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RS-FISH is a user-friendly software for accurate spot detection that is applicable to smFISH experiments, spatial transcriptomics, and spatial genomics. The approach enables fast spot detection in even very large volumetric datasets.
An improved version of the MS2-MCP system for imaging RNA dynamics involves tethering translation termination factors to tagged mRNAs to bypass destabilization caused by NMD machinery.
Iterative Synthetically Phosphorylated Isomers (iSPI) is a proteome-scale library of human-derived phosphoserine-containing phosphopeptides with precisely known positions of phosphorylation. This multi-purpose resource is available for optimization, standardization, and benchmarking of key steps in phosphoproteomics workflows.
SyConn2 is a machine learning-based framework for inferring and analyzing the connectomes contained in a volume electron microscopy dataset of brain tissue, for example from the zebra finch.
SVision is a deep-learning-based method that can sensitively and accurately detect and characterize complex structural variants using long-read sequencing data.
A systematic exploration of MINFLUX nanoscopy with DNA-PAINT labeling leads to improved nanoscopy in fixed cells and MINFLUX imaging with increased multiplexing, as exemplified by three-color imaging of mitochondria in mammalian cells.
This study demonstrates the feasibility of generating near-finished microbial genomes using only Oxford Nanopore R10.4 data from pure cultures or metagenomes.
Extensive analyses of mammalian phosphoproteomics datasets show that protein histidine phosphorylation in human cells may not be as prevalent as previously thought.
TrackMate 7 combines the benefits of machine and deep learning-based image segmentation with accurate object tracking to enable improved 2D and 3D tracking of diverse objects in biological research.
ColabFold is a free and accessible platform for protein folding that provides accelerated prediction of protein structures and complexes using AlphaFold2 or RoseTTAFold.
GLEAMS, a deep learning-based algorithm, embeds mass spectra such that spectra related to the same peptide are close to each other, enabling unknown spectra to be identified on a massive scale.
Two-color fluorogenic DNA-PAINT introduces self-quenching, kinetics-optimized probe designs. This approach improves imaging speed 26-fold and eliminates the need for optical sectioning.
This work describes a strategy for estimating the population frequency of structural variations by searching the raw alignments of large population sequencing samples using the STIX framework.