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Evaluation and optimization of sequence-based gene regulatory deep learning models.
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 C. Rafi AM, et al. bioRxiv [Preprint]. 2024 Feb 17:2023.04.26.538471. doi: 10.1101/2023.04.26.538471. bioRxiv. 2024. Update in: Nat Biotechnol. 2024 Oct 11. doi: 10.1038/s41587-024-02414-w PMID: 38405704 Free PMC article. Updated. Preprint.
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. Among authors: rafi am. Bioinformatics. 2023 Jun 1;39(6):btad328. doi: 10.1093/bioinformatics/btad328. Bioinformatics. 2023. PMID: 37208164 Free PMC article.
LegNet: a best-in-class deep learning model for short DNA regulatory regions.
Penzar D, Nogina D, Noskova E, Zinkevich A, Meshcheryakov G, Lando A, Rafi AM, de Boer C, Kulakovskiy IV. Penzar D, et al. Among authors: rafi am. Bioinformatics. 2023 Aug 1;39(8):btad457. doi: 10.1093/bioinformatics/btad457. Bioinformatics. 2023. PMID: 37490428 Free PMC article.
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: rafi am. 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
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. Nat Biotechnol. 2024 Oct 11. doi: 10.1038/s41587-024-02414-w. Online ahead of print. Nat Biotechnol. 2024. PMID: 39394483
18 results