Publications by authors named "Jeffrey Ruffolo"

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What does a language model know about proteins?
Jeffrey A Ruffolo

Nat Methods· October 2025

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Design of highly functional genome editors by modelling CRISPR-Cas sequences.
Jeffrey A Ruffolo, Stephen Nayfach, Joseph Gallagher, Aadyot Bhatnagar, Joel Beazer

Nature· September 2025

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How well do contextual protein encodings learn structure, function, and evolutionary context?
Sai Pooja Mahajan, Fátima A Dávila-Hernández, Jeffrey A Ruffolo, Jeffrey J Gray

Cell Syst· March 2025

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Engineering of CRISPR-Cas PAM recognition using deep learning of vast evolutionary data.
Stephen Nayfach, Aadyot Bhatnagar, Andrey Novichkov, Gabriella O Estevam, Nahye Kim, Jeffrey A Ruffolo

bioRxiv· January 2025

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Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.
Mark Hutchinson, Jeffrey A Ruffolo, Nantaporn Haskins, Michael Iannotti, Giuliana Vozza

MAbs· June 2024

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Flexible protein-protein docking with a multitrack iterative transformer.
Lee-Shin Chu, Jeffrey A Ruffolo, Ameya Harmalkar, Jeffrey J Gray

Protein Sci· February 2024

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Designing proteins with language models.
Jeffrey A Ruffolo, Ali Madani

Nat Biotechnol· February 2024

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IgLM: Infilling language modeling for antibody sequence design.
Richard W Shuai, Jeffrey A Ruffolo, Jeffrey J Gray

Cell Syst· November 2023

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ProGen2: Exploring the boundaries of protein language models.
Erik Nijkamp, Jeffrey A Ruffolo, Eli N Weinstein, Nikhil Naik, Ali Madani

Cell Syst· November 2023

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Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
Lee-Shin Chu, Jeffrey A Ruffolo, Ameya Harmalkar, Jeffrey J Gray

bioRxiv· July 2023

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Contextual protein and antibody encodings from equivariant graph transformers.
Sai Pooja Mahajan, Jeffrey A Ruffolo, Jeffrey J Gray

bioRxiv· July 2023

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Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies.
Jeffrey A Ruffolo, Lee-Shin Chu, Sai Pooja Mahajan, Jeffrey J Gray

Nat Commun· April 2023

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Hallucinating structure-conditioned antibody libraries for target-specific binders.
Sai Pooja Mahajan, Jeffrey A Ruffolo, Rahel Frick, Jeffrey J Gray

Front Immunol· November 2022

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A versatile design platform for glycoengineering therapeutic antibodies.
Seth D Ludwig, Zachary J Bernstein, Christian Agatemor, Kris Dammen-Brower, Jeffrey Ruffolo

MAbs· July 2022

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Simultaneous prediction of antibody backbone and side-chain conformations with deep learning.
Deniz Akpinaroglu, Jeffrey A Ruffolo, Sai Pooja Mahajan, Jeffrey J Gray

PLoS One· June 2022

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Antibody structure prediction using interpretable deep learning.
Jeffrey A Ruffolo, Jeremias Sulam, Jeffrey J Gray

Patterns (N Y)· February 2022

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Modeling of lamprey reticulospinal neurons: multiple distinct parameter sets yield realistic simulations.
Jeffrey A Ruffolo, Andrew D McClellan

J Neurophysiol· September 2020

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Geometric potentials from deep learning improve prediction of CDR H3 loop structures.
Jeffrey A Ruffolo, Carlos Guerra, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J Gray

Bioinformatics· July 2020

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