Unified rational protein engineering with sequence-based deep representation learning

• “EXPERT” A Practical and Forward-Looking Guide to Capturing Protein Expression and Purification Metadata to develop Machine Learning Models

  2026 Journal of Biological Chemistry article Decision Sciences Scientific Computing and Data Management Open access

  0

  citations
• AdventML: Advanced Enzyme Temperature Prediction with Transformer-Based Embeddings and Resampling Strategies

  2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access

  0

  citations
• Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort

  2024 Journal of Chemical Information and Modeling article Biochemistry, Genetics and Molecular Biology Protein Structure and Dynamics

  3

  citations
• 3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors

  2023 Journal of Cheminformatics article Computer Science Computational Drug Discovery Methods Open access

  6

  citations
• 3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors

  2023 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

  1

  citations
• Papyrus: a large-scale curated dataset aimed at bioactivity predictions

  2023 Journal of Cheminformatics article Computer Science Computational Drug Discovery Methods Open access

  84

  citations
• A hybrid model combining evolutionary probability and machine learning leverages data-driven protein engineering

  2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Protein Structure and Dynamics Open access

  11

  citations
• Rational evolution of a recombinant DNA polymerase for efficient incorporation of unnatural nucleotides by dual-site boosting

  2022 Research Square preprint Biochemistry, Genetics and Molecular Biology Enzyme Catalysis and Immobilization Open access

  0

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• Rational evolution of a recombinant DNA polymerase for efficient incorporation of unnatural nucleotides by dual-site boosting

  2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Enzyme Catalysis and Immobilization Open access

  0

  citations
• PyPEF—An Integrated Framework for Data-Driven Protein Engineering

  2021 Journal of Chemical Information and Modeling article Biochemistry, Genetics and Molecular Biology Enzyme Catalysis and Immobilization

  39

  citations
• Automatic Gene Function Prediction in the 2020’s

  2020 Genes article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  38

  citations
• Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function

  2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access cited by 2 patents

  137

  citations

12 results