publications

2025

  1. towards_annotation.jpg
    Towards functional annotation with latent protein language model features
    *Jake Silberg, *Elana Simon, and James Zou
    In ICML 2025 Generative AI and Biology (GenBio) Workshop , 2025
  2. escape_seq.png
    Massively parallel immunopeptidome by DNA sequencing provides insights into cancer antigen presentation
    Quanming Shi, Elana Simon, Cansu Cimen Bozkus, and 20 more authors
    Nature Genetics, 2025

2024

  1. primer.png
    Language models for biological research: a primer
    *Elana Simon, *Kyle Swanson, and James Zou
    Nature Methods, Aug 2024
  2. unitox.png
    UniTox: Leveraging LLMs to Curate a Unified Dataset of Drug-Induced Toxicity from FDA Labels
    Jake Silberg, Kyle Swanson, Elana Simon, and 5 more authors
    NeurIPS Datasets and Benchmarks, Dec 2024
  3. interplm.png
    InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders
    Elana Simon, and James Zou
    bioRxiv, Nov 2024

2022

  1. patent.png
    Compounds, compositions and methods of treating disorders
    Mark Rex Spyvee, Jonah Milton Kallenbach, Ankit Gupta, and 2 more authors
    Sep 2022
    US Patent App. 17/744,228

2021

  1. nanobody.png
    Protein design and variant prediction using autoregressive generative models
    Jung-Eun Shin, Adam J Riesselman, Aaron W Kollasch, and 6 more authors
    Nature communications, Apr 2021
  2. chemberta.png
    Chemberta-2: Towards chemical foundation models
    *Walid Ahmad, *Elana Simon, Seyone Chithrananda, and 2 more authors
    ELLIS Machine Learning for Molecule Discovery Workshop, Dec 2021

2020

  1. fibrolamellar.jpg
    The Fibrolamellar Registry: A patient-based medical registry can address medical care
    Julie Latone Newcomb, Siobhan Lett, Rachael D Migler, and 2 more authors
    Cancer Research, Dec 2020

2019

  1. autoregressive.png
    Accelerating protein design using autoregressive generative models
    Adam Riesselman, Jung-Eun Shin, Aaron Kollasch, and 6 more authors
    BioRxiv, Sep 2019
  2. fibrolamellar.jpg
    The fibrolamellar registry: A model for the study of rare diseases
    Michelle Desmond, Julie Latone, Siobhan Lett, and 3 more authors
    Cancer Research, Sep 2019

2018

  1. noncoding.png
    Non coding RNA analysis in fibrolamellar hepatocellular carcinoma
    Benjamin A Farber, Gadi Lalazar, Elana P Simon, and 5 more authors
    Oncotarget, Feb 2018

2015

  1. Molecular analysis of the pediatric cancer fibrolamellar hepatocellular carcinoma
    Elana P Simon, Joshua N Honeyman, David G Darcy, and 8 more authors
    Cancer Research, Apr 2015
  2. transcriptomic.png
    Transcriptomic characterization of fibrolamellar hepatocellular carcinoma
    Elana P Simon, Catherine A Freije, Benjamin A Farber, and 8 more authors
    Proceedings of the National Academy of Sciences, Apr 2015

2014

  1. chimera.png
    Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma
    *Joshua N Honeyman, *Elana P Simon, Nicolas Robine, and 8 more authors
    Science, Apr 2014