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Bolaños et al. present a realistic three-dimensional virtual mouse model that can be animated and that facilitates the training of pose estimation algorithms.
This work describes nanodisco, a tool for de novo identifying DNA methylation in bacterial species and microbiomes using nanopore sequencing and for performing metagenomic binning using microbial DNA methylation patterns.
ROSE-Z achieves axial interference through an asymmetrical optical scheme, yielding 2 nm axial localization precision with ~3,000 photons and a single objective, which offers improved multicolor three-dimensional localization microscopy for cellular structures.
Martini 3.0 is an updated and reparametrized force field for coarse-grained molecular dynamics simulations with new bead types and an expanded ability to model molecular packing and interactions.
A suite of generally applicable methods and tools, developed to enable single-molecule FRET-based studies of transmembrane proteins diffusing in the cell membrane of living cells, was used to study the oligomerization and dynamics of GPCRs.
Point-scanning super-resolution imaging uses deep learning to supersample undersampled images and enable time-lapse imaging of subcellular events. An accompanying ‘crappifier’ rapidly generates quality training data for robust performance.
Advances in single-cell sequencing technologies enable generation of datasets of millions of cells. scfind facilitates efficient and sophisticated gene search in massive single-cell datasets.
HD-fMOST is a microscopy technique for imaging large samples at high throughput and with high definition, which is achieved with a line-illumination modulation approach. The technology is illustrated by imaging fluorescently labeled neurons in whole mouse brains.
This work reports a dual transposase–peroxidase fusion to survey the accessible chromatin regions and the proximal proteome in one assay, providing a tool to capture both the genomic and proteomic contents of open chromatin.
Commonly used organic dyes can photoconvert to blue-shifted fluorescent species, especially under intense illumination. The mechanism of this process and how to avoid unwanted artifacts in super-resolution microscopy are explored here.
G-GESS is a serotonin biosensor, derived from a tick serotonin-binding protein. The biosensor has been applied here in cell culture, primary neurons, mouse brain slices and in vivo in the mouse brain.
The DRACO algorithm deconvolutes coexisting RNA structures from mutational profiling experiments, and can be applied to bacterial regulatory structures and elements from the SARS-CoV-2 genome.
Nuc-MS makes use of top–down mass spectrometry in ‘native’ mode to quantitatively interrogate histone proteoforms and their post-translational modifications in a single experiment.
Paired-Tag offers a multiomics assay for joint profiling of histone modifications and gene expression in single nuclei, and is applied to mouse frontal cortex and hippocampus for measuring cell-type-resolved chromatin state and transcriptome.
Total Variational Inference is a framework for end-to-end analysis of paired transcriptome and protein measurements such as CITE-seq data in single cells.
Reconstruction of light-field microscopy data with a deep-learning network achieves high reconstruction speed and reduces artifacts, as illustrated for moving C. elegans and beating zebrafish hearts.
The software M establishes a reference-based multi-particle refinement framework for cryo-EM data. Combined with CTF correction and map denoising, M enables residue-level structure determination inside cells.