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scVI is a ready-to-use generative deep learning tool for large-scale single-cell RNA-seq data that enables raw data processing and a wide range of rapid and accurate downstream analyses.
YETI puts individual -omics experiments in the context of public genomics data by creating an integrated dataset-specific functional network, thus allowing more thorough interpretation of the data.
Content-aware image restoration (CARE) uses deep learning to improve microscopy images. CARE bypasses the trade-offs between imaging speed, resolution, and maximal light exposure that limit fluorescence imaging to enable discovery.
The machine learning approach FIT leverages public mouse and human expression data to improve the translation of mouse model results to analogous human disease.
Proximity-CLIP, a method that combines proximity-based protein biotinylation and UV crosslinking, profiles RNAs and ribonucleoproteins in any cellular compartment.
An AAV-based platform achieves sparse yet bright labeling of neurons with cell-type specificity. This technology will facilitate the reconstruction of neurons in the mouse brain.
VARNAM is a red-shifted genetically encoded voltage sensor based on the Ace opsin. It is applied in Drosophila, mouse brain slices and behaving mice. It can be readily combined with blue-light-sensitive tools for dual-color applications.
A closed-loop all-optical strategy allows manipulation of neurons on the basis of their ongoing activity and can be used to clamp neuronal activity to a preset level, boost sensory-evoked activity or yoke together the activity of trigger and target neurons.
NATIVE is a correlative light and electron microscopy approach that is based on nanobody-mediated immunohistochemistry. The approach does not require harsh permeabilization and preserves ultrastructure well.
osmFISH applies automated cycles of single-molecule fluorescence in situ hybridization without barcoding to provide spatial gene expression in tissue sections at high sensitivity, accuracy and throughput.
This paper describes a platform for carrying out antibody-based capture and mass spectrometry in parallel, and tests the feasibility of this platform for high-throughput validation of antibodies.
A data-collection strategy using a fixed-target crystallography chip allows time-resolved serial synchrotron crystallography experiments to determine enzyme intermediate structures with time resolutions of milliseconds to seconds.
BLINK2 is a light-activated potassium channel for optogenetic inhibition of neuronal activity. Alberio et al. apply the tool in systems as diverse as cultured rat neurons, mouse brain slices, behaving zebrafish and a rat model of neuropathic pain.
A library of mutant mouse lung endothelial cells expressing a comprehensive repertoire of heparin sulfate structure modifications enables studies of the structure–function relationships of this complex polysaccharide.
Variants of the genetically encoded sensor iGluSnFR extend the range of conditions under which glutamate neurotransmission can be visualized. In addition, chromatic variants of iGluSnFR improve compatibility with various illumination schemes.
HUMAnN2 uses a tiered sequence search to provide rapid and accurate species-level functional profiles of microbial communities from metagenomic and metatranscriptomic data.
Multiple MS2 loops inserted in the first loop of an sgRNA after the spacer sequence stabilize the sgRNA and allow recruitment of multicolor fluorescent proteins for imaging of low-repeat genomic loci.
The deep neural network smNet extracts multiplexed parameters such as 3D position, orientation and wavefront distortion from emission patterns of single molecules.