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Wtdbg2 assembles genomes with comparable contiguity and accuracy to existing tools using long-read sequencing data, and is several times faster, especially for large genomes.
SIMFLUX combines elements of MINFLUX with structured illumination to double localization precision and improve resolution in localization microscopy. The approach was demonstrated on DNA origami and on cellular microtubules.
NicheNet uses expression data, in combination with a previous model built on known signaling and gene regulatory networks, to predict ligand–target links in cell-to-cell communications.
An adaptive excitation source enables two- and three-photon imaging of the awake mouse brain with high spatial and temporal resolution at 30-fold-reduced laser power relative to conventional approaches.
A deep learning-based software tool, DIA-NN, enables deep proteome analysis from data generated using fast chromatographic approaches and data-independent acquisition mass spectrometry.
A miniaturized NMR-on-a-chip needle can be implanted into rodent brains and can measure blood flow and oxygenation changes in vivo in a small volume at an unprecedentedly high temporal resolution of a few milliseconds.
An alternative to focused ion beam scanning electron microscopy (FIB-SEM), gas cluster ion beam scanning electron microscopy (GCIB-SEM) is compatible with large tissue samples while achieving similar isotropic resolution.
VarID is a computational method that quantifies the dynamics of transcriptional variability with the goal of identifying the role of highly variable genes, such as weakly expressed transcription factors, in cell differentiation or state transitions.
Micropatterning of cryo-EM grids enables controlled adhesion of mammalian cells for cryo-ET-based structural studies. This approach leads to reproducible cellular morphology and improves focused ion beam thinning of cells for in-cell structural analyses.
Tissue fixation with formaldehyde and a water-soluble carbodiimide crosslinker (EDC) leads to retention of extracellular vesicles within tissues and allows for reliable extracellular vesicle imaging for semiquantitative imaging applications.
FreeHi-C takes Hi-C sequencing data as input and simulates reads with random mutations and indels from the interacting fragment pairs. FreeHi-C-simulated replicates are used for benchmarking Hi-C analysis methods and enable data augmentation for differential chromatin interaction analysis.
A multi-beam two-photon microscope enables imaging of calcium activity or neurovascular dynamics in the brain with millisecond-scale temporal resolution.
Seamless integration of single-molecule localization microscopy and STED allows for correlative live imaging of protein position and movement at the nanoscale in the context of fine morphological features.
Optobodies combine split intracellular antibodies (intrabodies) with light-controlled dimerization tools for spatiotemporal control of intrabody activity. The developed tools demonstrate the versatility and power of this approach for probing protein function.
DNA-PAINT is sped up by an order of magnitude by optimizing sequences and buffer conditions, enabling faster imaging with no compromise to image quality or resolution, improved single-molecule counting and enhanced cellular imaging.
Functional ultrasound (fUS) imaging of neural activity has been extended to volumetric imaging across the whole brain. 4D fUS is demonstrated in the rat brain in response to sensory stimuli and during seizure-like activity.