Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain
the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in
Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles
and JavaScript.
Combining genome-wide CRISPR–Cas9-mediated base editors with temporally resolved phosphoproteomics enables the functional screening of thousands of post-translational modification sites involved in T cell activation.
ESI-cryoPrep is a cryo-EM specimen preparation method that employs electrospray ionization techniques to deposit charged macromolecule-containing droplets on EM grids. Demonstrated across various protein samples, this approach effectively prevents biomolecule adsorption at air–water or graphene–water interfaces, addressing challenges related to protein denaturation and preferred orientation.
Super-resolution imaging of reference and target structures enables precise determination of the labeling efficiency of high-affinity binding proteins in cells for improved quantitative assessment of protein organization at the single-molecule level.
Generating training data for training deep-learning-based tools is time consuming. The DELiVR pipeline facilitates this process as demonstrated in this study on detecting c-Fos+ cells or microglia in the brain, following tissue clearing and imaging with light-sheet microscopy.
LiMCA offers a tool for co-profiling 3D genome structure and gene expression at the single-cell level, enabling researchers to elucidate the olfactory receptor gene selection process.
A pretrained foundation model (UniFMIR) enables versatile and generalizable performance across diverse fluorescence microscopy image reconstruction tasks.
scGHOST offers a computational tool to annotate single-cell subcompartments from scHi-C or imaging data through graph representation learning with constrained random walk sampling.
Kilosort4 is a spike-sorting algorithm with improved performance compared to previous versions, owing to the use of a graph-based clustering approach. The tool extracts the activity of individual neurons from electrophysiological recordings acquired with, for example, Neuropixels electrodes.
The combination of light sheet illumination and reversibly switchable fluorophores enables improved structured illumination microscopy for fast, low-background super-resolution imaging in cells and spheroids.
Deep interactome profiling by mass spectrometry (DIP-MS) combines affinity purification with native BN-PAGE fractionation and mass spectrometry to resolve protein complexes sharing the same target protein. The paper also presents PPIprophet, a data-driven neural network-based protein complex deconvolution approach.
RoboEM enables automated proofreading of electron microscopy datasets using a strategy akin to that of self-steering cars. This decreases the need for manual proofreading of segmented datasets and facilitates connectomic analyses.
Improved green cAMP and red calcium sensors were developed to facilitate dual-color imaging in vivo. These sensors will allow studying the relationship between calcium and cAMP signaling.
scPROTEIN is a deep graph contrastive learning framework that can estimate the uncertainty of peptide quantification, denoise protein data, remove batch effects and encode single-cell proteomic-specific embeddings under a unified framework.
This work introduces two polishers for refining the draft genome generated from nanopore long reads, as well as an assembler pipeline for producing telomere-to-telomere diploid genome with low error rate.
An optogenetic system enables the controlled release of soluble and transmembrane proteins for precise exploration of cellular protein function at the single-molecule level and streamlined single-molecule imaging.
Implementation of ultralong transients on an Orbitrap mass spectrometer improves mass resolution, sensitivity and accuracy of charge determination in the analysis of large macromolecular ions.
Deng et al. expand the toolbox of neurotransmitter sensors with high-sensitivity green and red genetically encoded serotonin sensors. These are suitable for in vivo applications, as demonstrated in a variety of applications in mice.
A copper(II)-functionalized Mycobacteriumsmegmatis porin A nanopore enables direct identification of all 20 proteinogenic amino acids, one unnatural amino acid and two post-translational modifications, and shows potential for peptide discrimination and sequencing.