| Generative models for protein sequence modeling: recent advances and future directions M Mardikoraem, Z Wang, N Pascual, D Woldring Briefings in Bioinformatics 24 (6), bbad358, 2023 | 24 | 2023 |
| Protein fitness prediction is impacted by the interplay of language models, ensemble learning, and sampling methods M Mardikoraem, D Woldring Pharmaceutics 15 (5), 1337, 2023 | 17 | 2023 |
| Machine learning-driven protein library design: A path toward smarter libraries M Mardikoraem, D Woldring Yeast Surface Display, 87-104, 2022 | 4 | 2022 |
| AP-LASR: Automated Protein Libraries from Ancestral Sequence Reconstruction J VanAntwerp, M Mardikoraem, N Pascual, D Woldring bioRxiv, 2023.10. 09.561537, 2023 | 2 | 2023 |
| RecombiCraft library construction: A novel method for DNA library cloning and expansion using non-enzymatic single-step DNA recombination and liquid culture Y Kawai-Harada, M Mardikoraem, K Lauro, V Nimmagadda, Q Tong, ... PloS one 19 (12), e0312188, 2024 | | 2024 |
| Predicting Inhibitors of OATP1B1 via Heterogeneous OATP-Ligand Interaction Graph Neural Network (HOLI-GNN) M Mardikoraem, JN Eaves, T Belecciu, N Pascual, A Aljets, BJ Orlando, ... bioRxiv, 2024.10. 01.615464, 2024 | | 2024 |
| Navigating Protein Fitness Landscapes With Machine Learning and Biological Insights M Mardikoraem Michigan State University, 2024 | | 2024 |
| EvoSeq-ML: Advancing Data-Centric Machine Learning with Evolutionary-Informed Protein Sequence Representation and Generation M Mardikoraem, DR Woldring ICLR 2024 Workshop on Generative and Experimental Perspectives for …, 2024 | | 2024 |
| Affibody Sequence Design Using Deep Learning Generative Models Z Wang, M Mardikoraem, D Woldring PROTEIN SCIENCE 32, 2023 | | 2023 |
| Integration of protein engineering with machine learning to increase the efficiency of drug discovery J Eaves, M Mardikoraem, DR Woldring Biophysical Journal 121 (3), 46a, 2022 | | 2022 |
| Transfer Learning as a Superior Platform in Binding Affinity Prediction for Non-Immunoglobulin Scaffolds M Mardikoraem, D Woldring PROTEIN SCIENCE 30, 180-181, 2021 | | 2021 |
| Machine Learning Guides Combinatorial Protein Library Design M Mardikoraem, D Woldring 2020 Virtual AIChE Annual Meeting, 2020 | | 2020 |