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Illuminating protein space with a programmable generative model.
Nature. 2023 Nov;623(7989):1070-1078. doi: 10.1038/s41586-023-06728-8. Epub 2023 Nov 15.
Nature. 2023.
PMID: 37968394
Free PMC article.
Simultaneous enhancement of multiple functional properties using evolution-informed protein design.
Fram B, Truebridge I, Su Y, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler M, Marks DS, Bahl CD, Khan AR, Sander C, Gauthier NP.
Fram B, et al. Among authors: ingraham jb.
bioRxiv [Preprint]. 2023 May 9:2023.05.09.539914. doi: 10.1101/2023.05.09.539914.
bioRxiv. 2023.
PMID: 37214973
Free PMC article.
Preprint.
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Generating transition states of isomerization reactions with deep learning.
Pattanaik L, Ingraham JB, Grambow CA, Green WH.
Pattanaik L, et al. Among authors: ingraham jb.
Phys Chem Chem Phys. 2020 Oct 28;22(41):23618-23626. doi: 10.1039/d0cp04670a.
Phys Chem Chem Phys. 2020.
PMID: 33112304
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The EVcouplings Python framework for coevolutionary sequence analysis.
Hopf TA, Green AG, Schubert B, Mersmann S, Schärfe CPI, Ingraham JB, Toth-Petroczy A, Brock K, Riesselman AJ, Palmedo P, Kang C, Sheridan R, Draizen EJ, Dallago C, Sander C, Marks DS.
Hopf TA, et al. Among authors: ingraham jb.
Bioinformatics. 2019 May 1;35(9):1582-1584. doi: 10.1093/bioinformatics/bty862.
Bioinformatics. 2019.
PMID: 30304492
Free PMC article.
Item in Clipboard
Deep generative models of genetic variation capture the effects of mutations.
Riesselman AJ, Ingraham JB, Marks DS.
Riesselman AJ, et al. Among authors: ingraham jb.
Nat Methods. 2018 Oct;15(10):816-822. doi: 10.1038/s41592-018-0138-4. Epub 2018 Sep 24.
Nat Methods. 2018.
PMID: 30250057
Free PMC article.
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Mutation effects predicted from sequence co-variation.
Hopf TA, Ingraham JB, Poelwijk FJ, Schärfe CP, Springer M, Sander C, Marks DS.
Hopf TA, et al. Among authors: ingraham jb.
Nat Biotechnol. 2017 Feb;35(2):128-135. doi: 10.1038/nbt.3769. Epub 2017 Jan 16.
Nat Biotechnol. 2017.
PMID: 28092658
Free PMC article.
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3D RNA and Functional Interactions from Evolutionary Couplings.
Weinreb C, Riesselman AJ, Ingraham JB, Gross T, Sander C, Marks DS.
Weinreb C, et al. Among authors: ingraham jb.
Cell. 2016 May 5;165(4):963-75. doi: 10.1016/j.cell.2016.03.030. Epub 2016 Apr 14.
Cell. 2016.
PMID: 27087444
Free PMC article.
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Galactose metabolic genes in yeast respond to a ratio of galactose and glucose.
Escalante-Chong R, Savir Y, Carroll SM, Ingraham JB, Wang J, Marx CJ, Springer M.
Escalante-Chong R, et al. Among authors: ingraham jb.
Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1636-41. doi: 10.1073/pnas.1418058112. Epub 2015 Jan 20.
Proc Natl Acad Sci U S A. 2015.
PMID: 25605920
Free PMC article.
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