Publications

Sam Berry, Rachelle Gaudet, Debora S Marks (2026). Differences between protein fitness models can be used to design variants of altered specificity. In bioRxiv.

DOI Preprint

Aviv Spinner, Pascal Notin, Sam Berry, Dana Cortade, Zach Sisson, Svetlana Ikonomova, David Ross, Debora Marks (2026). Unified sampling framework and experimental benchmarking of sequence- and structure-based protein models. In bioRxiv.

DOI Preprint

Sam Berry, Camille B Freedman, Debora S Marks, Rachelle Gaudet (2026). Determinants of metal import and specificity in a bacterial transporter. In bioRxiv.

DOI Preprint

Shamayeeta Ray, Sam Berry, Rachelle Gaudet (2026). Structural and functional basis of proton-independent transition metal import by a canonical bacterial Nramp transporter. In bioRxiv.

DOI Preprint

Sam Berry, Rachelle Gaudet (2025). A structural window into the evolution of secondary transport mechanisms. In Nat Struct Mol Biol.

DOI Journal link

Jacob A Licht, Sam Berry, Michael A Gutierrez, Rachelle Gaudet (2024). They all rock: A systematic comparison of conformational movements in LeuT-fold transporters. In Structure.

DOI Journal link

Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Sam Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik (2024). GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. In Nat Struct Mol Biol.

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Shamayeeta Ray, Sam Berry, Eric A. Wilson, Casey H. Zhang, Mrinal Shekhar, Abhishek Singharoy (2023). High-resolution structures map the metal import pathway in an Nramp transporter. In eLife.

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Katherine Hummels, Sam Berry, Zhaoqi Li, Atsushi Taguchi, Joseph K Min, Suzanne Walker, Debora S Marks, Thomas G Bernhardt (2023). Coordination of bacterial cell wall and outer membrane biosynthesis. In Nature.

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Angela Steinauer, Jonathan R LaRochelle, Susan L Knox, Rebecca F Wissner, Sam Berry, Alanna Schepartz (2019). HOPS-dependent endosomal fusion required for efficient cytosolic delivery of therapeutic peptides and small proteins. In PNAS.

DOI Journal link