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DroNc-seq enables low-cost, high-throughput single-nucleus RNA-seq of tissues that are archived or difficult to dissociate, such as post-mortem human brain.
Negative feedback and incoherent feed-forward loops are the only circuit motifs that can adapt in response to stimuli. Rahi et al. describe signatures that allow discriminating between these two motifs and demonstrate the approach in yeast cell cycle timing and C. elegans olfaction.
The Omni-ATAC protocol improves the signal-to-background ratio in chromatin accessibility profiles and is suitable for a range of cell lines and primary cell types, as well as frozen tissue.
FreemoVR is a virtual reality system for freely moving animals. The versatile platform is demonstrated in various experiments with Drosophila, zebrafish, and mice.
Monocle 2 uses reversed graph embedding to automatically learn complex, branched pseudotime trajectories of differentiation or cellular state changes from single-cell expression data.
Monocle 2 uses reversed graph embedding to automatically learn complex, branched pseudotime trajectories of differentiation or cellular state changes from single-cell expression data.
The statistical concepts for false discovery rate control long applied in the field of data-dependent acquisition (DDA) mass spectrometry-based proteomics can be adapted for the emerging technique of data-independent acquisition (DIA) mass spectrometry.
ChromVar infers transcription-factor-associated accessibility from low-coverage or single-cell chromatin-accessibility data, thus enabling the clustering of cells and analysis of regulatory sequence motifs from sparse data sets.
Combining multielectrode arrays with an ex vivo preparation of the turtle brain allows identification of neurons as excitatory or inhibitory and mapping of their axonal projections.
A 9-nm-resolution structure of PR772 virus and a movie of its continuous conformational changes are determined from single-particle X-ray scattering data.
Structure determination of large molecular machines is facilitated by M3, a broadly applicable and user-friendly modeling method that takes diverse structural and biochemical data as inputs.
The histology topography cytometry analysis toolbox (histoCAT) enables quantitative analysis and exploration of highly multiplexed imaging data for better understanding of individual cells in the context of tissue architecture.
Informed-Proteomics, a software suite for top-down proteomics analysis, consists of a high-accuracy liquid chromatography–mass spectrometry feature-finding algorithm, an efficient database search tool, and an interactive results viewer.
Using established high-throughput single-cell RNA-seq platforms, CITE-seq combines highly multiplexed, antibody-based protein marker quantification with unbiased transcriptome profiling for thousands of single cells.
A rapidly inducible, autoinhibited SpCas9 and quantitative assessment of double-strand cleavage and indel formation allow insights into Cas9 kinetics in cell lines.
GROC-SVs enables the accurate detection and reconstruction of large and complex structural variants from read clouds generated by the 10x Genomics platform and subsequent Illumina sequencing.
The preferred specimen orientation problem limits accuracy and resolution in structure determination by cryo-EM. Collecting data at defined sample tilts yielded near-atomic-resolution structures for the influenza hemagglutinin trimer and ribosomal biogenesis intermediates.
A DNA-origami-based calibration method determines and accounts for labeling stoichiometry and fluorophore photophysics to improve protein counting in quantitative super-resolution imaging.