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19 results

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Page 1
A generative framework for enhanced cell-type specificity in rationally designed mRNAs.
Khoroshkin M, Zinkevich A, Aristova E, Yousefi H, Lee SB, Mittmann T, Manegold K, Penzar D, Raleigh DR, Kulakovskiy IV, Goodarzi H. Khoroshkin M, et al. Among authors: penzar d. bioRxiv [Preprint]. 2024 Dec 31:2024.12.31.630783. doi: 10.1101/2024.12.31.630783. bioRxiv. 2024. PMID: 39803435 Free PMC article. Preprint.
Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.
Vorontsov IE, Kozin I, Abramov S, Boytsov A, Jolma A, Albu M, Ambrosini G, Faltejskova K, Gralak AJ, Gryzunov N, Inukai S, Kolmykov S, Kravchenko P, Kribelbauer-Swietek JF, Laverty KU, Nozdrin V, Patel ZM, Penzar D, Plescher ML, Pour SE, Razavi R, Yang AWH, Yevshin I, Zinkevich A, Weirauch MT, Bucher P, Deplancke B, Fornes O, Grau J, Grosse I, Kolpakov FA; Codebook/GRECO-BIT Consortium; Makeev VJ, Hughes TR, Kulakovskiy IV. Vorontsov IE, et al. Among authors: penzar d. bioRxiv [Preprint]. 2024 Nov 13:2024.11.11.619379. doi: 10.1101/2024.11.11.619379. bioRxiv. 2024. PMID: 39605530 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: penzar d. Nat Biotechnol. 2024 Oct 11. doi: 10.1038/s41587-024-02414-w. Online ahead of print. Nat Biotechnol. 2024. PMID: 39394483
PhyloBench: A Benchmark for Evaluating Phylogenetic Programs.
Spirin S, Sigorskikh A, Efremov A, Penzar D, Karyagina A. Spirin S, et al. Among authors: penzar d. Mol Biol Evol. 2024 Jun 1;41(6):msae084. doi: 10.1093/molbev/msae084. Mol Biol Evol. 2024. PMID: 38860506 Free PMC article.
Ribonanza: deep learning of RNA structure through dual crowdsourcing.
He S, Huang R, Townley J, Kretsch RC, Karagianes TG, Cox DBT, Blair H, Penzar D, Vyaltsev V, Aristova E, Zinkevich A, Bakulin A, Sohn H, Krstevski D, Fukui T, Tatematsu F, Uchida Y, Jang D, Lee JS, Shieh R, Ma T, Martynov E, Shugaev MV, Bukhari HST, Fujikawa K, Onodera K, Henkel C, Ron S, Romano J, Nicol JJ, Nye GP, Wu Y, Choe C, Reade W; Eterna participants; Das R. He S, et al. Among authors: penzar d. bioRxiv [Preprint]. 2024 Jun 11:2024.02.24.581671. doi: 10.1101/2024.02.24.581671. bioRxiv. 2024. PMID: 38464325 Free PMC article. Preprint.
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: penzar 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.
Landscape of allele-specific transcription factor binding in the human genome.
Abramov S, Boytsov A, Bykova D, Penzar DD, Yevshin I, Kolmykov SK, Fridman MV, Favorov AV, Vorontsov IE, Baulin E, Kolpakov F, Makeev VJ, Kulakovskiy IV. Abramov S, et al. Among authors: penzar dd. Nat Commun. 2021 May 12;12(1):2751. doi: 10.1038/s41467-021-23007-0. Nat Commun. 2021. PMID: 33980847 Free PMC article.
19 results