| Improvements to the APBS biomolecular solvation software suite E Jurrus, D Engel, K Star, K Monson, J Brandi, LE Felberg, DH Brookes, ... Protein Science 27 (1), 112-128, 2018 | 1549 | 2018 |
| Conditioning by adaptive sampling for robust design DH Brookes, H Park, J Listgarten Proceedings of the 36th International Conference on Machine Learning 97, 773-782, 2019 | 209* | 2019 |
| Finding our way in the dark proteome A Bhowmick, DH Brookes, SR Yost, HJ Dyson, JD Forman-Kay, D Gunter, ... Journal of the American Chemical Society 138 (31), 9730-9742, 2016 | 125 | 2016 |
| Experimental inferential structure determination of ensembles for intrinsically disordered proteins DH Brookes, T Head-Gordon Journal of the American Chemical Society 138 (13), 4530-4538, 2016 | 79 | 2016 |
| On the sparsity of fitness functions and implications for learning DH Brookes, A Aghazadeh, J Listgarten Proceedings of the National Academy of Sciences 119 (1), e2109649118, 2022 | 35 | 2022 |
| Family of oxygen–oxygen radial distribution functions for water DH Brookes, T Head-Gordon The Journal of Physical Chemistry Letters 6 (15), 2938-2943, 2015 | 33 | 2015 |
| Epistatic Net allows the sparse spectral regularization of deep neural networks for inferring fitness functions A Aghazadeh, H Nisonoff, O Ocal, DH Brookes, Y Huang, OO Koyluoglu, ... Nature communications 12 (1), 5225, 2021 | 31 | 2021 |
| Optimal trade-off control in machine learning–based library design, with application to adeno-associated virus (AAV) for gene therapy D Zhu, DH Brookes, A Busia, A Carneiro, C Fannjiang, G Popova, D Shin, ... Science Advances 10 (4), eadj3786, 2024 | 20* | 2024 |
| A view of estimation of distribution algorithms through the lens of expectation-maximization D Brookes, A Busia, C Fannjiang, K Murphy, J Listgarten Proceedings of the 2020 Genetic and Evolutionary Computation Conference …, 2020 | 17 | 2020 |
| PB‐AM: An open‐source, fully analytical linear Poisson‐Boltzmann solver LE Felberg, DH Brookes, EH Yap, E Jurrus, NA Baker, T Head‐Gordon Journal of computational chemistry 38 (15), 1275-1282, 2017 | 13 | 2017 |
| Role of hydrophilicity and length of diblock arms for determining star polymer physical properties LE Felberg, DH Brookes, T Head-Gordon, JE Rice, WC Swope The Journal of Physical Chemistry B 119 (3), 944-957, 2015 | 10 | 2015 |
| Sparse epistatic regularization of deep neural networks for inferring fitness functions A Aghazadeh, H Nisonoff, O Ocal, Y Huang, OO Koyluoglu, J Listgarten, ... bioRxiv, 2020.11. 24.396994, 2020 | 4 | 2020 |
| Contrastive losses as generalized models of global epistasis DH Brookes, J Otwinowski, S Sinai arXiv preprint arXiv:2305.03136, 2023 | 1 | 2023 |
| Beyond the training set: an intuitive method for detecting distribution shift in model-based optimization F Damani, DH Brookes, T Sternlieb, C Webster, S Malina, R Jajoo, K Lin, ... arXiv preprint arXiv:2311.05363, 2023 | | 2023 |
| Generative design for gene therapy: An validated method F Damani, D Brookes, J Chan, R Jajoo, A Mijalis, J Samson, F Vadan, ... NeurIPS 2023 Generative AI and Biology (GenBio) Workshop, 2023 | | 2023 |
| Forward and Inverse Problems in Machine Learning Approaches to Biological Sequence Design DH Brookes UC Berkeley, 2021 | | 2021 |
| PB-SAM, a novel solution to the Poisson-Boltzmann equation for applications ranging from protein simulations to polymer membrane design L Felberg, M Soniat, D Brookes, E Yap, T Head-Gordon ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 252, 2016 | | 2016 |
