Publications

2024

Unlocking Guidance for Discrete State-Space Diffusion and Flow Models
Hunter Nisonoff*, Junhao Xiong*, Stephan Allenspach*, Jennifer Listgarten
arXiv preprint arXiv:2406.01572, 2024

RNA Language Models Predict Mutations that Improve RNA Function
Yekaterina Shulgina*, Marena I Trinidad*, Conner J Langeberg*, Hunter Nisonoff*, Seyone Chithrananda*, Petr Skopintsev*, Amos J Nissley*, Jaymin Patel, Ron S Boger, Honglue Shi, others
Nature Communications (In press), 2024

A Map of the Rubisco Biochemical Landscape
Noam Prywes, Naiya R Philips, Luke M Oltrogge, Sebastian Lindner, Yi-Chin Candace Tsai, Benoit de Pins, Aidan E Cowan, Leah J Taylor-Kearney, Hana A Chang, Laina N Hall, et al., Hunter Nisonoff, et al., David F Savage
Nature (In press), 2024

GENTANGLE: Integrated Computational Design of Gene Entanglements
Jose Manuel Marti, Chloe Hsu, Charlotte Rochereau, Chenling Xu, Tomasz Blazejewski, Hunter Nisonoff, Sean P Leonard, Christina S Kang-Yun, Jennifer Chlebek, Dante P Ricci, others
Bioinformatics, 40(7), btae380, 2024

2023

Coherent Blending of Biophysics-Based Knowledge with Bayesian Neural Networks for Robust Protein Property Prediction
Hunter Nisonoff, Yixin Wang, Jennifer Listgarten
ACS Synthetic Biology, 12(11), 3242–3251, 2023

Eukaryotic RNA-guided Endonucleases Evolved From a Unique Clade of Bacterial Enzymes
Peter H Yoon, Petr Skopintsev, Honglue Shi, Lin-Xing Chen, Benjamin A Adler, Muntathar Al-Shimary, Rory J Craig, Zheng Li, Jasmine Amerasekera, Marena Trinidad, Hunter Nisonoff, et al., Jennifer Doudna
Nucleic Acids Research, 51(22), 12414–12427, 2023

Identification of GDC-1971 (RLY-1971), a SHP2 Inhibitor Designed for the Treatment of Solid Tumors
Alexander M Taylor, Bret R Williams, Fabrizio Giordanetto, Elizabeth H Kelley, Andre Lescarbeau, Kelley Shortsleeves, Yong Tang, W Patrick Walters, Alfonso Arrazate, Christine Bowman, et al., Hunter Nisonoff, et al., Lindsay Willmore
Journal of Medicinal Chemistry, 66(19), 13384–13399, 2023

Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1B: From Molecular Dynamics Simulations to X-ray Crystallography
Jack B Greisman, Lindsay Willmore, Christine Y Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter Nisonoff, Paul Maragakis, David E Shaw
Journal of Chemical Information and Modeling, 63(9), 2644–2650, 2023

2022

Learning Protein Fitness Models from Evolutionary and Assay-Labeled Data
Chloe Hsu, Hunter Nisonoff, Clara Fannjiang, Jennifer Listgarten
Nature Biotechnology, 1–9, 2022

2021

Epistatic Net Allows the Sparse Spectral Regularization of Deep Neural Networks for Inferring Fitness Functions
Amirali Aghazadeh, Hunter Nisonoff, Orhan Ocal, David H Brookes, Yijie Huang, O Ozan Koyluoglu, Jennifer Listgarten, Kannan Ramchandran
Nature Communications, 12(1), 1–10, 2021

XYZeq: Spatially Resolved Single-Cell RNA Sequencing Reveals Expression Heterogeneity in the Tumor Microenvironment
Youjin Lee, Derek Bogdanoff, Yutong Wang, George C Hartoularos, Jonathan M Woo, Cody T Mowery, Hunter Nisonoff, David S Lee, Yang Sun, James Lee, others
Science Advances, 7(17), eabg4755, 2021

2020

A Deep-Learning View of Chemical Space Designed to Facilitate Drug Discovery
Paul Maragakis*, Hunter Nisonoff*, Brian Cole, David E Shaw
Journal of Chemical Information and Modeling, 60(10), 4487-4496, 2020

2016

Algorithms for Protein Design
Pablo Gainza, Hunter Nisonoff, Bruce R Donald
Current Opinion in Structural Biology, 39, 16–26, 2016

* Indicates co-first authorship