Zachary Flamholz

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

Maxim V. Kuleshov, Jennifer E. L. Diaz, Zachary Flamholz et al. · Nucleic Acids Research · 2019 · 107 citations · Full text

Large language models improve annotation of prokaryotic viral proteins

Zachary Flamholz, Steven J. Biller, Libusha Kelly · Nature Microbiology · 2024 · 73 citations · Full text

Natural Language Processing, Large Language Models, Engineering +7

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources

Daniel Clarke, Lily Wang, Alex L. Jones et al. · Cell Systems · 2019 · 62 citations · Full text

Algorithmic Fairness, Research Digital Resources, Research Ethics +4

Word embeddings trained on published case reports are lightweight, effective for clinical tasks, and free of protected health information

Zachary Flamholz, Andrew Crane‐Droesch, Lyle Ungar et al. · Journal of Biomedical Informatics · 2021 · 15 citations · Full text

Natural Language Processing, Engineering, Clinical Data +11

H/ACA snRNP–dependent ribosome biogenesis regulates translation of polyglutamine proteins

Shane Breznak, Yingshi Peng, Limin Deng et al. · Science Advances · 2023 · 12 citations · Full text