| Learning protein fitness models from evolutionary and assay-labeled data C Hsu, H Nisonoff, C Fannjiang, J Listgarten Nature biotechnology 40 (7), 1114-1122, 2022 | 106 | 2022 |
| XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment Y Lee, D Bogdanoff, Y Wang, GC Hartoularos, JM Woo, CT Mowery, ... Science advances 7 (17), eabg4755, 2021 | 77 | 2021 |
| Algorithms for protein design P Gainza, HM Nisonoff, BR Donald Current opinion in structural biology 39, 16-26, 2016 | 75 | 2016 |
| OSPREY 3.0: Open‐source protein redesign for you, with powerful new features MA Hallen, JW Martin, A Ojewole, JD Jou, AU Lowegard, MS Frenkel, ... Journal of computational chemistry 39 (30), 2494-2507, 2018 | 67 | 2018 |
| A deep-learning view of chemical space designed to facilitate drug discovery P Maragakis, H Nisonoff, B Cole, DE Shaw Journal of Chemical Information and Modeling 60 (10), 4487-4496, 2020 | 36 | 2020 |
| 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 |
| Combining evolutionary and assay-labelled data for protein fitness prediction C Hsu, H Nisonoff, C Fannjiang, J Listgarten bioRxiv, 2021.03. 28.437402, 2021 | 28 | 2021 |
| Discovery and validation of the binding poses of allosteric fragment hits to protein tyrosine phosphatase 1b: From molecular dynamics simulations to X-ray crystallography JB Greisman, L Willmore, CY Yeh, F Giordanetto, S Shahamadtar, ... Journal of Chemical Information and Modeling 63 (9), 2644-2650, 2023 | 7 | 2023 |
| Identification of GDC-1971 (RLY-1971), a SHP2 inhibitor designed for the treatment of solid tumors AM Taylor, BR Williams, F Giordanetto, EH Kelley, A Lescarbeau, ... Journal of Medicinal Chemistry 66 (19), 13384-13399, 2023 | 6 | 2023 |
| Efficient Partition Function Estimatation in Computational Protein Design: Probabalistic Guarantees and Characterization of a Novel Algorithm H Nisonoff Duke University Durham, 2015 | 6 | 2015 |
| Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes PH Yoon, P Skopintsev, H Shi, LX Chen, BA Adler, M Al-Shimary, ... Nucleic Acids Research 51 (22), 12414-12427, 2023 | 4 | 2023 |
| Augmenting neural networks with priors on function values H Nisonoff, Y Wang, J Listgarten arXiv preprint arXiv:2202.04798, 2022 | 4 | 2022 |
| 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 |
| Coherent Blending of Biophysics-Based Knowledge with Bayesian Neural Networks for Robust Protein Property Prediction H Nisonoff, Y Wang, J Listgarten ACS Synthetic Biology 12 (11), 3242-3251, 2023 | 3 | 2023 |
| Molecular Graph Generation from Structural Features Using an Artificial Neural Network P Maragakis, H Nisonoff, P Skopp, J Salmon US Patent App. 17/614,856, 2022 | 3 | 2022 |
| Discovery and validation of the binding poses of allosteric fragment hits to PTP1B: From molecular dynamics simulations to X-ray crystallography JB Greisman, L Willmore, CY Yeh, F Giordanetto, S Shahamadtar, ... bioRxiv, 2022.11. 14.516467, 2022 | 2 | 2022 |
| RNA language models predict mutations that improve RNA function Y Shulgina, MI Trinidad, CJ Langeberg, H Nisonoff, S Chithrananda, ... bioRxiv, 2024.04. 05.588317, 2024 | | 2024 |
| GENTANGLE: integrated computational design of gene entanglements JM Martí, C Hsu, C Rochereau, T Blazejewski, H Nisonoff, SP Leonard, ... bioRxiv, 2023.11. 09.565696, 2023 | | 2023 |
Jennifer ListgartenProfessor, UC Berkeley EECS and Center for Computational BiologyVerified email at berkeley.edu
