publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

2026

  1. GATSBI: Improving context-aware protein embeddings through biologically motivated data splits
    Gowri Nayar and Russ B. Altman
    Bioinformatics, 2026
    ISMB 2026
  2. Interpreting protein language models for cancer discovery: High attention hotspots predict pathogenic mutation positions and novel drug binding sites
    Samuel J. Pribus, Gowri Nayar, and Russ B. Altman
    Cancer Research, 2026
    AACR Annual Meeting abstract

2025

  1. Paying attention to attention: High attention sites as indicators of protein family and function in language models
    Gowri Nayar, Alp Tartici, and Russ B. Altman
    PLOS Computational Biology, 2025
    DOI
  2. Pool PaRTI: a PageRank-based pooling method for identifying critical residues and enhancing protein sequence representations
    Alp Tartici, Gowri Nayar, and Russ B. Altman
    Bioinformatics, 2025
    DOI Code
  3. Exposing the molecular reaction blind spots of LLMs with PathwayQA
    Kristen A. Carpenter, Dylan A. Smith, Bo Xiong, and 2 more authors
    bioRxiv, 2025
    Preprint
  4. Material representation in computational systems
    Nathaniel H. Park, Gowri Nayar, Dmitry Zubarev, and 1 more author
    2025
    US Patent 12,456,542

2024

  1. Heterogeneous network approaches to protein pathway prediction
    Gowri Nayar and Russ B. Altman
    Computational and Structural Biotechnology Journal, 2024
    DOI
  2. Computational Approaches to Drug Repurposing: Methods, Challenges, and Opportunities
    Henry C. Cousins, Gowri Nayar, and Russ B. Altman
    Annual Review of Biomedical Data Science, 2024
    DOI
  3. Longitudinal modeling of multimorbidity trajectories using large language models
    Lawrence Yang, Elliot Bolton, Gowri Nayar, and 1 more author
    medRxiv, 2024
    Preprint

2022

  1. IBM Functional Genomics Platform, a cloud-based platform for studying microbial life at scale
    Edward E. Seabolt, Gowri Nayar, Harsha Krishnareddy, and 4 more authors
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022
  2. Predicting epitope candidates for SARS-CoV-2
    Akshay Agarwal, Kristen L. Beck, Sara Capponi, and 4 more authors
    Viruses, 2022
  3. ggMOB: elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus–genus mobilization networks
    Ignacio Terrizzano, Edward Seabolt, Akshay Agarwal, and 4 more authors
    Frontiers in Genetics, 2022

2021

  1. Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2
    Gowri Nayar, Edward E. Seabolt, Mark Kunitomi, and 4 more authors
    Scientific Reports, 2021
    DOI
  2. Semi-supervised pipeline for autonomous annotation of SARS-CoV-2 genomes
    Kristen L. Beck, Edward Seabolt, Akshay Agarwal, and 4 more authors
    Viruses, 2021

2020

  1. Survey of public assay data: opportunities and challenges to understanding antimicrobial resistance
    Gowri Nayar, Akshay Agarwal, and James H. Kaufman
    In Proceedings of the 35th Annual ACM Symposium on Applied Computing (SAC), 2020
  2. Integrative and conjugative elements (ICE) and associated cargo genes within and across hundreds of bacterial genera
    James H. Kaufman, Ignacio Terrizzano, Gowri Nayar, and 4 more authors
    bioRxiv, 2020
    Preprint