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This analysis comprehensively compares methods for gene regulatory network inference submitted through the DREAM5 challenge. It demonstrates that integration of predictions from multiple methods shows the most robust performance across data sets.
Primary rat oligodendocytes were cultured in the presence of electron-spun nanofibers of varying sizes as a model to study myelination processes in the mammalian central nervous system. The authors study the role of fiber diameter on the initiation of concentric wrapping by oligodendrocytes.
pLink, software for data analysis of cross-linked proteins coupled with mass spectrometry, estimates false discovery rate and enables analysis of protein complexes without extensive purification.
This method achieves simultaneous and spatially colocalized excitation of three fluorophores with distinct spectra, doing so via two-photon microscopy using a femtosecond laser and an optical parametric oscillator and by temporally overlapping the beams. Imaging of 'Brainbow'-labeled mouse and chicken nervous tissue and of developing fly embryos is shown.
A machine learning–based structural-variant discovery approach that incorporates prior knowledge shows high sensitivity and specificity even on single genomes.
Due to an unexpected cell-penetrating property, zinc-finger nucleases (ZFNs) can be delivered to several mammalian cell types as proteins. Dose-dependent disruption of an endogenous gene was achieved with reduced activity at known off-target sites.
This paper reports a fluorescence imaging method based on interference contrast in which the incidence angle of the excitation light is actively scanned. The high axial precision and temporal resolution are used for dynamic nanoscale imaging of cytoskeleton and adhesion proteins in living cells.
Two large-scale resources for studying microRNA function are presented: one is a library of fluorescent sensors with a corresponding assay for global profiling of microRNA activity in different cell types; the other is a decoy library for suppressing microRNA activity individually or in pooled loss-of-function screens.
A rare cutting protease that creates large peptides is well suited for differentiating protein isoforms and detecting combinations of post-translational modifications by tandem mass spectrometry.
An imaging and registration framework called Virtual Brain Explorer for Zebrafish (ViBE-Z) allows mapping of gene expression patterns and anatomical structures in the zebrafish larval brain. ViBE-Z is provided via a web interface and contains software for image processing, data sets from several developmental stages and a brain atlas.
An analytically exact approach that determines the radial symmetry center of the image of any radially symmetric particle allows faster localization than iterative methods while also giving localization accuracies approaching theoretical limits.
MetaPhlAn (metagenomic phylogenetic analysis) allows the rapid and accurate identification of microbial species and higher clades from shotgun sequencing data.
The authors describe a method for realigning images from serially sectioned biological specimens that minimizes the effect of artificial deformations in the alignment by applying global elastic constraints. The method is applied to transmission electron microscopy and array tomography image series and is made available through the Fiji platform.
Simultaneous multiview light-sheet microscopy using two illumination and two detection arms with one- or two-photon illumination is coupled to a fast data acquisition framework and analysis pipeline for quantitative imaging and tracking of individual cells and the developing nervous system throughout a living fly embryo. A related paper by Krzic et al. is also in this issue.
A selective-plane illumination microscope with two illumination and two detection objectives rapidly records four three-dimensional images of an entire developing fly embryo and processes them into a single high-content image in real time. This allows for cell tracking and quantification of cell shape changes across the embryo. A related paper by Tomer et al. is also in this issue.
Super-resolution microscopy of fluorescently labeled oligonucleotides bound to individual mRNA transcripts is used for highly multiplexed imaging and quantification of transcripts in single cells. The method is used to profile transcripts from 32 stress-response genes in single yeast cells in response to extracellular stress.
The authors present a bioinformatic method for the accurate unsupervised classification of time-lapse images. This method should enable reproducible and unbiased annotation of large-scale image data sets.
Genotyping based on restriction site7ndash;associated (RAD) sequencing around type IIB enzyme recognition sites is reported. The streamlined reduced-representation approach features even and tunable genome coverage and enables large-scale genotyping studies by maximizing the amount of genotypic information that can be obtained from individuals for a given amount of sequencing.
The combination of cell-free protein expression and combinatorial dual labeling–aided NMR analysis allows for the rapid backbone structure assessment of human membrane proteins.
