Amy Wang

Hi! I'm a Senior Scientist at Prescient Design (Genentech) working in Large Molecule Drug Discovery led by Franziska Seeger. My research lies at the intersection of machine learning and biophysics. My work is guided by the principle that integrating deep mechanistic understanding of biological systems with AI will address critical bottlenecks in therapeutic development.


I completed my PhD in 2023 at Stanford University, where I studied mechanosensitive cell adhesion proteins using biophysical (molecular biology, single-molecule force spectroscopy) and computational approaches with Alex Dunn and Bill Weis. I also interned with Microsoft Research's BioML Team in 2022 with Kevin Yang, Ava Amini, and Alex Lu to study how biophysical priors could improve ML models for protein property prediction. Additionally, I briefly worked with Ron Dror to study protein electrostatic binding interactions with MD simulations.

I received my bachelor's degree in Chemical Engineering with a minor in Polymers & Soft Matter at MIT. I worked in Brad Olsen's lab, where I studied the physics governing protein-block copolymer self-assembly, and in the Langer and Anderson labs, where I characterized protein-polymer interactions for drug delivery applications.

CV | Google Scholar | Twitter
amywangsci [at] gmail.com

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Publications

Lab-in-the-loop therapeutic antibody design with deep learning
N.C. Frey, I. Hötzel, S.D. Stanton, R. Kelly, R.G. Alberstein, ..., A. Wang, ..., A.Regev, Y. Wu, K. Cho, R. Bonneau, V. Gligorijević

bioRxiv 2025

Concept Bottleneck Language Models For Protein Design
A.A. Ismail, T. Oikarinen, A. Wang, J. Adebayo, S.D. Stanton, H.C. Bravo, K. Cho, N.C. Frey

International Conference on Learning Representations (ICLR) 2025

Fine-tuning discrete diffusion models via reward optimization with applications to dna and protein design
C. Wang, M. Uehara, Y. He, A. Wang, A. Lal, T. Jaakola, S. Levine, A. Regev, H. Wang, T. Biancalani

International Conference on Learning Representations (ICLR) 2025

Multi-level force-dependent allosteric enhancement of αE-catenin binding to F-actin by vinculin
N.A. Bax*, A. Wang*, D.L. Huang, S. Pokutta, A.R. Dunn, W.I. Weis

Journal of Molecular Biology 2023 | PDF

Mechanism of the cadherin-catenin F-actin catch bond interaction
A. Wang, A.R. Dunn, W.I. Weis

eLife 2022 | PDF

A retrievable implant for the long-term encapsulation and survival of therapeutic xenogeneic cells
S. Bose, L.R. Volpatti*, D. Thiono*, V. Yesilyurt, C. McGladrigan, Y. Tang, A. Facklam, A. Wang, S. Jhunjhunwala, O. Veiseh, J. Hollister-Lock, C. Bhattacharya, G.C. Weir, D.L. Greiner, R. Langer, D.G. Anderson

Nature Biomedical Engineering 2020 | PDF

Structure and mechanism of the cation–chloride cotransporter NKCC1
T.A. Chew*, B.J. Orlando*, J. Zhang*, N.R. Latorraca, A. Wang, S.A. Hollingsworth, D.H. Chen, R.O. Dror, M. Liao, L. Feng

Nature 2019 | PDF

Predicting protein–polymer block copolymer self-assembly from protein properties
A. Huang, J.M. Paloni, A. Wang, A.C. Obermeyer, H.V. Sureka, H. Yao, B.D. Olsen

Biomacromolecules 2019 | PDF

Design of insulin-loaded nanoparticles enabled by multistep control of nanoprecipitation and zinc chelation
S. Chopra, N. Bertrand, J. Lim, A. Wang, O. Farokhzad, R. Karnik

ACS Applied Materials & Interfaces 2017 | PDF
Patent Filed October 7, 2015.

Workshops

A guided design framework for the optimization of therapeutic-like antibodies
A. Wang, Z. Sang, S.D. Stanton, J.L. Hofmann, S. Izadi, E. Park, J. Ludwiczak, M. Kirchmeyer, D. Davidson, A. Maier, T. Pritsky, N.C. Frey, A.M. Watkins, F. Seeger

Generative and Experimental Perspectives for Biomolecular Design, ICLR 2025 | PDF

The Effects of Structural Conditioning on Antibody Inverse Folding
Z. Ma, D. Davidson, A. Wang, N. Frey, F. Seeger

Women in ML Workshop, NeurIPS 2023

Learning from physics-based features improves protein property prediction
A. Wang, A.X. Lu, A.P. Amini, K.K. Yang

Machine Learning in Structural Biology Workshop, NeurIPS 2022 | PDF | Poster

Awards and Affiliations
Webpage design courtesy of Jon Barron.