| Opportunities and obstacles for deep learning in biology and medicine T Ching, DS Himmelstein, BK Beaulieu-Jones, AA Kalinin, BT Do, ... Journal of the royal society interface 15 (141), 20170387, 2018 | 1930 | 2018 |
| FAAH genetic variation enhances fronto-amygdala function in mouse and human I Dincheva, AT Drysdale, CA Hartley, DC Johnson, D Jing, EC King, S Ra, ... Nature communications 6 (1), 6395, 2015 | 279 | 2015 |
| Forebrain elimination of cacna1c mediates anxiety-like behavior in mice AS Lee, S Ra, AM Rajadhyaksha, JK Britt, D Jesus-Cortes, KL Gonzales, ... Molecular psychiatry 17 (11), 1054-1055, 2012 | 110 | 2012 |
| OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization G Ahdritz, N Bouatta, S Kadyan, Q Xia, W Gerecke, TJ O’Donnell, ... Biorxiv, 2022.11. 20.517210, 2022 | 98 | 2022 |
| Cav1. 2 L-type Ca2+ channels mediate cocaine-induced GluA1 trafficking in the nucleus accumbens, a long-term adaptation dependent on ventral tegmental area Cav1. 3 channels K Schierberl, J Hao, TF Tropea, S Ra, TP Giordano, Q Xu, SM Garraway, ... Journal of Neuroscience 31 (38), 13562-13575, 2011 | 86 | 2011 |
| Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data AM Smith, JR Walsh, J Long, CB Davis, P Henstock, MR Hodge, ... BMC bioinformatics 21, 1-18, 2020 | 61 | 2020 |
| Behavioral characterization of cereblon forebrain-specific conditional null mice: a model for human non-syndromic intellectual disability AM Rajadhyaksha, S Ra, S Kishinevsky, AS Lee, P Romanienko, ... Behavioural brain research 226 (2), 428-434, 2012 | 56 | 2012 |
| Function-guided protein design by deep manifold sampling V Gligorijević, D Berenberg, S Ra, A Watkins, S Kelow, K Cho, R Bonneau bioRxiv, 2021.12. 22.473759, 2021 | 34 | 2021 |
| Equifold: Protein structure prediction with a novel coarse-grained structure representation JH Lee, P Yadollahpour, A Watkins, NC Frey, A Leaver-Fay, S Ra, K Cho, ... Biorxiv, 2022.10. 07.511322, 2022 | 24 | 2022 |
| FAAH genetic variation enhances fronto-amygdala function in mouse and human. Nat Commun 6: 6395 I Dincheva, AT Drysdale, CA Hartley, DC Johnson, D Jing, EC King, S Ra, ... | 22 | 2015 |
| Learning causal representations of single cells via sparse mechanism shift modeling R Lopez, N Tagasovska, S Ra, K Cho, J Pritchard, A Regev Conference on Causal Learning and Reasoning, 662-691, 2023 | 19 | 2023 |
| PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design JW Park, S Stanton, S Saremi, A Watkins, H Dwyer, V Gligorijevic, ... arXiv preprint arXiv:2210.04096, 2022 | 11 | 2022 |
| Deep learning of representations for transcriptomics-based phenotype prediction AM Smith, JR Walsh, J Long, CB Davis, P Henstock, MR Hodge, ... BioRxiv, 574723, 2019 | 8 | 2019 |
| A Pareto-optimal compositional energy-based model for sampling and optimization of protein sequences N Tagasovska, NC Frey, A Loukas, I Hötzel, J Lafrance-Vanasse, RL Kelly, ... arXiv preprint arXiv:2210.10838, 2022 | 5 | 2022 |
| Black box recursive translations for molecular optimization F Damani, V Sresht, S Ra arXiv preprint arXiv:1912.10156, 2019 | 5 | 2019 |
| OpenProteinSet: Training data for structural biology at scale G Ahdritz, N Bouatta, S Kadyan, L Jarosch, D Berenberg, I Fisk, A Watkins, ... Advances in Neural Information Processing Systems 36, 2024 | 4 | 2024 |
| Protein discovery with discrete walk-jump sampling NC Frey, D Berenberg, K Zadorozhny, J Kleinhenz, J Lafrance-Vanasse, ... arXiv preprint arXiv:2306.12360, 2023 | 4 | 2023 |
| 3D molecule generation by denoising voxel grids PO O Pinheiro, J Rackers, J Kleinhenz, M Maser, O Mahmood, A Watkins, ... Advances in Neural Information Processing Systems 36, 2024 | 3 | 2024 |
| Multi-segment preserving sampling for deep manifold sampler D Berenberg, JH Lee, S Kelow, JW Park, A Watkins, V Gligorijević, ... arXiv preprint arXiv:2205.04259, 2022 | 3 | 2022 |
| Learning protein family manifolds with smoothed energy-based models NC Frey, D Berenberg, J Kleinhenz, I Hotzel, J Lafrance-Vanasse, ... ICLR 2023 Workshop on Physics for Machine Learning, 2023 | 2 | 2023 |
Kyunghyun ChoNew York University, GenentechVerified email at nyu.edu
