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Tiling of regulatory DNA with mutations introduced by genome editing nucleases and linking the resulting alleles to a phenotypic readout allows the precise determination of functional sequence motifs within these regions.
An sgRNA-scoring algorithm (CRISPRscan) based on molecular features that enhance activity allows users to predict the most efficient sgRNA for in vivo targets.
DNA-programmed assembly of cells (DPAC) allows the reconstitution of organoid-like structures with controlled size, shape, cell-type composition and spatial heterogeneity.
Cycler constructs a trajectory of cell-cycle progression from fixed images of cells enabling the correlation of an individual cell's position in the cell cycle with multiple cellular readouts.
DeepSEA, a deep-learning algorithm trained on large-scale chromatin-profiling data, predicts chromatin effects from sequence alone, has single-nucleotide sensitivity and can predict effects of noncoding variants.
Spectrally resolved STORM (stochastic optical reconstruction microscopy) uses wide-field spectral measurements of sparsely activated single-molecule emitters to image cells labeled with fluorophores with highly overlapping emission spectra, opening the door to multiplexed super-resolution imaging.
Small, lightweight LED implants and a radio-frequency transducer as a power source enable wireless optogenetic stimulation in the brain, spinal cord and peripheral nervous system of behaving mice.
SpeedSeq is an open-source software suite offering very fast, accurate and comprehensive analysis of single-nucleotide and structural variants from whole genome sequencing data.
Screening for tertiary-interaction responsiveness in large RNA ribozyme-aptamer libraries to ligands identifies RNA devices with improved activation ratios and ligand sensitivities.
Functional ultrasound imaging and electroencephalography are combined to assess brain activity in mobile rats. The methodology is applied to the analysis of theta rhythms in a maze task and of epileptic seizures.
ARM-seq enables enhanced sequencing of modified tRNAs and tRNA fragments. Treatment of RNA with the demethylase AlkB prior to reverse transcription removes three ‘hard-stop’ modifications, allowing for discovery of modified tRNA fragments and their precursors by RNA sequencing.
Functionally important residues in a long RNA can be identified by mutational interference mapping experiment (MIME), a method which uses random mutagenesis of RNA followed by selection for function and high-throughput sequencing.
ProteoPlex optimizes buffer conditions for the isolation and purification of macromolecular complexes. The concurrent complex stabilization is beneficial for structure determination using X-ray crystallography or cryo-electron microscopy.