| Protein complex prediction with AlphaFold-Multimer R Evans, M O’Neill, A Pritzel, N Antropova, A Senior, T Green, A Žídek, ... biorxiv, 2021.10. 04.463034, 2021 | 3754 | 2021 |
| De novo design of protein structure and function with RFdiffusion JL Watson, D Juergens, NR Bennett, BL Trippe, J Yim, HE Eisenach, ... Nature 620 (7976), 1089-1100, 2023 | 2355* | 2023 |
| Diffusion probabilistic modeling of protein backbones in 3d for the motif-scaffolding problem BL Trippe, J Yim, D Tischer, D Baker, T Broderick, R Barzilay, T Jaakkola arXiv preprint arXiv:2206.04119, 2022 | 377 | 2022 |
| Predicting conversion to wet age-related macular degeneration using deep learning J Yim, R Chopra, T Spitz, J Winkens, A Obika, C Kelly, H Askham, M Lukic, ... Nature Medicine 26 (6), 892-899, 2020 | 333 | 2020 |
| SE (3) diffusion model with application to protein backbone generation J Yim, BL Trippe, V De Bortoli, E Mathieu, A Doucet, R Barzilay, ... arXiv preprint arXiv:2302.02277, 2023 | 330 | 2023 |
| Generative flows on discrete state-spaces: Enabling multimodal flows with applications to protein co-design A Campbell, J Yim, R Barzilay, T Rainforth, T Jaakkola arXiv preprint arXiv:2402.04997, 2024 | 247 | 2024 |
| Scalable emulation of protein equilibrium ensembles with generative deep learning S Lewis, T Hempel, J Jiménez-Luna, M Gastegger, Y Xie, AYK Foong, ... Science 389 (6761), eadv9817, 2025 | 165 | 2025 |
| Fast protein backbone generation with se (3) flow matching J Yim, A Campbell, AYK Foong, M Gastegger, J Jiménez-Luna, S Lewis, ... arXiv preprint arXiv:2310.05297, 2023 | 140 | 2023 |
| Sparse projection oblique randomer forests TM Tomita, J Browne, C Shen, J Chung, JL Patsolic, B Falk, CE Priebe, ... Journal of machine learning research 21 (104), 1-39, 2020 | 76 | 2020 |
| Diffusion models in protein structure and docking J Yim, H Stärk, G Corso, B Jing, R Barzilay, TS Jaakkola Wiley Interdisciplinary Reviews: Computational Molecular Science 14 (2), e1711, 2024 | 72 | 2024 |
| Improved motif-scaffolding with SE (3) flow matching J Yim, A Campbell, E Mathieu, AYK Foong, M Gastegger, J Jiménez-Luna, ... ArXiv, arXiv: 2401.04082 v2, 2024 | 68 | 2024 |
| Proteina: Scaling flow-based protein structure generative models T Geffner, K Didi, Z Zhang, D Reidenbach, Z Cao, J Yim, M Geiger, ... arXiv preprint arXiv:2503.00710, 2025 | 61 | 2025 |
| Improving protein optimization with smoothed fitness landscapes A Kirjner, J Yim, R Samusevich, S Bracha, T Jaakkola, R Barzilay, I Fiete arXiv preprint arXiv:2307.00494, 2023 | 43* | 2023 |
| Atom-level enzyme active site scaffolding using RFdiffusion2 W Ahern, J Yim, D Tischer, S Salike, SM Woodbury, D Kim, I Kalvet, ... Nature Methods, 1-10, 2025 | 42 | 2025 |
| Generator matching: Generative modeling with arbitrary markov processes P Holderrieth, M Havasi, J Yim, N Shaul, I Gat, T Jaakkola, B Karrer, ... arXiv preprint arXiv:2410.20587, 2024 | 42 | 2024 |
| Computational design of metallohydrolases D Kim, SM Woodbury, W Ahern, D Tischer, A Kang, E Joyce, AK Bera, ... Nature, 1-8, 2025 | 25 | 2025 |
| MotifBench: A standardized protein design benchmark for motif-scaffolding problems Z Zheng, B Zhang, K Didi, KK Yang, J Yim, JL Watson, HF Chen, ... arXiv preprint arXiv:2502.12479, 2025 | 9 | 2025 |
| Fast non-autoregressive inverse folding with discrete diffusion JJ Yang, J Yim, R Barzilay, T Jaakkola arXiv preprint arXiv:2312.02447, 2023 | 6 | 2023 |
| ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids H Stark, B Jing, T Geffner, J Yim, T Jaakkola, A Vahdat, K Kreis arXiv preprint arXiv:2503.05025, 2025 | 5 | 2025 |
| Hierarchical protein backbone generation with latent and structure diffusion J Yim, M Jaakik, G Liu, J Gershon, K Kreis, D Baker, R Barzilay, ... arXiv preprint arXiv:2504.09374, 2025 | 4 | 2025 |
Tommi JaakkolaMITVerified email at csail.mit.edu
