ChemBERTa-2: Towards Chemical Foundation Models. - Walid Ahmad; Elana Simon; Seyone Chithrananda; Gabriel Grand; Bharath Ramsundar (CoRR, 2022)

UniTox: Leveraging LLMs to Curate a Unified Dataset of Drug-Induced Toxicity from FDA Labels. - Jacob Silberg; Kyle Swanson; Elana Simon; Angela Zhang; Zaniar Ghazizadeh; Scott Ogden; Hisham Hamadeh; James Y. Zou (NeurIPS, 2024)

InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders. - Elana Simon; James Zou (CoRR, 2024)

Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop. - Elizabeth Fahsbender; Alma Andersson; Jeremy Ash; Polina Binder; Daniel Burkhardt; Benjamin Chang; Georg K. Gerber; Anthony Gitter; Patrick Godau; Ankit Gupta; Genevieve Haliburton; Siyu He; et al. (CoRR, 2025)