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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: nogina d. Nat Biotechnol. 2024 Oct 11. doi: 10.1038/s41587-024-02414-w. Online ahead of print. Nat Biotechnol. 2024. PMID: 39394483
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. Among authors: nogina d. 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.
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: nogina d. Bioinformatics. 2023 Aug 1;39(8):btad457. doi: 10.1093/bioinformatics/btad457. Bioinformatics. 2023. PMID: 37490428 Free PMC article.
GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks.
Kamal A, Arnold C, Claringbould A, Moussa R, Servaas NH, Kholmatov M, Daga N, Nogina D, Mueller-Dott S, Reyes-Palomares A, Palla G, Sigalova O, Bunina D, Pabst C, Zaugg JB. Kamal A, et al. Among authors: nogina d. Mol Syst Biol. 2023 Jun 12;19(6):e11627. doi: 10.15252/msb.202311627. Epub 2023 Apr 19. Mol Syst Biol. 2023. PMID: 37073532 Free PMC article.
A hierarchy in clusters of cephalopod mRNA editing sites.
Moldovan MA, Chervontseva ZS, Nogina DS, Gelfand MS. Moldovan MA, et al. Among authors: nogina ds. Sci Rep. 2022 Mar 2;12(1):3447. doi: 10.1038/s41598-022-07460-5. Sci Rep. 2022. PMID: 35236910 Free PMC article.
Ribosomal leaky scanning through a translated uORF requires eIF4G2.
Smirnova VV, Shestakova ED, Nogina DS, Mishchenko PA, Prikazchikova TA, Zatsepin TS, Kulakovskiy IV, Shatsky IN, Terenin IM. Smirnova VV, et al. Among authors: nogina ds. Nucleic Acids Res. 2022 Jan 25;50(2):1111-1127. doi: 10.1093/nar/gkab1286. Nucleic Acids Res. 2022. PMID: 35018467 Free PMC article.