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LOVTRAP enables rapid optogenetic control of protein dissociation and is complementary to related optogenetic tools that mediate light-induced protein association. LOVTRAP is applied to the study of oscillatory processes at the cell membrane.
Reversible cryo-arrest allows consecutive super-resolution and functional imaging of molecular patterns in the same mammalian cell. This method was used to study the evolution of receptor tyrosine kinase reaction patterns at multiple scales.
ExFISH extends expansion microscopy to single-molecule RNA imaging, enabling super-resolution imaging of diverse RNAs in cells and tissues on conventional microscopes. The method enables multiplexed imaging of RNA and improved RNA quantitation.
UMI-4C is a rapid, simplified barcoding approach to targeted chromatin conformation capture that produces high-complexity libraries from low sample input, is easily multiplexed and gives a quantitative, statistically defined readout.
A newly developed algorithm enabled clustering of all 256 million (66 million identified and 190 million unidentified) peptide MS/MS spectra available in the PRIDE Archive database, allowing the detection of millions of consistently unidentified spectra across different data sets, of which roughly 20% could be identified using multiple complementary analysis tools.
PALM and STORM are powerful methods for studying membrane-protein clustering. However, fluorophore blinking can lead to miscounting artifacts. A new method shows that varying label density works for artifact-free analysis of membrane-protein nanoclusters.
Structural Variant Search, a combination of a chimera-free library preparation and a non-consensus-based SV-calling algorithm, enables the quantitative detection of rare somatic variants.
Correlation fluorescent in situ hybridization (corrFISH) makes it possible to quantify abundant transcripts using sequential barcoded hybridization, despite high spot density in images.
When studying neural circuitry, the ablation of synapses may be an alternative to optogenetic manipulation of neurons. A genetically encoded tool called GFE3 eliminates inhibitory inputs into neurons expressing GFE3.
For multiple hypothesis testing in genomics and other large-scale data analyses, the independent hypothesis weighting (IHW) approach uses data-driven P-value weight assignment to improve power while controlling the false discovery rate.
This Analysis provides a head-to-head comparison of >40 monomeric fluorescent proteins in terms of photophysical properties, photostability and performance in fusions to help users choose the best-performing tools.
DADA2 is an open-source software package that denoises and removes sequencing errors from Illumina amplicon sequence data to distinguish microbial sample sequences differing by as little as a single nucleotide.
The open-source Single Cell Genotyper software addresses common artifacts in single-cell sequencing data in order to robustly infer clonal genotypes, enabling the study of tumor heterogeneity and evolution.
X-shift software allows automated mapping of phenotypic space from large mass cytometry data sets. X-shift and the new representation algorithm Divisive Marker Tree provide a rapid, deterministic approach to navigating complex cellular systems.
Flyception is a tracking and imaging system that enables the monitoring of brain activity in freely walking fruit flies, making the analysis of calcium dynamics possible in studies of neural mechanisms such as those that underlie social behaviors.
Optogenetic tools such as a BphP1–PpsR2 pair can be harnessed to exert spatiotemporal control over signaling pathways or transcriptional events. The BphP1–PpsR2 system is activated by near-infrared light, making it suitable for in vivo applications.