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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.
An approach combining in situ tagmentation and transcription with MERFISH enables spatial profiling of the epigenome in tissues with single-cell resolution.
We developed a FAIR (findable, accessible, interoperable, reusable) framework for researchers to share spatially standardized brain models. TemplateFlow enables the implementation of more reliable data processing pipelines by maximizing the accessibility of such models. It equips neuroimaging researchers with a foundational tool to bridge gaps between populations and species in neuroscience research.
The ability to measure protein complexes in single cells is currently limited to a very small number of targets. Combining a proximity ligation assay with single-cell sequencing creates the ability to measure hundreds of extracellular protein complexes and thousands of mRNAs in individual cells.
To accelerate data acquisition for in situ cryo-electron tomography, we created a method that takes into consideration sample geometry for the robust prediction of sample movement while the microscope stage is tilted. This approach enabled the parallel collection of tens to hundreds of tilt series.
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.
Image-seq isolates cells from specific tissue locations under image guidance for analysis by single-cell RNA sequencing. The technique can be combined with in vivo imaging to document the temporal and dynamic history of the cells prior to sequencing.
The AlphaFill algorithm transplants missing small molecules and ions from experimentally determined structures to predicted protein models in the AlphaFold protein structure database. All AlphaFill entries are available for visual inspection and download through the AlphaFill website.