| Flexible and stretchable nanowire-coated fibers for optoelectronic probing of spinal cord circuits C Lu, S Park, TJ Richner, A Derry, I Brown, C Hou, S Rao, J Kang, ... Science advances 3 (3), e1600955, 2017 | 227 | 2017 |
| Protein sequence design with a learned potential N Anand, R Eguchi, II Mathews, CP Perez, A Derry, RB Altman, PS Huang Nature communications 13 (1), 746, 2022 | 191 | 2022 |
| Atom3d: Tasks on molecules in three dimensions RJL Townshend, M Vögele, P Suriana, A Derry, A Powers, Y Laloudakis, ... arXiv preprint arXiv:2012.04035, 2020 | 130 | 2020 |
| Simulating 500 million years of evolution with a language model T Hayes, R Rao, H Akin, NJ Sofroniew, D Oktay, Z Lin, R Verkuil, VQ Tran, ... Science, eads0018, 2025 | 122 | 2025 |
| A literature-based knowledge graph embedding method for identifying drug repurposing opportunities in rare diseases DN Sosa, A Derry, M Guo, E Wei, C Brinton, RB Altman Pacific Symposium on Biocomputing 2020, 463-474, 2019 | 121 | 2019 |
| Homology modeling of TMPRSS2 yields candidate drugs that may inhibit entry of SARS-CoV-2 into human cells. S Rensi, A Keys, YC Lo, A Derry, G McInnes, T Liu, R Altman ChemRxiv, 2020 | 48 | 2020 |
| Convolutional neural networks A Derry, M Krzywinski, N Altman Nature Methods 20 (9), 1269-1270, 2023 | 40 | 2023 |
| COLLAPSE: A representation learning framework for identification and characterization of protein structural sites A Derry, RB Altman Protein Science 32 (2), e4541, 2023 | 14 | 2023 |
| Neural networks primer A Derry, M Krzywinski, N Altman Nature Methods, 2023 | 10 | 2023 |
| Explainable protein function annotation using local structure embeddings A Derry, RB Altman bioRxiv, 2023 | 7 | 2023 |
| Training data composition affects performance of protein structure analysis algorithms A Derry, KA Carpenter, RB Altman PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022, 10-21, 2021 | 7 | 2021 |
| Simulating 500 million years of evolution with a language model, July 2024 T Hayes, R Rao, H Akin, NJ Sofroniew, D Oktay, Z Lin, R Verkuil, VQ Tran, ... URL https://www. biorxiv. org/content/10.1101/2024.07 1, v1, 2024 | 6 | 2024 |
| Prospector heads: generalized feature attribution for large models & data G Machiraju, A Derry, A Desai, N Guha, AH Karimi, J Zou, RB Altman, ... ArXiv, arXiv: 2402.11729 v2, 2024 | 2 | 2024 |
| Deep Learning on Local Sites for Protein Structure and Function Analysis AWF Derry Stanford University, 2024 | | 2024 |
| Unsupervised learning reveals landscape of local structural motifs across protein classes A Derry, RB Altman bioRxiv, 2023.12. 04.569990, 2023 | | 2023 |
| Interaction of amphiphilic nanoparticles with structurally perturbed lipid membranes A Derry Massachusetts Institute of Technology, 2018 | | 2018 |