Tan J, Shenker-Tauris N, Rodriguez-Hernaez J, et al. Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening. Nature biotechnology. 2023. doi:10.1038/s41587-022-01612-8
Gene Regulation Observatory
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
Mangiameli SM, Chen H, Earl AS, et al. Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nature methods. 2023;20(5):686-694. doi:10.1038/s41592-023-01845-8
Joung J, Ma S, Tay T, et al. A transcription factor atlas of directed differentiation. Cell. 2023;186(1):209-229.e26. doi:10.1016/j.cell.2022.11.026
Simonson B, Chaffin M, Hill MC, et al. Single-nucleus RNA sequencing in ischemic cardiomyopathy reveals common transcriptional profile underlying end-stage heart failure. Cell reports. 2023;42(2):112086. doi:10.1016/j.celrep.2023.112086
De Rop F V, Hulselmans G, Flerin C, et al. Systematic benchmarking of single-cell ATAC-sequencing protocols. Nature biotechnology. 2023. doi:10.1038/s41587-023-01881-x
Wang L, Trasanidis N, Wu T, et al. Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics. Nature methods. 2023. doi:10.1038/s41592-023-01971-3
Cheong JG, Ravishankar A, Sharma S, et al. Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. Cell. 2023. doi:10.1016/j.cell.2023.07.019
Hu Y, Ma S, Kartha VK, et al. Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.03.28.533945
Martyn GE, Montgomery MT, Jones H, et al. Rewriting regulatory DNA to dissect and reprogram gene expression. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.12.20.572268