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
558 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
112 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
33 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
21 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
17 2021 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
15 2022 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 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
12 * 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
5 * 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 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
3 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 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
2 2024 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
1 2023 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 ( ) 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