Sotabase

Career

· PhD Student, MIT2021–
· PhD Student, University of California, Berkeley2015–2020
· Software Engineer, DeepMind
· B.S. in Computer Science, Johns Hopkins University
· Software Engineer, MIT CSAIL
· Graduate Student, University of California, Berkeley
· AI Scientist, Xaira Therapeutics

Publications (24)

Protein complex prediction with AlphaFold-Multimer
bioRxiv · 2021
2,781
cited
Deep indel mutagenesis reveals the regulatory and modulatory architecture of alternative exon splicing
Nature Communications · 2025
811
cited
De novo design of protein structure and function with RFdiffusion
Nature · 2023
630
cited
Conductance stable and mechanically durable bi-layer EGaIn composite-coated stretchable fiber for 1D bioelectronics
Nature Communications · 2023
614
cited
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem
International Conference on Learning Representations · 2022
307
cited
SE(3) diffusion model with application to protein backbone generation
International Conference on Machine Learning · 2023
287
cited
Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design
International Conference on Machine Learning · 2024
230
cited
Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models
bioRxiv · 2022
194
cited
Scalable emulation of protein equilibrium ensembles with generative deep learning
bioRxiv · 2025
170
cited
Fast protein backbone generation with SE(3) flow matching
2023
114
cited
Diffusion models in protein structure and docking
WIREs Computational Molecular Science · 2024
60
cited
Improved motif-scaffolding with SE(3) flow matching
Trans. Mach. Learn. Res. · 2024
51
cited
Sparse Projection Oblique Randomer Forests
Journal of machine learning research · 2015
50
cited
Atom-level enzyme active site scaffolding using RFdiffusion2
bioRxiv · 2025
49
cited
Generator Matching: Generative modeling with arbitrary Markov processes
arXiv.org · 2024
45
cited
Improving protein optimization with smoothed fitness landscapes
International Conference on Learning Representations · 2023
25
cited
Computational design of metallohydrolases
bioRxiv · 2025
16
cited
ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids
International Conference on Learning Representations · 2025
8
cited
Random Projection Forests
2015
7
cited
Fast non-autoregressive inverse folding with discrete diffusion
2023
5
cited
Sotabase
Jason Yim | Researcher Profile | Sotabase | Sotabase