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Garnett uses a hierarchical markup language and machine learning to define cell types and their marker genes and identifies these cell types in scRNA-seq datasets from tissues and whole organisms and across species.
Repetitive optical selective exposure (ROSE) is an interferometric single-molecule localization microscopy method offering twofold improvement in lateral resolution with the same photon budget compared with conventional approaches.
Pepper, an RNA aptamer that prevents degradation of degron-tagged fluorescent proteins, enables fully genetically encoded fluorescence imaging of mRNA in living cells.
SAVER-X trains a deep neural network for transfer learning that improves the quality of scRNA-seq data using prior information learnt from existing public studies.
An optimized F-box protein–degron pair enables efficient auxin-mediated protein degradation with minimal basal degradation in human cells and is suitable for transmembrane, cytoplasmic and nuclear proteins.
Single-molecule oblique-plane microscopy (obSTORM) enables deep volumetric super-resolution imaging in a light-sheet microscopy platform that is convenient for standard tissues and small intact animals.
By embedding DNA sequences that are known to bind transcription factors in vitro together with labels for the TFs in a high-dimensional space, the machine learning approach BindSpace distinguishes between the binding preferences of even closely related TFs.
Methyl-HiC combines the elucidation of chromatin architecture with the reading of DNA methylomes in pools and single cells. Regions that are distant on the linear-genome but close in three-dimensional space show coordinated DNA methylation.
The search engine Thesaurus detects and quantifies phosphopeptide positional isomers from data-independent acquisition and parallel reaction monitoring mass spectrometry data, enabling studies of how neighboring phosphosites are regulated.
A genetically encodable protein synthesis inhibitor (gePSI) for cell-specific inhibition of protein synthesis that is efficient and reversible enables the study of structural plasticity following single-synapse activation in neurons.
Conos constructs a joint graph between single cells in different samples based on multiple pairwise alignments of the samples and identifies recurrent subpopulations across all of the datasets.
The red form of the photoconvertible fluorescent protein mEos4b has a long-lived dark state with specific chromophore conformation. Weak 488-nm light depopulates this state, improving track lengths in single-particle tracking experiments.
The automated structures analysis program (ASAP) enables rapid and objective detection, classification and analysis of cellular assemblies in super-resolution images.
Pathway-level information extractor (PLIER) uses prior knowledge of pathways to extract biologically interpretable latent variables from large gene expression datasets.
Two-photon microscopy in combination with adaptive optics enables diffraction-limited morphological and functional imaging up to around 800 μm below the pia. This is achieved with the help of fluorescent microvessels serving as guidestars.
HiChIRP combines a modified chromosome conformation capture protocol with enrichment of RNA-associated chromosome conformation to visualize genome-wide looping linked to an RNA of interest.