DeepViFi: detecting oncoviral infections in cancer genomes using transformers. - Utkrisht Rajkumar; Sara Javadzadeh; Mihir Bafna; Dongxia Wu; Rose Yu; Jingbo Shang; Vineet Bafna (BCB, 2022)

CLARIFY: cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics. - Mihir Bafna; Hechen Li; Xiuwei Zhang 002 (Bioinform., 2023)