publications

2026

  1. evo2.png
    Genome Modelling and Design across All Domains of Life with Evo 2
    Garyk Brixi, Matthew G Durrant, Jerome Ku, and 59 more authors
    Nature, Mar 2026

2025

  1. interplm.png
    InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders
    Elana Simon, and James Zou
    Nature Methods, Oct 2025
  2. towards_annotation.jpg
    Towards functional annotation with latent protein language model features
    *Jacob Silberg, *Elana Simon, and James Zou
    In Proceedings of the 20th Machine Learning in Computational Biology Meeting (MLCB) , Oct 2025
  3. circuit_tracing.png
    Replicating Circuit Tracing for a Simple Known Mechanism
    *Jack Merullo, *Connor Watts, Max Loeffler, and 4 more authors
    Goodfire Research Blog, Jun 2025
  4. phylogeny_manifold.png
    Finding the Tree of Life in Evo 2
    Michael Pearce, Elana Simon, Michael Byun, and 1 more author
    Goodfire Research Blog, Aug 2025
  5. Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop
    Elizabeth Fahsbender, Alma Andersson, Jeremy Ash, and 32 more authors
    arXiv, Jul 2025
  6. 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, Jul 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

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