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Illuminating protein space with a programmable generative model.
Ingraham JB, Baranov M, Costello Z, Barber KW, Wang W, Ismail A, Frappier V, Lord DM, Ng-Thow-Hing C, Van Vlack ER, Tie S, Xue V, Cowles SC, Leung A, Rodrigues JV, Morales-Perez CL, Ayoub AM, Green R, Puentes K, Oplinger F, Panwar NV, Obermeyer F, Root AR, Beam AL, Poelwijk FJ, Grigoryan G. Ingraham JB, et al. 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.
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.
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.
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.
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.