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Page 1
Silent silencers: Leave no trace.
Ozturan D, de Boer CG. Ozturan D, et al. Among authors: de boer cg. Mol Cell. 2024 Dec 5;84(23):4473-4475. doi: 10.1016/j.molcel.2024.11.005. Mol Cell. 2024. PMID: 39642851
GIL: a python package for designing custom indexing primers.
Mateyko N, Tariq O, Chen XE, Cheney W, Salaudeen AL, Luthra I, Nikpour N, Rafi AM, Kamali Deghan H, Jensen C, de Boer C. Mateyko N, et al. Bioinformatics. 2023 Jun 1;39(6):btad328. doi: 10.1093/bioinformatics/btad328. Bioinformatics. 2023. PMID: 37208164 Free PMC article.
Linking candidate causal autoimmune variants to T cell networks using genetic and epigenetic screens in primary human T cells.
Ho CH, Dippel MA, McQuade MS, Mishra A, Pribitzer S, Nguyen LP, Hardy S, Chandok H, Chardon F, McDiarmid TA, DeBerg HA, Buckner JH, Shendure J, de Boer CG, Guo MH, Tewhey R, Ray JP. Ho CH, et al. Among authors: de boer cg. bioRxiv [Preprint]. 2024 Oct 11:2024.10.07.617092. doi: 10.1101/2024.10.07.617092. bioRxiv. 2024. PMID: 39416200 Free PMC article. Preprint.
A community effort to optimize sequence-based deep learning models of gene regulation.
Rafi AM, Nogina D, Penzar D, Lee D, Lee D, Kim N, Kim S, Kim D, Shin Y, Kwak IY, Meshcheryakov G, Lando A, Zinkevich A, Kim BC, Lee J, Kang T, Vaishnav ED, Yadollahpour P; Random Promoter DREAM Challenge Consortium; Kim S, Albrecht J, Regev A, Gong W, Kulakovskiy IV, Meyer P, de Boer CG. Rafi AM, et al. Among authors: de boer cg. Nat Biotechnol. 2024 Oct 11. doi: 10.1038/s41587-024-02414-w. Online ahead of print. Nat Biotechnol. 2024. PMID: 39394483
Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput.
Kennedy PH, Alborzian Deh Sheikh A, Balakar M, Jones AC, Olive ME, Hegde M, Matias MI, Pirete N, Burt R, Levy J, Little T, Hogan PG, Liu DR, Doench JG, Newton AC, Gottschalk RA, de Boer CG, Alarcón S, Newby GA, Myers SA. Kennedy PH, et al. Among authors: de boer cg. Nat Methods. 2024 Jun;21(6):1033-1043. doi: 10.1038/s41592-024-02256-z. Epub 2024 Apr 29. Nat Methods. 2024. PMID: 38684783
Regulatory activity is the default DNA state in eukaryotes.
Luthra I, Jensen C, Chen XE, Salaudeen AL, Rafi AM, de Boer CG. Luthra I, et al. Among authors: de boer cg. Nat Struct Mol Biol. 2024 Mar;31(3):559-567. doi: 10.1038/s41594-024-01235-4. Epub 2024 Mar 6. Nat Struct Mol Biol. 2024. PMID: 38448573
30 results