publications

2025

  1. Evaluation of Machine Learning-Assisted Directed Evolution Across Diverse Combinatorial Landscapes
    Francesca-Zhoufan Li, Jason Yang, Kadina E Johnston, and 3 more authors
    Cell Systems, Sep 2025
  2. Sequence-Based Generative AI-Guided Design of Versatile Tryptophan Synthases
    Theophile Lambert, Amin Tavakoli, Gautham Dharuman, and 5 more authors
    bioRxiv, Aug 2025
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    Illuminating the universe of enzyme catalysis in the era of artificial intelligence
    Jason Yang, Francesca-Zhoufan Li, Yueming Long, and 1 more author
    Cell Systems, Aug 2025
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    Steering Generative Models with Experimental Data for Protein Fitness Optimization
    Jason Yang, Wenda Chu, Daniel Khalil, and 4 more authors
    arXiv, May 2025
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    Active Learning-Assisted Directed Evolution
    Jason Yang, Ravi G Lal, James C Bowden, and 6 more authors
    Nature Communications, Jan 2025

2024

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    CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes
    Jason Yang, Ariane Mora, Shengchao Liu, and 4 more authors
    NeurIPS Datasets & Benchmarks, Dec 2024
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    Function-Guided Conditional Generation Using Protein Language Models with Adapters
    Jason Yang, Aadyot Bhatnagar, Jeffrey A. Ruffolo, and 1 more author
    MLSB Workshop, Dec 2024
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    A combinatorially complete epistatic fitness landscape in an enzyme active site
    Kadina E Johnston, Patrick J Almhjell, Ella J Watkins-Dulaney, and 4 more authors
    PNAS, Jul 2024
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    Opportunities and Challenges for Machine Learning-Assisted Enzyme Engineering
    Jason Yang, Francesca-Zhoufan Li, and Frances H. Arnold
    ACS Central Science, Feb 2024

2023

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    DeCOIL: Optimization of Degenerate Codon Libraries for Machine Learning-Assisted Protein Engineering
    Jason Yang, Julie Ducharme, Kadina E. Johnston, and 3 more authors
    ACS Synthetic Biology, Jul 2023

2022

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    Machine learning enables interpretable discovery of innovative polymers for gas separation membranes
    Jason Yang, Lei Tao, Jinlong He, and 2 more authors
    Science Advances, Jul 2022
  2. Molecular insights into the structure-property relationships of 3D printed polyamide reverse-osmosis membrane for desalination
    Jinlong He, Jason Yang, Jeffrey R. McCutcheon, and 1 more author
    Journal of Membrane Science, Sep 2022
  3. Designing polymeric membranes with coordination chemistry for high-precision ion separations
    Ryan M. DuChanois, Mohammad Heiranian, Jason Yang, and 5 more authors
    Science Advances, Mar 2022

2021

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    Efficient separation of small organic contaminants in water using functionalized nanoporous graphene membranes: Insights from molecular dynamics simulations
    Jason Yang, Zhiqiang Shen, Jinlong He, and 1 more author
    Journal of Membrane Science, Jul 2021

2019

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    Shape-Dependent Interactions of Manganese Oxide Nanomaterials with Lipid Bilayer Vesicles
    Ines Zucker, Sara M. Hashmi, Jason Yang, and 3 more authors
    Langmuir, Oct 2019