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Page 1
Global reference mapping of human transcription factor footprints.
Vierstra J, Lazar J, Sandstrom R, Halow J, Lee K, Bates D, Diegel M, Dunn D, Neri F, Haugen E, Rynes E, Reynolds A, Nelson J, Johnson A, Frerker M, Buckley M, Kaul R, Meuleman W, Stamatoyannopoulos JA. Vierstra J, et al. Nature. 2020 Jul;583(7818):729-736. doi: 10.1038/s41586-020-2528-x. Epub 2020 Jul 29. Nature. 2020. PMID: 32728250 Free PMC article.
Index and biological spectrum of human DNase I hypersensitive sites.
Meuleman W, Muratov A, Rynes E, Halow J, Lee K, Bates D, Diegel M, Dunn D, Neri F, Teodosiadis A, Reynolds A, Haugen E, Nelson J, Johnson A, Frerker M, Buckley M, Sandstrom R, Vierstra J, Kaul R, Stamatoyannopoulos J. Meuleman W, et al. Nature. 2020 Aug;584(7820):244-251. doi: 10.1038/s41586-020-2559-3. Epub 2020 Jul 29. Nature. 2020. PMID: 32728217 Free PMC article.
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.
Schreiber J, Boix C, 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 R, Farrell N, Halow J, Lee K, Jiang L, Yang X, Epstein C, Strattan JS, Bernstein B, Snyder M, Kellis M, Stafford W, Kundaje A; ENCODE Imputation Challenge Participants. Schreiber J, 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.
Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling.
Lazar JE, Stehling-Sun S, Nandakumar V, Wang H, Chee DR, Howard NP, Acosta R, Dunn D, Diegel M, Neri F, Castillo A, Ibarrientos S, Lee K, Lescano N, Van Biber B, Nelson J, Halow J, Sandstrom R, Bates D, Urnov FD, Stamatoyannopoulos JA, Funnell APW. Lazar JE, et al. Cell Rep. 2020 May 26;31(8):107676. doi: 10.1016/j.celrep.2020.107676. Cell Rep. 2020. PMID: 32460018 Free article.