Amy Wang

I am a computational researcher with a decade of wet-lab experience, focused on accelerating drug development by integrating biological data and domain expertise with scalable ML pipelines.

As a Senior ML Scientist in Large Molecule Drug Discovery at Prescient Design (Genentech), I develop frameworks deployed in 10+ drug discovery programs and lead AI method development in close partnership with experimental teams.

I earned my PhD in 2023 at Stanford University studying force-sensitive cell adhesion proteins with Alex Dunn and Bill Weis, while collaborating on GNN models for protein prediction with Microsoft Research's BioML Team (Kevin Yang, Ava Amini, Alex Lu) and MD simulation analysis with Ron Dror's group. As a Chemical Engineering undergraduate at MIT, I studied protein-polymer systems with applications to drug delivery in the Olsen, Langer, and Anderson labs.

My technical depth in AI/ML coupled with hands-on experimental experience, enables me to accelerate cross-functional collaboration and drive method adoption in biotech.

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

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, [...], N.C. Frey, A.M. Watkins, Franziska SeegerF. Seeger

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

SurfProp: A surface-based property prediction framework for antibody developability and screening
P. Rao, H. Isaacson, J.L. Hofmann, D. Davidson, A. Wang, A.M. Watkins, R. Bonneau, S. Izadi, J.H. Lee, N.C. Frey, F. Seeger

GenBio Workshop, 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

University Nominee for the 2023 Schmidt Science Fellows Program
Valuation of Public Companies in the Life Sciences Pitch Competition (INDE209) - First Place (2020)
NSF Graduate Research Fellowship (2018-2023)
Stanford ChEM-H Chemistry/Biology Interface Predoctoral Training Program (2018-2023)
Stanford Graduate Fellowship (2018-2023)
MIT Tau Beta Pi (2017)
MIT Chemical Engineering Departmental BP Academic Achievement Award (2016)

Webpage design courtesy of Jon Barron.

	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.