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Machine learning and deep learning models are used to predict high-quality tandem mass spectra, providing benefits over traditional analysis methods for interpreting proteomics data.
A dataset made up of single cancer cells or their mixtures serves as a benchmark for testing almost 4,000 combinations of scRNA-seq data analysis methods.
A deep learning–based tool, Prosit, predicts high-quality peptide tandem mass spectra, improving peptide-identification performance compared with that of traditional proteomics analysis methods.
CancerMine, a resource based on literature mining, offers a database of drivers, oncogenes and tumor suppressors for gene–cancer associations, updated monthly.
Fluorescence intensity fluctuation spectrometry provides a rapid and accurate measurement of the identity, abundance and stability of protein oligomers.
Using primer-exchange reactions, SABER extends FISH probes with repetitive sequences that can accommodate multiple fluorescent imager strands, resulting in up to 450-fold signal amplification. SABER is showcased in DNA and RNA FISH experiments across a range of complex biological samples.
A bioluminescent glucose-uptake probe enables accurate, real-time, non-invasive longitudinal imaging of d-glucose absorption both in vitro and in vivo.
Light-sheet microscopy in the NIR-II window enables rapid volumetric imaging of tissues at impressive depths in vivo without invasive preparations owing to the reduced light scattering and tissue autofluorescence at these wavelengths.
High-density arrays of optical fibers enable monitoring and manipulation of neural activity at large scale across many brain regions. The multi-fiber arrays can be used in head-fixed tasks, in freely behaving animals and during social interactions.
Epi-illumination SPIM enables fast, volumetric, high-resolution, subcellular imaging of any sample compatible with a standard inverted fluorescence microscope.
Iso-LFM enables rapid, instantaneous volumetric imaging of biological processes with isotropic and improved resolution by simultaneously capturing orthogonal light fields.
Replication initiation is stochastic and obscured in population sequencing; D-NAscent reports the use of long nanopore reads to detect base analogs and thus to assess replication initiation at the individual molecule level.
ECCITE-seq combines the single-cell analysis of multiple modalities, for example transcriptome, immune cell receptors, cell surface proteins and single-guide RNAs.
A method for protein binder selection and identification, NestLink, uses barcoding peptides detectable by mass spectrometry to select and biophysically characterize thousands of binders without requiring the handling of individual clones.
A mass-spectrometry-compatible surfactant called Azo effectively solubilizes proteins, is rapidly degraded by ultraviolet irradiation and enables top-down proteomic analysis of membrane proteins.
To address the issue of intra-tissue heterogeneity in cancer genomics, we developed Texomer, which enables joint analysis of bulk DNA and RNA sequencing data for allele-specific deconvolution and quantification of tumor heterogeneity.
Ribonucleotidyl transferases tethered to an RNA reporter add untemplated RNA tails. TRAID-seq identifies the activities of 22 enzymes, including the addition of poly(UG).
Among 17 measures of association tested, measures of proportionality consistently performed well for inference of gene and cellular networks, cell clusters and links to disease from scRNA-seq data. In contrast, several widely used measures of association performed well on only a subset of tasks.
High-throughput screening of fragment libraries of yeast genes yields dominant negative polypeptides on the basis of their decreased frequencies in cells after a growth selection.
This study reports results from the second community-wide single-molecule localization microscopy software challenge, which tested over 30 software packages on realistic simulated data for multiple popular 3D image acquisition modes, as well as 2D localization microscopy.