Hu Y, Horlbeck MA, Zhang R, et al. Multiscale footprints reveal the organization of cis-regulatory elements. Nature. 2025. doi:10.1038/s41586-024-08443-4
Epigenomics
Vinyard ME, Rasmussen AW, Li R, Klein AM, Getz G. Learning cell dynamics with neural differential equations. Nature Machine Intelligence. 2025;7. doi:10.1038/s42256-025-01150-3
Goel VY, Aboreden NG, Jusuf JM, et al. Dynamics of microcompartment formation at the mitosis-to-G1 transition. Nature structural & molecular biology. 2025. doi:10.1038/s41594-025-01687-2
Roseman SA, Siegenfeld AP, Lee C, Lue NZ, Waterbury AL, Liau BB. DNA methylation insulates genic regions from CTCF loops near nuclear speckles. eLife. 2025;13. doi:10.7554/eLife.102930
Labade A, Chiang Z, Comenho C, et al. Expansion genome sequencing links nuclear abnormalities to hotspots of aberrant euchromatin repression. bioRxiv : the preprint server for biology. 2024. doi:10.1101/2024.09.24.614614
Waterbury AL, Kwok HS, Lee C, et al. An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing. Molecular cell. 2024. doi:10.1016/j.molcel.2024.05.017
Kim KL, Rahme GJ, Goel VY, Farran CAE, Hansen AS, Bernstein BE. Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation. Molecular cell. 2024. doi:10.1016/j.molcel.2024.02.007
Najm FJ, DeWeirdt P, Moore MM, et al. Chromatin complex dependencies reveal targeting opportunities in leukemia. Nature communications. 2023;14(1):448. doi:10.1038/s41467-023-36150-7
Rozowsky J, Gao J, Borsari B, et al. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell. 2023;186(7):1493-1511.e40. doi:10.1016/j.cell.2023.02.018
Kwok HS, Freedy AM, Siegenfeld AP, et al. Drug addiction unveils a repressive methylation ceiling in EZH2-mutant lymphoma. Nature chemical biology. 2023. doi:10.1038/s41589-023-01299-1