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Page 1
Massively parallel characterization of transcriptional regulatory elements.
Agarwal V, Inoue F, Schubach M, Penzar D, Martin BK, Dash PM, Keukeleire P, Zhang Z, Sohota A, Zhao J, Georgakopoulos-Soares I, Noble WS, Yardımcı GG, Kulakovskiy IV, Kircher M, Shendure J, Ahituv N. Agarwal V, et al. Among authors: penzar d. Nature. 2025 Mar;639(8054):411-420. doi: 10.1038/s41586-024-08430-9. Epub 2025 Jan 15. Nature. 2025. PMID: 39814889 Free PMC article.
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. 2025 Aug;43(8):1373-1383. doi: 10.1038/s41587-024-02414-w. Epub 2024 Oct 11. Nat Biotechnol. 2025. PMID: 39394483 Free PMC article.
GAME: Genomic API for Model Evaluation.
Luthra I, Priyadarshi S, Guo R, Mahieu L, Kempynck N, Dooley D, Penzar D, Vorontsov I, Sheng Y, Tu X, Klie A, Drusinsky S, Floren A, Armand E, Alasoo K, Seelig G, Tewhey R, Koo P, Agarwal V, Gosai S, Pinello L, White MA, Lal A, Zeitlinger J, Pollard KS, Libbrecht M, Carter H, Mostafavi S, Kulakovskiy I, Hsiao W, Aerts S, Zhou J, de Boer CG. Luthra I, et al. Among authors: penzar d. bioRxiv [Preprint]. 2025 Jul 8:2025.07.04.663250. doi: 10.1101/2025.07.04.663250. bioRxiv. 2025. PMID: 40672207 Free PMC article. 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.
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. 2025 Aug;43(8):1373-1383. doi: 10.1038/s41587-024-02414-w. PMID: 38405704 Free PMC article. Updated. Preprint.
22 results