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Cellpose is a generalist, deep learning-based approach for segmenting structures in a wide range of image types. Cellpose does not require parameter adjustment or model retraining and outperforms established methods on 2D and 3D datasets.
A careful analysis of how carrier proteome levels used in the SCoPE-MS method affect the quantitative accuracy of single-cell proteomics results, yields guidelines for method users.
Click-ExM uses click-chemistry-based labeling to increase the versatility of expansion microscopy. Click-ExM enables imaging of numerous classes of biomolecules including lipids, glycans, proteins, DNA, RNA and small molecules.
nnU-Net is a deep learning-based image segmentation method that automatically configures itself for diverse biological and medical image segmentation tasks. nnU-Net offers state-of-the-art performance as an out-of-the-box tool.
This paper describes a CRISPR–Cas13 system to effectively target circRNAs and screen their functions in vitro and in vivo, which enables the study of relevant circRNA phenotypes in human cell proliferation and in mouse embryogenesis.
A new method should be thoroughly tested, applied, described — and peer-reviewed — before biological discoveries generated using the method are published.
Membrane proteins exhibit spatial variation in rigidity and disorder, which poses a challenge for traditional cryo-EM reconstruction algorithms. Non-uniform refinement accounts for this spatial variability, yielding improved 3D reconstruction quality even for small membrane proteins.
diaPASEF makes use of the correlation between the ion mobility and the m/z of peptides to trap and release precursor ions in a TIMS-TOF mass spectrometer for an almost complete sampling of the precursor ion beam with data-independent acquisition.
Using nanopore sequencing as readout, nanoNOMe–seq enables chromosome-level allele-specific profiles of CpG methylation and chromatin accessibility on human cells, in which the chromatin accessibility is profiled through exogenous GpC methylation introduced by a GpC methyltransferase.
Direct infusion–shotgun proteome analysis (DI-SPA) using data-independent acquisition mass spectrometry (DIA-MS) achieves fast and reproducible results by omitting the liquid-chromatography fractionation step and directly performing gas-phase peptide fractionation by ion mobility.
Engineered deubiquitinases (enDUBs) use nanobodies to bring deubiquitinases to target proteins for selective ubiquitin chain removal. enDUBs can rescue the functional expression of mutant ion channels like those responsible for cystic fibrosis.