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This paper presents nonnegative spatial factorization, a general framework for spatially aware and interpretable dimension reduction for high-dimensional spatial data, and its application to spatial transcriptomics analysis.
A statistical approach for optimal design of multiplexed imaging studies has been developed. It determines experimental parameters that facilitate cell phenotype identification.
During segmentation of neurons in electron microscopy datasets, auxiliary learning via the prediction of local shape descriptors increases efficiency, which is important for the processing of datasets of ever-increasing size.
Antibody-barcode eCLIP (ABC) uses proximity ligation to couple DNA-barcoded antibodies to RNA-binding protein (RBP)-protected RNA fragments for multiplexed eCLIP. ABC can be used to interrogate several RBPs in a single tube with results on par with eCLIP.
Nano3P-seq presents a nanopore-based sequencing tool to profile polyA-tailed and non-polyA-tailed transcripts, as well as capture polyA tail length and composition.
Localization Model Fit (LocMoFit) is an open-source tool for extracting meaningful parameters from individual structures in localization microscopy data. The framework was used for quantitative analysis of diverse biological structures.
This paper shows that the uniformity of vitreous ice thickness relies on the surface flatness of the supporting film, and presents a method to use ultraflat graphene as the support for cryo-EM specimen preparation.
DEDAL is a deep learning-based protein sequence alignment method that improves the quality of predicted alignment for remote homologs and better discriminates remote homologs from evolutionarily unrelated sequences.
Chemically activated protein domains are chemogenetic tools that inhibit the activity of short peptides in the absence of a small molecule. Their versatility was demonstrated on a range of peptides and in both cells and mice.
miRFP718nano is a rationally designed small near-infrared fluorescent protein with an emission tail that extends into the short-wave infrared range for improved multiplexed and deep-tissue imaging applications.
The parallel cryo electron tomography (PACE-tomo) method increases the throughput on in situ samples by parallelizing acquisition. It maximizes the usable sample area on individual lamellae without compromising data quality.
This work presents Prox-seq that couples sequencing and proximity ligation assay to simultaneously measure extracellular proteins, protein–protein interactions and mRNA in single cells.