Nature Methods, Published online: 09 May 2024; doi:10.1038/s41592-024-02261-2We developed a two-pronged strategy to functionally probe the enormous repertoire of noncoding DNA within genomes. Our approach markedly improved signal-to-noise ratio and successfully intersected single-cell genomics with reporter assays. The result delivers a multiplex and...

Nature Methods, Published online: 09 May 2024; doi:10.1038/s41592-024-02274-xBy learning to embed DNA k-mers and cells into a joint space, CellSpace improves single-cell ATAC-seq analysis in multiple tasks such as latent structure discovery, transcription factor activity inference and batch effect mitigation.

Nature Methods, Published online: 09 May 2024; doi:10.1038/s41592-024-02260-3Single-cell quantitative expression reporters enable high-sensitivity quantitative characterization of cis-regulatory elements at the single-cell level in multicellular systems.

Nature Methods, Published online: 08 May 2024; doi:10.1038/s41592-024-02268-9Molecular Pixelation is an optics-free method that uses DNA-tagged antibodies to enable identification of the relative location of proteins on single cells.

Nature Methods, Published online: 07 May 2024; doi:10.1038/s41592-024-02296-5Author Correction: brainlife.io: a decentralized and open-source cloud platform to support neuroscience research

Nature Methods, Published online: 06 May 2024; doi:10.1038/s41592-024-02265-yCustom-built mathematical models make the immune response more predictable and offer mechanistic insights into fundamental immunology.