QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. - Asa Thibodeau; Eladio J. Márquez; Oscar Luo; Yijun Ruan; Francesca Menghi; Dong-Guk Shin; Michael L. Stitzel; Paola Vera-Licona; Duygu Ucar (PLoS Comput. Biol., 2016)

TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators. - Asa Thibodeau; Dong-Guk Shin (Bioinform., 2019)

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data. - Asa Thibodeau; Shubham Khetan; Alper Eroglu; Ryan Tewhey; Michael L. Stitzel; Duygu Ucar (PLoS Comput. Biol., 2021)