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DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools.
Jha A, Bohaczuk SC, Mao Y, Ranchalis J, Mallory BJ, Min AT, Hamm MO, Swanson E, Dubocanin D, Finkbeiner C, Li T, Whittington D, Noble WS, Stergachis AB, Vollger MR. Jha A, et al. bioRxiv [Preprint]. 2023 Dec 11:2023.04.20.537673. doi: 10.1101/2023.04.20.537673. bioRxiv. 2023. Update in: Genome Res. 2024 Nov 20;34(11):1976-1986. doi: 10.1101/gr.279095.124. PMID: 37131601 Free PMC article. Updated. Preprint.
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.
Schreiber JM, Boix CA, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, Carman MJ, Pinoli P, Hong C, Yip KY, Spence JP, Batra SS, Song YS, Mahony S, Zhang Z, Tan W, Shen Y, Sun Y, Shi M, Adrian J, Sandstrom RS, Farrell NP, Halow JM, Lee K, Jiang L, Yang X, Epstein CB, Strattan JS, Bernstein BE, Snyder MP, Kellis M, Noble WS, Kundaje AB; ENCODE Imputation Challenge Participants. Schreiber JM, et al. Genome Biol. 2023 Apr 18;24(1):79. doi: 10.1186/s13059-023-02915-y. Genome Biol. 2023. PMID: 37072822 Free PMC article.