Nature Methods, Published online: 14 May 2024; doi:10.1038/s41592-024-02279-6The Consortium for Top-Down Proteomics conducted a study to develop and test protocols for native mass spectrometry combined with top-down fragmentation of proteins and protein complexes across eleven instruments in nine laboratories. They report the summary of the outcomes...

Nature Methods, Published online: 14 May 2024; doi:10.1038/s41592-024-02272-zOpenFold is a trainable open-source implementation of AlphaFold2. It is fast and memory efficient, and the code and training data are available under a permissive license.

Nature Methods, Published online: 10 May 2024; doi:10.1038/s41592-024-02269-8By effective and efficient integration of PacBio HiFi, Oxford Nanopore Technologies ultra-long and other sequencing data types, hifiasm (UL) enables telomere-to-telomere diploid and polyploid genome assembly at a population scale.

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.