah Dukler; Gilad Barshad; Shushan Toneyan; Charles G. Danko; Adam C. Siepel (Bioinform., 2021)

Selecting deep neural networks that yield consistent attribution-based interpretations for genomics. - Antonio Majdandzic; Chandana Rajesh; Ziqi Tang; Shushan Toneyan; Ethan L. Labelson; Rohit K. Tripathy 001; Peter K. Koo (MLCB, 2022)

Evaluating deep learning for predicting epigenomic profiles. - Shushan Toneyan; Ziqi Tang; Peter K. Koo (Nat. Mac. Intell., 2022)