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Nature Methods



A multidisciplinary journal that publishes significant novel methods for life scientists and chemists.



 



Seeing red

2017-06-29

The growing advantages of red to near-infrared fluorescent probes should move them beyond being a 'second color' in biological imaging.



The Author File: Alexis Battle

2017-06-29

Calculating gene–environment interactions, and the role of a 'why' machine.



Points of Significance: Principal component analysis

2017-06-29

PCA helps you interpret your data, but it will not always find the important patterns.















Microbiology: Better tools for Bacteroides

2017-06-29

Two sets of complementary tools extend our capacity to manipulate the gut microbiome.



Proteomics: Charting the subcellular proteome

2017-06-29

Human protein subcellular locations light up in the Cell Atlas resource.



Biochemistry: CRISPR kinetics

2017-06-29

In vitro Cas9-binding assays show the effects of mutations in the target sequence on binding kinetics.



Neuroscience: Zooming into the larval zebrafish brain

2017-06-29

A serial-section electron microscopy data set of larval zebrafish brain—imaged at several scales—provides a resource for structure–function analyses of the animals' neural circuitry.



























Stem cells: Organoid variability examined

2017-06-29

Single-cell transcriptomics is used to determine what cell types are present in brain organoids and how much these cell types vary across organoids.



Assessing phototoxicity in live fluorescence imaging

2017-06-29

This Commentary discusses the problem of phototoxicity in live imaging and suggests guidelines to improve its assessment and reporting.



Towards a perceptive understanding of size in cellular biology

2017-06-29

This piece tackles the question of how to make biological scale more intuitive to human beings, bringing to bear the author's background in scientific visualization.



Metabolism: sweeter paths in glycoscience

2017-06-29

Carbohydrates are tough molecules to study, but glycoscientists are developing and democratizing the needed tools.



Illuminating redox biology using NADH- and NADPH-specific sensors

2017-06-29

Genetically encoded NAD and NADP sensors will revolutionize the study of redox biology.



FISH-ing for captured contacts: towards reconciling FISH and 3C

2017-06-12

This Analysis explores the relationship between chromosome conformation capture (for example, Hi-C) and FISH datasets, and uses simulations to reconcile measurements from the two technologies.



Comparison of computational methods for Hi-C data analysis

2017-06-12

Six tools to call chromatin interactions and seven tools for topologically associating domain calling are systematically compared with real and simulated data. The strengths and weaknesses of each tool are discussed.



Differential analysis of RNA-seq incorporating quantification uncertainty

2017-06-05

By using bootstraps that estimate inferential variance, the sleuth method and software provide fast and highly accurate differential gene expression analysis in an interactive Shiny app.



webKnossos: efficient online 3D data annotation for connectomics

2017-06-12

webKnossos is a browser-based tracing and annotation tool for 3D electron microscopy data sets that is optimized for seamless data viewing. The tool’s flight-mode view facilitates fast neurite tracing because of its egocentric viewpoint.



Nm-seq maps 2′-O-methylation sites in human mRNA with base precision

2017-05-15

Iterative oxidation, elimination and dephosphorylation steps remove nucleotides from the 3′ end of RNA until a 2′-O-methylated ribose that cannot be oxidized is encountered and brings the process to a stop. High-throughput sequencing of these fragments exposes 2′-O-methyl sites at base resolution.



Allele-specific expression reveals interactions between genetic variation and environment

2017-05-22

The EAGLE algorithm and software identifies replicable gene-by-environment interactions based on associations between environment and allele-specific expression.



Quantitative mRNA imaging throughout the entire Drosophila brain

2017-06-05

Improved fluorescence in situ hybridization enables smFISH in cleared whole-mount Drosophila brains with confocal microscopy; a custom Bessel beam structured illumination microscope allows single-mRNA detection across the entire brain.



Testing for differential abundance in mass cytometry data

2017-05-15

A statistical approach makes it possible to detect differentially abundant cell populations across biological conditions from high-dimensional mass cytometry data without relying on cell clustering.



CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations

2017-06-05

Early STOP codons created with CRISPR base editors leads to gene knockout with high efficiency and does not stress cells with double-strand DNA breaks. CRISPR-STOP can target the majority of human genes and is useful for genetic screens.



Fast high-resolution miniature two-photon microscopy for brain imaging in freely behaving mice

2017-05-29

FHIRM-TPM is a miniature two-photon microscope capable of imaging fluorescently labeled neurons in the brains of freely behaving mice. It allows for imaging of spines or recording of neural activity with a frame rate up to 40 Hz.



Genetically encoded fluorescent sensors reveal dynamic regulation of NADPH metabolism

2017-06-05

Genetically encoded iNap sensors allow imaging of NADPH with high spatiotemporal resolution in living systems. The iNaps cover physiologically relevant NADPH concentrations and are demonstrated in mammalian cells and live zebrafish.



Biosynthesis and genetic encoding of phosphothreonine through parallel selection and deep sequencing

2017-05-29

A new approach to evolve novel aminoacyl-tRNA synthetase–tRNA pairs with orthogonal substrate specificity is applied to generate a system to site-specifically incorporate phosphothreonine into proteins, enabling functional studies of this post-translational modification.



A quantitative and multiplexed approach to uncover the fitness landscape of tumor suppression in vivo

2017-05-22

The combination of tumor barcoding with CRISPR-mediated targeting of tumor suppressors allows quantitative analysis of tumor-suppressor function during tumor growth in vivo.



Fused cerebral organoids model interactions between brain regions

2017-05-10

The fusion of patterned cerebral organoids into more complex structures enables modeling of inter-regional processes such as neuronal migration.