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Nature Methods

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


Sharing images


Images are among the richest data types that biologists collect, yet most biological images are not available for reanalysis or reuse. This may be changing.

The Author File: Melike Lakadamyali


DNA origami, super-resolution microscopy and creative flashes on a bike.

Points of Significance: Classification and regression trees


Decision trees are a simple but powerful prediction method.

Neuroscience: Tailoring optogenetic illumination through tapered fibers


A tapered optical fiber delivers spatially precise and efficient optogenetic illumination to the rodent brain.

Synthetic biology: Synthetic epigenetic memory


Combining an inducible methyltransferase with a methylation-sensitive zinc finger creates an epigenetic memory circuit.

Proteomics: Bottoms-up!


Developments in data-independent-acquisition mass spectrometry allow efficient and accurate quantitation of peptidoforms across large sample cohorts.

Lab-on-a-chip: A community repository for microfluidics


The Metafluidics initiative encourages researchers to upload and share open-source microfluidics designs.

Sensors and probes: Super-resolution imaging with mCherry


A chemical caging strategy allows mCherry to be used for localization microscopy.

Genetics: new tales from ancient DNA


Coaxing ancient DNA to reveal its history delivers surprises and even improves ways of working with badly damaged present-day DNA.

Image Data Resource: a bioimage data integration and publication platform


This Resource describes the Image Data Resource (IDR), a prototype online system for biological image data that links experimental and analytic data across multiple data sets and promotes image data sharing and reanalysis.

Comparison of algorithms for the detection of cancer drivers at subgene resolution


13 algorithms for the detection of cancer driver genes at the subgene level are assessed for their advantages and limitations.

A DNA origami platform for quantifying protein copy number in super-resolution


A DNA-origami-based calibration method determines and accounts for labeling stoichiometry and fluorophore photophysics to improve protein counting in quantitative super-resolution imaging.

Addressing preferred specimen orientation in single-particle cryo-EM through tilting


The preferred specimen orientation problem limits accuracy and resolution in structure determination by cryo-EM. Collecting data at defined sample tilts yielded near-atomic-resolution structures for the influenza hemagglutinin trimer and ribosomal biogenesis intermediates.

RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps


RosettaES, an algorithm that uses a fragment-based sampling strategy, improves macromolecular structure modeling from cryo-EM data at 3–5-Å resolution.

Visualizing adenosine-to-inosine RNA editing in single mammalian cells


inoFISH uses fluorescence in situ hybridization to visualize and localize adenosine-to-inosine-edited transcripts.

High-speed fixed-target serial virus crystallography


A new sample-delivery method for serial X-ray crystallography exploits the full repetition rate of the X-ray free-electron laser at the LCLS facility, thus enabling efficient, high-speed data collection to solve the three-dimensional structures of viruses.

Video rate volumetric Ca2+ imaging across cortex using seeded iterative demixing (SID) microscopy


The seeded iterative demixing strategy, when used in combination with light-field microscopy, enables calcium imaging at single-neuron resolution in the mouse brain at high volumetric imaging rates and depths of up to 380 μm.

CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping


CrY2H-seq, a Cre recombinase reporter-mediated yeast two-hybrid method coupled with next-generation sequencing, enables ultra-high-throughput screening of transcription factor interactions in Arabidopsis thaliana.