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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. Among authors: poelwijk fj. 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.
Predicting Evolution Using Regulatory Architecture.
Nghe P, de Vos MGJ, Kingma E, Kogenaru M, Poelwijk FJ, Laan L, Tans SJ. Nghe P, et al. Among authors: poelwijk fj. Annu Rev Biophys. 2020 May 6;49:181-197. doi: 10.1146/annurev-biophys-070317-032939. Epub 2020 Feb 4. Annu Rev Biophys. 2020. PMID: 32040932 Review.
Protein Structure from Experimental Evolution.
Stiffler MA, Poelwijk FJ, Brock KP, Stein RR, Riesselman A, Teyra J, Sidhu SS, Marks DS, Gauthier NP, Sander C. Stiffler MA, et al. Among authors: poelwijk fj. Cell Syst. 2020 Jan 22;10(1):15-24.e5. doi: 10.1016/j.cels.2019.11.008. Epub 2019 Dec 11. Cell Syst. 2020. PMID: 31838147 Free article.
Inferring protein 3D structure from deep mutation scans.
Rollins NJ, Brock KP, Poelwijk FJ, Stiffler MA, Gauthier NP, Sander C, Marks DS. Rollins NJ, et al. Among authors: poelwijk fj. Nat Genet. 2019 Jul;51(7):1170-1176. doi: 10.1038/s41588-019-0432-9. Epub 2019 Jun 17. Nat Genet. 2019. PMID: 31209393 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: poelwijk fj. 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.
The Context-Dependence of Mutations: A Linkage of Formalisms.
Poelwijk FJ, Krishna V, Ranganathan R. Poelwijk FJ, et al. PLoS Comput Biol. 2016 Jun 23;12(6):e1004771. doi: 10.1371/journal.pcbi.1004771. eCollection 2016 Jun. PLoS Comput Biol. 2016. PMID: 27337695 Free PMC article. No abstract available.
Environmental dependence of genetic constraint.
de Vos MG, Poelwijk FJ, Battich N, Ndika JD, Tans SJ. de Vos MG, et al. Among authors: poelwijk fj. PLoS Genet. 2013 Jun;9(6):e1003580. doi: 10.1371/journal.pgen.1003580. Epub 2013 Jun 27. PLoS Genet. 2013. PMID: 23825963 Free PMC article.
21 results