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
1552 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
210 * 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
36 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
32 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 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 