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Single-lysosome mass spectrometry (SLMS) integrates lysosomal patch-clamp recording and induced nanoESI/MS for concurrent metabolic and electrophysiological profiling of individual enlarged lysosomes.
ABEL-FRET combines anti-Brownian trapping for tether-free observation of biomolecules in solution with smFRET. ABEL-FRET offers ultrahigh resolution of FRET efficiency and enables simultaneous hydrodynamic profiling of molecular composition.
Super-resolution structured illumination microscopy reconstruction algorithms are described that can handle structured noise artifacts in two and three dimensions. The algorithms lack adjustable parameters and enhance objective representation of imaged objects.
Detect-seq, built upon chemical labeling and enrichment of intermediate deoxyuridine, offers an approach to profile different types of off-target mutation induced by cytosine base editors including unexpected edits outside of protospacer and on the target strand.
This work presents NeoLoopFinder, a computational method, for identifying chromatin interactions of structurally rearranged genomes. NeoLoopFinder was applied in 50 cancer datasets and identified genes associated with enhancer-hijacking events.
Distance distribution correction (DDC) eliminates repeat localizations caused by fluorophore blinking without the need for calibrations. Use of DDC yields accurate and quantifiable single-molecule localization microscopy data.
Combining whole-transcriptome preindexing with standard droplet microfluidics, scifi-RNA-seq enables single-cell RNA-seq with massive throughput and built-in sample multiplexing.
Surveying targets by APOBEC-mediated profiling identifies binding sites of RBPs by C-to-U RNA editing. STAMP is isoform specific, can be multiplexed and enables detection of ribosome association in single cells.
A deep learning–based algorithm enables efficient reconstruction of light-field microscopy data at video rate. In addition, concurrently acquired light-sheet microscopy data provide ground truth data for training, validation and refinement of the algorithm.
This paper reports CoTECH, which couples chromatin binding enrichment with RNA sequencing for concurrent measurements of histone modification and transcriptome in single cells, offering a multiomics tool for studying epigenetic regulations.
The CEPT cocktail comprising four small molecules enhances pluripotent stem cell survival, biobanking, organoid formation, and single-cell cloning efficiency by reducing cellular stress.
This work describes the identification of Cas13 proteins from two families by mining public metagenomic data. The newly identified Cas13X.1 shows efficient target knockdown and can be used to degrade SARS-CoV-2 and H1N1 genomes. In addition, the truncated Cas13X.1 offers an advantage in generating mini-RNA base editors.
DANNCE enables robust 3D tracking of animals’ limbs and other features in naturalistic environments by making use of a deep learning approach that incorporates geometric reasoning. DANNCE is demonstrated on behavioral sequences from rodents, marmosets, and chickadees.
PCprophet combines complex-level scoring and machine learning to predict novel protein complexes from protein cofractionation mass spectrometry data and to perform differential analysis across experimental conditions.
Phasor S-FLIM combines novel electronics for multichannel fluorescence lifetime acquisition and a phasor-based unmixing algorithm for real-time analysis of reliable spectral lifetime imaging data, enabling new biological observations.
A deep-learning-guided approach enables protein engineering using only a small number (‘low N’) of functionally characterized variants of target proteins.
This work describes nanodisco, a tool for de novo identifying DNA methylation in bacterial species and microbiomes using nanopore sequencing and for performing metagenomic binning using microbial DNA methylation patterns.