Publications

Dolgikh B, Schulte S, Woldring DR. Development of Approaches and Identifying Limitations toward Functional Yeast Surface Display of FLS2. ACS Synthetic Biology. 2026;15(9):3566–3578.

Eaves J, Needs A, Woldring D. Critical Artifacts Improve Reproducibility of Protein–Ligand Binding Affinity Prediction Models on CASF-2016. Journal of Chemical Information and Modeling. 2026. Published online June 24.

Eaves J, Woldring D. Robustness of Protein-Ligand Binding Affinity Prediction Models to Docked and Predicted Structures. Journal of Chemical Information and Modeling. 2026.

Woldring D, Belecciu T, Garland L, Amalfitano A, Shapiro E. Hepatic organic anion transporting polypeptides (OATPs) as MRI reporter proteins. npj Imaging. 2026;4:3.

Dey S, Naser A, Woldring D, Hickey D. Utilizing Engineered Monobodies for the Electrochemical Quantification of Lysozyme. Analytical Chemistry. 2025;97(50):27589–27597.

Hussain E, Prokop J, Nonnemacher E, Ashrafi N, Yilmaz A, Mimi R, Khalid A, Krinickis K, Lomeikaite V, Sanfilippo L, Maxton K, Charron J, Subrahmanya C, Goodyke A, Needs A, Woldring D, Bupp C, Hartog N, Gordevicius J, Graham S, Rajasekaran S. The molecular architecture of severe pediatric traumatic brain injury: integrated omics reveal therapeutic pathways. Critical Care. 30(1):23. Published online December 9, 2025.

Kawai-Harada Y, Mardikoraem M, Makela A, Lauro K, Lam J, Contag C, Woldring D, Harada M. VesicleVoyager: In Vivo Selection of Surface Displayed Proteins That Direct Extracellular Vesicles to Tissue-Specific Targets. Journal of Extracellular Vesicles. 2025;14(11):e70184.

Chatterjee S, Rankin J, Farrugia M, Delaney B, Pascual N, VanAntwerp J, Woldring D, Hu J, Hausinger R. Ancestral Sequence Reconstruction of the Ethylene-Forming Enzyme. Biochemistry. 2025;64(15):3432–3445.

Mardikoraem M, Eaves J, Belecciu T, Pascual N, Aljets A, Hagenbuch B, Shapiro E, Orlando B, Woldring D. Predicting inhibitors of OATP1B1 via heterogeneous OATP-ligand interaction graph neural network (HOLIgraph). Journal of Cheminformatics. 2025;17:69.

Kawai-Harada Y, Mardikoraem M, Lauro K, Nimmagadda V, Tong Q, Bello K, Woldring D, Harada M. RecombiCraft library construction: A novel method for DNA library cloning and expansion using non-enzymatic single-step DNA recombination and liquid culture. PLOS ONE. 2024;19(12):e0312188.

Nakisa A, Sempere L, Chen X, Qu L, Woldring D, Crawford H, Huang X. Tumor-Associated Carbohydrate Antigen 19–9 (CA 19–9), a Promising Target for Antibody-Based Detection, Diagnosis, and Immunotherapy of Cancer. ChemMedChem. 2024;19:e202400491.

Mardikoraem M, Wang Z, Pascual N, Woldring D. Generative Models for Protein Sequence Modeling: Recent Advances and Future Directions. Briefings in Bioinformatics. 2023;24(6):bbad358.

Ricker B, Mitra S, Castellanos E, Grady C, Woldring D, Pelled G, Gilad A. Proposed three-phenylalanine motif involved in magnetoreception signalling of an Actinopterygii protein expressed in mammalian cells. Open Biology. 2023;13(11):230019.

Chen J, Woldring D, Huang F, Huang X, Wei G. Topological deep learning based deep mutational scanning. Computers in Biology and Medicine. 2023;164:107258.

Mardikoraem M, Woldring D. Protein Fitness Prediction Is Impacted by the Interplay of Language Models, Ensemble Learning, and Sampling Methods. Pharmaceutics 2023. Download PDF

Pascual N, Belecciu T, Schmidt S, Nakisa A, Huang X, Woldring DR. Single-Cell B-cell Sequencing to Generate Natively-paired scFab Yeast Surface Display Libraries. Genotype Phenotype Coupling. Methods in Molecular Biology 2023. Download PDF

Wang Z, Belecciu T, Eaves J, Reimers M, Bachmann M, Woldring DR. Phytochemical Drug Discovery for COVID-19 Using High-resolution Computational Docking and Machine Learning Assisted Binder Prediction. J Biomol Struc Dyn 2022. Download PDF

Komuro H, Aminova S, Lauro K, Woldring DR, Harada M. Design and Evaluation of Engineered Extracellular Vesicle (EV)-Based Targeting for EGFR-Overexpressing Tumor Cells Using Monobody Display. Bioengineering 2022. Download PDF

Traxlmayr MW. Yeast Surface Display. Book. Methods in Molecular Biology 2022

  • VanAntwerp J, Finneran P, Dolgikh B, Woldring DR. Ancestral Sequence Reconstruction and Alternate Amino Acid States Guide Protein Library Design for Directed Evolution Download PDF
  • Mardikoraem M, Woldring DR. Machine Learning-driven Protein Library Design: A Path Toward Smarter Libraries Download PDF
  • Dolgikh B, Woldring DR. Site-wise Diversification of Combinatorial Libraries Using Insights from Structure-guided Stability Calculations. Download PDF

Woldring DR, Holec PV, Stern LA, Du Y & Hackel BJ. A gradient of sitewise diversity promotes evolutionary fitness for binder discovery in a three-helix bundle protein scaffold. Biochemistry 2017. Download PDF

Stern LA, Csizmar CM, Woldring DR, Wagner CR, Hackel BJ. Titratable avidity reduction enhances affinity discrimination in mammalian cellular selections of yeast-displayed ligands. ACS combinatorial science 2017. Download PDF

Hackel BJ, Woldring DR, Zhou H. Compositions and methods that involve protein scaffolds that specifically bind to hepatocyte growth factor receptor. US Patent App. 16/158,957

Woldring DR, Holec PV & Hackel BJ. ScaffoldSeq: Software for Characterization of Directed Evolution Populations. Proteins: Structure, Function and Bioinformatics 2016. Download PDF

Kruziki MA, Case BA, Chan JY, Zudock EJ, Woldring DR, Yee D & Hackel BJ. 64Cu-Labeled Gp2 Domain for PET Imaging of Epidermal Growth Factor Receptor. Molecular Pharma. 2016

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Woldring DR, Holec PV, Zhou H & Hackel BJ. High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains. PLoS One 2016. Download PDF

Kruziki MA, Bhatnagar S, Woldring DR, Duong VT, Hackel BJ. A 45-amino-acid scaffold mined from the PDB for high-affinity ligand engineering. Chemistry & biology. 2015. Download PDF