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Jason Yim
Jason Yim
Verified email at csail.mit.edu - Homepage
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Cited by
Year
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
37542021
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
3772022
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
3332020
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
3302023
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
2472024
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
1652025
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
1402023
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
762020
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
722024
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
682024
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
612025
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
422025
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
422024
Computational design of metallohydrolases
D Kim, SM Woodbury, W Ahern, D Tischer, A Kang, E Joyce, AK Bera, ...
Nature, 1-8, 2025
252025
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
92025
Fast non-autoregressive inverse folding with discrete diffusion
JJ Yang, J Yim, R Barzilay, T Jaakkola
arXiv preprint arXiv:2312.02447, 2023
62023
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
52025
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
42025
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Articles 1–20