Sotabase

Career

· Machine Learning Engineer, Prescient Design, Computational Sciences, Genentech2021–
· Research Intern, The Flatiron Institute2021–
· PhD in Computer Science, New York University2020–
· MS in Computer Science, University of Vermont2017–2019
· BS in Mathematics, University of Vermont2015–2017

Publications (38)

Structure-based protein function prediction using graph convolutional networks
Nature Communications · 2021
814
cited
OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
bioRxiv · 2023
336
cited
Protein remote homology detection and structural alignment using deep learning
Nature Biotechnology · 2023
103
cited
Sequence-structure-function relationships in the microbial protein universe
bioRxiv · 2022
70
cited
Protein Discovery with Discrete Walk-Jump Sampling
International Conference on Learning Representations · 2023
51
cited
Structure-Based Function Prediction using Graph Convolutional Networks
bioRxiv · 2019
47
cited
Function-guided protein design by deep manifold sampling
bioRxiv · 2021
31
cited
Lab-in-the-loop therapeutic antibody design with deep learning
bioRxiv · 2025
23
cited
OpenProteinSet: Training data for structural biology at scale
Neural Information Processing Systems · 2023
23
cited
Protein Structural Alignments From Sequence
bioRxiv · 2020
21
cited
TM-Vec: template modeling vectors for fast homology detection and alignment
bioRxiv · 2022
11
cited
Efficient Crowd Exploration of Large Networks
Proc. ACM Hum. Comput. Interact. · 2018
9
cited
L EARNING PROTEIN FAMILY MANIFOLDS WITH SMOOTHED ENERGY - BASED MODELS
2023
6
cited
Multi-segment preserving sampling for deep manifold sampler
arXiv.org · 2022
5
cited
Comparative genomics of the parasite Trichomonas vaginalis reveals genes involved in spillover from birds to humans
Nature Communications · 2025
2
cited
Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans
bioRxiv · 2024
1
cited
flatironinstitute/DeepFRI: First release
2021
Inferring the size of the causal universe: features and fusion of causal attribution networks
arXiv.org · 2018
Neural language representations predict outcomes of scientific research
arXiv.org · 2018
PlasmoFP: leveraging deep learning to predict protein function of uncharacterized proteins across the malaria parasite genus
bioRxiv · 2025
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Daniel Berenberg | Researcher Profile | Sotabase | Sotabase