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Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference.
Tjärnberg A, Beheler-Amass M, Jackson CA, Christiaen LA, Gresham D, Bonneau R. Tjärnberg A, et al. Among authors: bonneau r. bioRxiv [Preprint]. 2023 Feb 3:2023.02.02.526909. doi: 10.1101/2023.02.02.526909. bioRxiv. 2023. Update in: Genome Biol. 2024 Jan 18;25(1):24. doi: 10.1186/s13059-023-03134-1 PMID: 36778259 Free PMC article. Updated. Preprint.
OpenProteinSet: Training data for structural biology at scale.
Ahdritz G, Bouatta N, Kadyan S, Jarosch L, Berenberg D, Fisk I, Watkins AM, Ra S, Bonneau R, AlQuraishi M. Ahdritz G, et al. Among authors: bonneau r. ArXiv [Preprint]. 2023 Aug 10:arXiv:2308.05326v1. ArXiv. 2023. PMID: 37608940 Free PMC article. Preprint.
Supercharged Phosphotriesterase for improved Paraoxon activity.
Kronenberg J, Britton D, Halvorsen L, Chu S, Kulapurathazhe MJ, Chen J, Lakshmi A, Renfrew PD, Bonneau R, Montclare JK. Kronenberg J, et al. Among authors: bonneau r. Protein Eng Des Sel. 2024 Jan 29;37:gzae015. doi: 10.1093/protein/gzae015. Protein Eng Des Sel. 2024. PMID: 39292622
Sequence-structure-function relationships in the microbial protein universe.
Koehler Leman J, Szczerbiak P, Renfrew PD, Gligorijevic V, Berenberg D, Vatanen T, Taylor BC, Chandler C, Janssen S, Pataki A, Carriero N, Fisk I, Xavier RJ, Knight R, Bonneau R, Kosciolek T. Koehler Leman J, et al. Among authors: bonneau r. Nat Commun. 2023 Apr 26;14(1):2351. doi: 10.1038/s41467-023-37896-w. Nat Commun. 2023. PMID: 37100781 Free PMC article.
327 results