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In this DREAM challenge, 75 methods for the identification of disease-relevant modules from molecular networks are compared and validated with GWAS data. The authors provide practical guidelines for users and establish benchmarks for network analysis.
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.
Decorrelation analysis offers an improved method for assessing image resolution that works on a single image and is insensitive to common image artifacts. The method can be applied generally to any type of microscopy images.
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.
A single transcript encoding Cas12a and an array of CRISPR RNAs enables multiplexed genome engineering, from multiple knockouts to transcriptional activation or repression to orthogonal transcriptional control and editing in the same sample.
FLAM-seq implements a cDNA library preparation followed by single-molecule sequencing, for determining full-length mRNA molecules, including poly(A) tails.
A massively parallel biophysical approach, Hotspot Thermal Profiling, analyzes the effects of phosphorylation on protein stability across the proteome in live cells.
O-glycopeptides and O-glycan structures can be identified and quantified on a proteome-wide scale with Glyco-DIA, a data-independent-acquisition mass spectrometry-based method.
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.
A technique to ‘lift out’ samples of interest from high-pressure-frozen specimens expands applications of cryo-electron tomography to multicellular organisms and tissue.
A nuclear magnetic resonance spectroscopy-based approach to monitor multiple molecule and reaction types at once, Systems NMR, provides in vitro insights into complex biomolecular network dynamics.
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 two-photon computed tomography approach, called scanned line angular projection microscopy, enables high-speed imaging at over 1 kHz frame rates, as demonstrated for glutamate imaging in the in vivo mouse brain.