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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. Among authors: gong w. 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.
Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees.
Gong W, Granados AA, Hu J, Jones MG, Raz O, Salvador-Martínez I, Zhang H, Chow KK, Kwak IY, Retkute R, Prusokiene A, Prusokas A, Khodaverdian A, Zhang R, Rao S, Wang R, Rennert P, Saipradeep VG, Sivadasan N, Rao A, Joseph T, Srinivasan R, Peng J, Han L, Shang X, Garry DJ, Yu T, Chung V, Mason M, Liu Z, Guan Y, Yosef N, Shendure J, Telford MJ, Shapiro E, Elowitz MB, Meyer P. Gong W, et al. Cell Syst. 2021 Aug 18;12(8):810-826.e4. doi: 10.1016/j.cels.2021.05.008. Epub 2021 Jun 18. Cell Syst. 2021. PMID: 34146472 Free 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: gong w. Nat Biotechnol. 2024 Oct 11. doi: 10.1038/s41587-024-02414-w. Online ahead of print. Nat Biotechnol. 2024. PMID: 39394483
Pathologic Stimulus Determines Lineage Commitment of Cardiac C-kit+ Cells.
Chen Z, Zhu W, Bender I, Gong W, Kwak IY, Yellamilli A, Hodges TJ, Nemoto N, Zhang J, Garry DJ, van Berlo JH. Chen Z, et al. Among authors: gong w. Circulation. 2017 Dec 12;136(24):2359-2372. doi: 10.1161/CIRCULATIONAHA.117.030137. Epub 2017 Oct 11. Circulation. 2017. PMID: 29021323 Free PMC article.
4,746 results