Publications by authors named "John B Ingraham"

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Simultaneous enhancement of multiple functional properties using evolution-informed protein design.
Benjamin Fram, Yang Su, Ian Truebridge, Adam J Riesselman, John B Ingraham

Nat Commun· June 2024

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Illuminating protein space with a programmable generative model.
John B Ingraham, Max Baranov, Zak Costello, Karl W Barber, Wujie Wang

Nature· November 2023

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Simultaneous enhancement of multiple functional properties using evolution-informed protein design.
Benjamin Fram, Ian Truebridge, Yang Su, Adam J Riesselman, John B Ingraham

bioRxiv· May 2023

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Generating transition states of isomerization reactions with deep learning.
Lagnajit Pattanaik, John B Ingraham, Colin A Grambow, William H Green

Phys Chem Chem Phys· October 2020

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The EVcouplings Python framework for coevolutionary sequence analysis.
Thomas A Hopf, Anna G Green, Benjamin Schubert, Sophia Mersmann, Charlotta P I Schärfe, John B Ingraham

Bioinformatics· May 2019

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Deep generative models of genetic variation capture the effects of mutations.
Adam J Riesselman, John B Ingraham, Debora S Marks

Nat Methods· October 2018

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Mutation effects predicted from sequence co-variation.
Thomas A Hopf, John B Ingraham, Frank J Poelwijk, Charlotta P I Schärfe, Michael Springer

Nat Biotechnol· February 2017

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3D RNA and Functional Interactions from Evolutionary Couplings.
Caleb Weinreb, Adam J Riesselman, John B Ingraham, Torsten Gross, Chris Sander

Cell· May 2016

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Galactose metabolic genes in yeast respond to a ratio of galactose and glucose.
Renan Escalante-Chong, Yonatan Savir, Sean M Carroll, John B Ingraham, Jue Wang

Proc Natl Acad Sci U S A· February 2015

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