Amini, Ava P.

Protein structure generation via folding diffusion

Wu, K. E., Yang, K. K., Berg, R. V. D., Zou, J. Y., Lu, A. X., & Amini, A. P. (2022) · arXiv

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 193

Protein generation with evolutionary diffusion: sequence is all you need

Alamdari, S., Thakkar, N., van den Berg, R., Tenenholtz, N., Strome, R., Moses, A. M., Lu, A. X., Fusi, N., Amini, A. P., & Yang, K. K. (2023) · eLife

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 154

Zero-shot evaluation reveals limitations of single-cell foundation models

Kedzierska, K. Z., Crawford, L., Amini, A. P., & Lu, A. X. (2025) · Genome Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 109

Assessing the limits of zero-shot foundation models in single-cell biology

Kedzierska, K. Z., Crawford, L., Amini, A. P., & Lu, A. X. (2023) · bioRxiv (Cold Spring Harbor Laboratory)

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 61

Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models

Li, F.-Z., Amini, A. P., Yue, Y., Yang, K. K., & Lu, A. X. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 51

Deeper evaluation of a single-cell foundation model

Boiarsky, R., Singh, N. M., Buendia, A., Amini, A. P., Getz, G., & Sontag, D. (2024) · Nature Machine Intelligence

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 25