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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.
An optogenetic strategy enables selection of proteases with improved catalytic rates. The developed TEV protease variants are well suited for biotechnology applications, including FLARE assays with substantially improved temporal resolution.
MaSIF, a deep learning-based method, finds common patterns of chemical and geometric features on biomolecular surfaces for predicting protein–ligand and protein–protein interactions.
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.
The 2018 Human Protein Atlas Image Classification competition sought to improve automated classification of protein subcellular localizations from fluorescence images. The winning strategies involved innovative deep learning approaches for multi-label classification.
The unique advantages of single-particle cryo-electron microscopy and cryo-electron tomography are combined in a method called TYGRESS, here applied to determine the structure of the intact ciliary axoneme at a resolution of 12 Å.
An approach combining cryo-electron microscopy and mass spectrometry analysis of protein complexes enriched directly from cells enables structure determination of unknown complexes at atomic resolution.
Single-cell isolation following time-lapse imaging (SIFT) enables high-throughput screening of complex and dynamic phenotypes from pooled bacterial libraries. SIFT was used to generate ultraprecise synthetic gene oscillators.
A new method of autophagy measurement is based on the detection of phospho-ATG16L1, a conserved early marker of autophagy. Sensitive detection can be achieved in multiple biological systems and assays with advantages over standard methods.
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.
Harmony, for the integration of single-cell transcriptomic data, identifies broad and fine-grained populations, scales to large datasets, and can integrate sequencing- and imaging-based data.
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.
Directly sequencing RNA strands through a nanopore retains the full length of the transcript and allows for analysis of polyA tail length, transcript haplotypes and base modifications.
DuMPLING (dynamic μ-fluidic microscopy phenotyping of a library before in situ genotyping) enables screening of dynamic phenotypes in strain libraries and was used here to study genes that coordinate replication and cell division in Escherichia coli.