| Machine learning-aided engineering of hydrolases for PET depolymerization H Lu, DJ Diaz, NJ Czarnecki, C Zhu, W Kim, R Shroff, DJ Acosta, ... Nature 604 (7907), 662-667, 2022 | 519 | 2022 |
| Discovery of novel gain-of-function mutations guided by structure-based deep learning R Shroff, AW Cole, DJ Diaz, BR Morrow, I Donnell, A Annapareddy, ... ACS synthetic biology 9 (11), 2927-2935, 2020 | 108* | 2020 |
| Improved Bst DNA Polymerase Variants Derived via a Machine Learning Approach I Paik, PHT Ngo, R Shroff, DJ Diaz, AC Maranhao, DJF Walker, S Bhadra, ... Biochemistry 62 (2), 410-418, 2021 | 30 | 2021 |
| Using machine learning to predict the effects and consequences of mutations in proteins DJ Diaz, AV Kulikova, AD Ellington, CO Wilke Current Opinion in Structural Biology 78, 102518, 2023 | 17 | 2023 |
| Learning the local landscape of protein structures with convolutional neural networks AV Kulikova, DJ Diaz, JM Loy, AD Ellington, CO Wilke Journal of Biological Physics 47 (4), 435-454, 2021 | 16 | 2021 |
| HotProtein: A novel framework for protein thermostability prediction and editing T Chen*, C Gong*, DJ Diaz, X Chen, JT Wells, Q Liu, Z Wang, ... International Conference of Learning Representations 2023, 2022 | 13* | 2022 |
| GroovDB: A database of ligand-inducible transcription factors S d’Oelsnitz, JD Love, DJ Diaz, AD Ellington ACS Synthetic Biology 11 (10), 3534-3537, 2022 | 12 | 2022 |
| Stability Oracle: a structure-based graph-transformer for identifying stabilizing mutations DJ Diaz, C Gong, J Ouyang-Zhang, JM Loy, J Wells, D Yang, AD Ellington, ... BioRxiv, 2023.05. 15.540857, 2023 | 11* | 2023 |
| Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme S d’Oelsnitz, DJ Diaz, W Kim, DJ Acosta, TL Dangerfield, MW Schechter, ... Nature Communications 15 (1), 2084, 2024 | 4* | 2024 |
| Two sequence-and two structure-based ML models have learned different aspects of protein biochemistry AV Kulikova, DJ Diaz, T Chen, TJ Cole, AD Ellington, CO Wilke Scientific Reports 13 (1), 13280, 2023 | 4* | 2023 |
| Pushing Differential Sensing Further: The Next Steps in Design and Analysis of Bio‐Inspired Cross‐Reactive Arrays HA Fargher, S d'Oelsnitz, DJ Diaz, EV Anslyn Analysis & Sensing 3 (2), e202200095, 2023 | 3 | 2023 |
| Predicting a Protein's Stability under a Million Mutations J Ouyang-Zhang, DJ Diaz, AR Klivans, P Krähenbühl 37th Conference on Neural Information Processing Systems, 2023 | 2 | 2023 |
| Asymmetric Synthesis of α-Chloroamides via Photoenzymatic Hydroalkylation of Olefins Y Liu, SG Bender, D Sorigue, DJ Diaz, AD Ellington, G Mann, ... Journal of the American Chemical Society 146 (11), 7191-7197, 2024 | 1 | 2024 |
| Institute for Foundations of Machine Learning (IFML): Advancing AI systems that will transform our world A Klivans, AG Dimakis, K Grauman, JI Tamir, DJ Diaz, K Davidson AI Magazine 45 (1), 35-41, 2024 | | 2024 |
| Recombinant proteins with increased solubility and stability A Ellington, P Inyup, A Maranhao, S Bhadra, D Walker, NGO Phuoc, ... US Patent App. 18/044,909, 2024 | | 2024 |
| Microenvironment Flows as Protein Engineers C Gong, L Wu, D Diaz, X Liu, J Loy, A Klivans NeurIPS 2023 Generative AI and Biology (GenBio) Workshop, 2023 | | 2023 |
| Binding Oracle: Fine-Tuning From Stability to Binding Free Energy C Gong, A Klivans, J Wells, J Loy, A Dimakis, D Diaz NeurIPS 2023 Generative AI and Biology (GenBio) Workshop, 2023 | | 2023 |
| () redicting nzym romiscuity with its Molecule Mate – an Attentive Metric Learning Solution X Chen, DJ Diaz, C Gong, A Dimakis, A Klivans, Z Wang, T Chen | | 2023 |
| The Coming Congruence of Synthetic Biology and Machine Learning for Engineering Life A Ellington, D Diaz, I Paik The Astrobiology Science Conference (AbSciCon) 2022, 144-01, 2022 | | 2022 |
| ENGINEERING PROTEINS WITH 3D CONVOLUTIONAL NEURAL NETWORKS 8 D Diaz | | 2022 |
