Nature Methods, Published online: 22 May 2024; doi:10.1038/s41592-024-02267-wSpatial transcriptomics and mRNA splicing measurements encode rich spatiotemporal information for cell states and their transitions. We present a multiscale dynamical system method for reconstructing cell-state-specific dynamics and spatial state transitions. This theory-based...

Nature Methods, Published online: 20 May 2024; doi:10.1038/s41592-024-02273-yMetabuli enhances metagenomic read classification by jointly analyzing DNA and amino acid sequences for specificity and sensitivity, respectively.

Nature Methods, Published online: 17 May 2024; doi:10.1038/s41592-024-02295-6DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible

Nature Methods, Published online: 16 May 2024; doi:10.1038/s41592-024-02281-yPebblescout navigates vast, rapidly growing nucleotide content in resources by providing indexing and search capabilities. We used Pebblescout to index a metagenomic subset of Sequence Read Archive and seven other resources into databases spanning over 3.7 petabases and searchable...

Nature Methods, Published online: 16 May 2024; doi:10.1038/s41592-024-02280-zThe Pebblescout tool achieves an efficient search for subjects in a large nucleotide database such as runs in Sequence Read Archive data.

Nature Methods, Published online: 16 May 2024; doi:10.1038/s41592-024-02266-xSTT is a method that connects mRNA splicing and cell-state transitions across spatiotemporal scales and at single-cell resolution.