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This Analysis study compares computational methods for single-cell multi-omics prediction and integration, generating useful insights for method users and developers working with different analysis purposes and biological problems.
The dyes chosen for DNA-PAINT microscopy are pivotal for data quality. This Analysis shows a comprehensive comparison of 18 fluorescent dyes in DNA-PAINT and offers guidance for optimum dye selection in single-color and multiplexed imaging.
This analysis presents a systematic comparison of 11 sequencing-based spatial transcriptomics methods using well-characterized references, which offers insights into performance variations in spatial transcriptomic techniques.
The EMDataResource Ligand Model Challenge aimed at assessing the reliability and reproducibility of modeling ligands bound to protein and protein–nucleic acid complexes in cryo-EM maps determined at near-atomic resolution. This analysis presents the results and recommends best practices for assessing cryo-EM structures of liganded macromolecules.
The 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 and their recommendations in this Analysis.
Cell segmentation is crucial in many image analysis pipelines. This analysis compares many tools on a multimodal cell segmentation benchmark. A Transformer-based model performed best in terms of performance and general applicability.
This analysis provides 108 noncoding CRISPR screens collated by the ENCODE4 consortium and establishes experimental guidelines for future CRISPRi screens characterizing functional cis-regulatory elements.
