| Designing proteins with language models JA Ruffolo, A Madani Nature Biotechnology 42 (2), 200-202, 2024 | 10 | 2024 |
| Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences JA Ruffolo, S Nayfach, J Gallagher, A Bhatnagar, J Beazer, R Hussain, ... bioRxiv, 2024.04. 22.590591, 2024 | 3 | 2024 |
| Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE (3)-Discrete Diffusion A Morehead, J Ruffolo, A Bhatnagar, A Madani arXiv preprint arXiv:2401.06151, 2023 | 31 | 2023 |
| Large language models generate functional protein sequences across diverse families A Madani, B Krause, ER Greene, S Subramanian, BP Mohr, JM Holton, ... Nature Biotechnology, 1-8, 2023 | 426 | 2023 |
| Designing active and thermostable enzymes with sequence-only predictive models C Fannjiang, M Olivas, ER Greene, CJ Markin, B Wallace, B Krause, ... NeurIPS 2022 Workshop on Learning Meaningful Representations of Life, 2022 | 1 | 2022 |
| A language model beats alphafold2 on orphans JM Michaud, A Madani, JS Fraser Nature Biotechnology, 1-2, 2022 | 17 | 2022 |
| ProGen2: exploring the boundaries of protein language models E Nijkamp, JA Ruffolo, EN Weinstein, N Naik, A Madani Cell Systems, 2022 | 155 | 2022 |
| Systems and methods for alignment-based pre-training of protein prediction models P Sturmfels, A Madani, J Vig, N Rajani US Patent App. 17/153,164, 2022 | | 2022 |
| Generative Adversarial Network Medical Image Generation for Training of a Classifier A Madani, M Moradi, TF Syeda-Mahmood US Patent App. 17/528,566, 2022 | 5 | 2022 |
| Deep Extrapolation for Attribute-Enhanced Generation A Chan, A Madani, B Krause, N Naik Advances in Neural Information Processing Systems 34, 14084-14096, 2021 | 21 | 2021 |
| Don’t throw away that linear head: Few-shot protein fitness prediction with generative models B Krause, N Naik, W Liu, A Madani | 1 | 2021 |
| Machine-learned hormone status prediction from image analysis N Naik, A Madani, NS Keskar US Patent App. 16/895,983, 2021 | | 2021 |
| Systems and methods for language modeling of protein engineering A Madani, B McCann, N Naik US Patent App. 17/001,045, 2021 | | 2021 |
| Medical image classification based on a generative adversarial network trained discriminator A Madani, M Moradi, TF Syeda-Mahmood US Patent 10,937,540, 2021 | 31 | 2021 |
| Deep learning-enabled medical computer vision A Esteva, K Chou, S Yeung, N Naik, A Madani, A Mottaghi, Y Liu, E Topol, ... NPJ Digital Medicine 4 (1), 1-9, 2021 | 840 | 2021 |
| FLIP: Benchmark tasks in fitness landscape inference for proteins C Dallago, J Mou, KE Johnston, BJ Wittmann, N Bhattacharya, S Goldman, ... bioRxiv, 2021 | 88 | 2021 |
| Deep neural language modeling enables functional protein generation across families A Madani, B Krause, ER Greene, S Subramanian, BP Mohr, JM Holton, ... bioRxiv, 2021 | 57 | 2021 |
| Profile Prediction: An Alignment-Based Pre-Training Task for Protein Sequence Models P Sturmfels, J Vig, A Madani, NF Rajani arXiv preprint arXiv:2012.00195, 2020 | 20 | 2020 |
| Deep learning-enabled breast cancer hormonal receptor status determination from base-level H&E stains N Naik, A Madani, A Esteva, NS Keskar, MF Press, D Ruderman, DB Agus, ... Nature Communications 11 (1), 1-8, 2020 | 186 | 2020 |
| Machine learning for endoleak detection after endovascular aortic repair S Talebi, MH Madani, A Madani, A Chien, J Shen, D Mastrodicasa, ... Scientific Reports 10 (1), 1-8, 2020 | 23 | 2020 |
