| Progen2: exploring the boundaries of protein language models E Nijkamp, JA Ruffolo, EN Weinstein, N Naik, A Madani Cell systems 14 (11), 968-978. e3, 2023 | 280* | 2023 |
| Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies JA Ruffolo, LS Chu, SP Mahajan, JJ Gray Nature communications 14 (1), 2389, 2023 | 233 | 2023 |
| Antibody structure prediction using interpretable deep learning JA Ruffolo, J Sulam, JJ Gray Patterns 3 (2), 2022 | 182 | 2022 |
| IgLM: Infilling language modeling for antibody sequence design RW Shuai, JA Ruffolo, JJ Gray Cell Systems 14 (11), 979-989. e4, 2023 | 129* | 2023 |
| Deciphering antibody affinity maturation with language models and weakly supervised learning JA Ruffolo, JJ Gray, J Sulam arXiv preprint arXiv:2112.07782, 2021 | 127 | 2021 |
| Geometric Potentials from Deep Learning Improve Prediction of CDR H3 Loop Structures JA Ruffolo, C Guerra, SP Mahajan, J Sulam, JJ Gray Bioinformatics 36 (Supplement_1), i268–i275, 2020 | 72 | 2020 |
| Designing proteins with language models JA Ruffolo, A Madani nature biotechnology 42 (2), 200-202, 2024 | 40 | 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 | 33 | 2023 |
| 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 | 20 | 2024 |
| Hallucinating structure-conditioned antibody libraries for target-specific binders SP Mahajan, JA Ruffolo, R Frick, JJ Gray bioRxiv, 2022.06. 06.494991, 2022 | 19 | 2022 |
| Flexible protein–protein docking with a multitrack iterative transformer LS Chu, JA Ruffolo, A Harmalkar, JJ Gray Protein Science 33 (2), e4862, 2024 | 17 | 2024 |
| Simultaneous prediction of antibody backbone and side-chain conformations with deep learning D Akpinaroglu, JA Ruffolo, SP Mahajan, JJ Gray PloS one 17 (6), e0258173, 2022 | 15* | 2022 |
| Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen M Hutchinson, JA Ruffolo, N Haskins, M Iannotti, G Vozza, T Pham, ... mAbs 16 (1), 2362775, 2024 | 6* | 2024 |
| FLAb: Benchmarking deep learning methods for antibody fitness prediction M Chungyoun, J Ruffolo, J Gray BioRxiv, 2024.01. 13.575504, 2024 | 6 | 2024 |
| A versatile design platform for glycoengineering therapeutic antibodies SD Ludwig, ZJ Bernstein, C Agatemor, K Dammen-Brower, J Ruffolo, ... Mabs 14 (1), 2095704, 2022 | 4 | 2022 |
| Adapting protein language models for structure-conditioned design JA Ruffolo, A Bhatnagar, J Beazer, S Nayfach, J Russ, E Hill, R Hussain, ... bioRxiv, 2024.08. 03.606485, 2024 | 3 | 2024 |
| Conditional enzyme generation using protein language models with adapters J Yang, A Bhatnagar, JA Ruffolo, A Madani arXiv preprint arXiv:2410.03634, 2024 | 2 | 2024 |
| Contextual protein and antibody encodings from equivariant graph transformers SP Mahajan, JA Ruffolo, JJ Gray bioRxiv, 2023 | 2 | 2023 |
| Towards deep learning models for target-specific antibody design SP Mahajan, J Ruffolo, R Frick, JJ Gray Biophysical Journal 121 (3), 528a, 2022 | 1 | 2022 |
| Engineering of CRISPR-Cas PAM recognition using deep learning of vast evolutionary data S Nayfach, A Bhatnagar, A Novichkov, GO Estevam, N Kim, E Hill, ... bioRxiv, 2025.01. 06.631536, 2025 | | 2025 |
Jeffrey J. GrayJohns Hopkins University, Chemical and Biomolecular Engineering / Program in Molecular BiophysicsEmail verificata su jhu.edu