publications

2025

  1. bioRxiv
    DANGO: Predicting Higher-Order Genetic Interactions
    Ruochi ZhangMihir Bafna, Jianzhu Ma, and Jian Ma
    bioRxiv Jan 2025

2023

  1. MLSB
    DiffRNAFold: Generating RNA Tertiary Structures with Latent Space Diffusion
    Mihir Bafna, Vikranth Keerthipati, Subhash Kanaparthi, and Ruochi Zhang
    NeurIPS MLSB Dec 2023
  2. ISMB
    CLARIFY: Cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics
    Mihir BafnaHechen Li, and Xiuwei Zhang
    ISMB and Bioinformatics Jun 2023

2022

  1. NSUR
    Benchmarking and Refining Cell-Cell Interactions with Spatial Transcriptomics and Deep Learning
    Mihir Bafna, and Xiuwei Zhang
    NSUR Oct 2022
  2. ACM-BCB
    DeepViFi: Detecting Oncoviral Infections in Cancer Genomes Using Transformers
    Utkrisht Rajkumar, Sara Javadzadeh,  Mihir Bafna, Dongxia Wu, Rose Yu, Jingbo Shang, and Vineet Bafna
    ACM-BCB Oct 2022

2021

  1. Patent
    Computer-implemented methods for quantitation of features of interest in whole slide imaging
    Nam Nguyen, Lorena Mora-Blanco, Kristen Turner, Julie Weise, Jason Christiansen, and Mihir Bafna
    Provisional patent. PCT/US2021/022308 Mar 2021